Starting /dee2/code/volunteer_pipeline.sh ERR5262814 current disk space = 1551381204992 free memory = 1595559472 ERR5262814 SRAfilesize fc63c783f8c874da67cc143d4aee915d ERR5262814.sra ERR5262814.sra file validated ERR5262814 is paired end ERR5262814 is conventional basespace ERR5262814 read1 length is 101-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5262814_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101-150 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.747 37.0 37.0 37.0 37.0 37.0 2 36.59175 37.0 37.0 37.0 37.0 37.0 3 36.6975 37.0 37.0 37.0 37.0 37.0 4 36.7455 37.0 37.0 37.0 37.0 37.0 5 36.739 37.0 37.0 37.0 37.0 37.0 6 36.7515 37.0 37.0 37.0 37.0 37.0 7 36.7475 37.0 37.0 37.0 37.0 37.0 8 36.733 37.0 37.0 37.0 37.0 37.0 9 36.725 37.0 37.0 37.0 37.0 37.0 10-14 36.7247 37.0 37.0 37.0 37.0 37.0 15-19 36.6803 37.0 37.0 37.0 37.0 37.0 20-24 36.6279 37.0 37.0 37.0 37.0 37.0 25-29 36.6135 37.0 37.0 37.0 37.0 37.0 30-34 36.5744 37.0 37.0 37.0 37.0 37.0 35-39 36.58540000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.563100000000006 37.0 37.0 37.0 37.0 37.0 45-49 36.556 37.0 37.0 37.0 37.0 37.0 50-54 36.561800000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.4841 37.0 37.0 37.0 37.0 37.0 60-64 36.4778 37.0 37.0 37.0 37.0 37.0 65-69 36.4402 37.0 37.0 37.0 37.0 37.0 70-74 36.418400000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.4349 37.0 37.0 37.0 37.0 37.0 80-84 36.4499 37.0 37.0 37.0 37.0 37.0 85-89 36.4495 37.0 37.0 37.0 37.0 37.0 90-94 36.437400000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.5051 37.0 37.0 37.0 37.0 37.0 100-104 35.898182845711425 37.0 37.0 37.0 34.6 37.0 105-109 35.64494969695899 37.0 37.0 37.0 31.8 37.0 110-114 36.41097258442098 37.0 37.0 37.0 37.0 37.0 115-119 36.30239195122869 37.0 37.0 37.0 37.0 37.0 120-124 36.45164161508989 37.0 37.0 37.0 37.0 37.0 125-129 36.24006340940481 37.0 37.0 37.0 37.0 37.0 130-134 36.2866740542986 37.0 37.0 37.0 37.0 37.0 135-139 36.22071593418592 37.0 37.0 37.0 37.0 37.0 140-144 36.206183802789624 37.0 37.0 37.0 37.0 37.0 145-149 36.13653212395063 37.0 37.0 37.0 37.0 37.0 150 36.177464788732394 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 1.0 26 2.0 27 2.0 28 0.0 29 8.0 30 15.0 31 24.0 32 32.0 33 42.0 34 82.0 35 265.0 36 2748.0 37 778.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 8.799999999999999 83.1 1.4000000000000001 6.7 2 27.934918648310386 2.202753441802253 43.4793491864831 26.382978723404253 3 19.475 11.625 13.100000000000001 55.800000000000004 4 22.15 32.574999999999996 22.825 22.45 5 26.25 30.725 21.4 21.625 6 24.125 31.45 19.225 25.2 7 15.825 25.95 41.225 17.0 8 20.200000000000003 23.45 29.825000000000003 26.525 9 19.85 20.5 31.175000000000004 28.475 10-14 22.555 28.134999999999998 24.085 25.224999999999998 15-19 21.875 26.46 25.855 25.81 20-24 22.29 26.1 26.31 25.3 25-29 22.400000000000002 26.895000000000003 25.119999999999997 25.585 30-34 23.205000000000002 26.43 24.55 25.814999999999998 35-39 22.400000000000002 26.974999999999998 24.845 25.779999999999998 40-44 23.26 26.284999999999997 24.834999999999997 25.619999999999997 45-49 22.075 25.6 24.805 27.52 50-54 21.615000000000002 25.919999999999998 25.924999999999997 26.540000000000003 55-59 22.264999999999997 25.645 26.57 25.52 60-64 24.325 25.25 24.165 26.26 65-69 23.345 24.975 26.08 25.6 70-74 22.495 25.775 25.275 26.455000000000002 75-79 24.845 25.5 23.919999999999998 25.735000000000003 80-84 23.515 25.635 25.41 25.44 85-89 24.36 26.029999999999998 24.15 25.46 90-94 23.22 25.75 24.355 26.674999999999997 95-99 24.474999999999998 24.4 26.009999999999998 25.115 100-104 20.838125718857828 26.58898834825224 28.219232884932737 24.353653047957195 105-109 24.35527328714396 21.564665127020785 21.41070053887606 32.6693610469592 110-114 28.113968734241052 21.381744831064044 24.53353504790721 25.970751386787693 115-119 17.426545086119553 27.583586626139816 25.835866261398177 29.15400202634245 120-124 18.074756784434204 30.952380952380953 27.62416794674859 23.34869431643625 125-129 16.997167138810198 27.581766675251096 26.706155034766933 28.714911151171773 130-134 19.39203354297694 24.528301886792452 25.707547169811324 30.372117400419285 135-139 18.898056960340696 25.765238221985626 30.822464732499334 24.51424008517434 140-144 19.859497433126183 23.399081329370443 26.614428532828967 30.12699270467441 145-149 19.66354109211252 21.897407611693325 24.407060121345836 34.03199117484832 150 21.12676056338028 13.521126760563378 34.92957746478873 30.422535211267604 >>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 0.5 13 0.5 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 0.5 28 0.5 29 1.0 30 2.0 31 5.0 32 12.0 33 13.5 34 29.0 35 60.0 36 75.5 37 88.0 38 101.0 39 105.5 40 122.0 41 166.0 42 183.5 43 205.0 44 224.5 45 205.0 46 190.0 47 187.0 48 178.5 49 139.5 50 153.0 51 174.5 52 166.0 53 173.5 54 144.0 55 85.0 56 62.5 57 62.5 58 62.5 59 73.0 60 64.0 61 51.0 62 47.5 63 44.5 64 42.5 65 42.0 66 40.0 67 34.5 68 32.0 69 29.0 70 26.5 71 21.5 72 17.0 73 16.5 74 11.0 75 7.0 76 5.5 77 4.5 78 5.5 79 3.5 80 0.5 81 1.0 82 1.0 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 0.125 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 100-101 1.0 102-103 0.0 104-105 1.0 106-107 3198.0 108-109 6.0 110-111 1.0 112-113 0.0 114-115 2.0 116-117 4.0 118-119 4.0 120-121 3.0 122-123 0.0 124-125 0.0 126-127 5.0 128-129 7.0 130-131 7.0 132-133 2.0 134-135 7.0 136-137 2.0 138-139 8.0 140-141 2.0 142-143 1.0 144-145 11.0 146-147 6.0 148-149 12.0 150-151 710.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 62.025 #Duplication Level Percentage of deduplicated Percentage of total 1 69.36719064893188 43.025000000000006 2 20.15316404675534 25.0 3 5.360741636436921 9.975000000000001 4 2.2168480451430876 5.5 5 0.8061265618702136 2.5 6 0.6852075775896815 2.55 7 0.24183796856106407 1.05 8 0.16122531237404272 0.8 9 0.12091898428053204 0.675 >10 0.8867392180572351 8.924999999999999 >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 GGCAAACAGAAGTGATCTTGAGCAAAGTCCAGTGATCTAGGACGTGCCCA 42 1.05 No Hit CCTGTATGTTCAGTAGCAGCACTTACTCCTCGTCATCATCGTCGTCGCTG 32 0.8 No Hit GTTCAGTAGCAGCACTTACTCCTCGTCATCATCGTCGTCGCTGTCCTTCT 30 0.75 No Hit GCTGGTTGTTCAAGCTAAAAGTTGCAGCCCACCAAGAAAAACAAAACATC 20 0.5 No Hit GTTCTAACATTGCTGGTTGTTCAAGCTAAAAGTTGCAGCCCACCAAGAAA 18 0.44999999999999996 No Hit GCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACTTACTCCTCGT 17 0.42500000000000004 No Hit CTGTATGTTCAGTAGCAGCACTTACTCCTCGTCATCATCGTCGTCGCTGT 16 0.4 No Hit GTTCAAGCTAAAAGTTGCAGCCCACCAAGAAAAACAAAACATCTTTATCC 15 0.375 No Hit CCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACTTACTCCTCGTCAT 15 0.375 No Hit GGTGATACAAGTGTGTTTGCATATTGTGATGGGACTTCAGGTGAAATATC 14 0.35000000000000003 No Hit GCATCCTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCA 14 0.35000000000000003 No Hit GACATGTTCTAACATTGCTGGTTGTTCAAGCTAAAAGTTGCAGCCCACCA 14 0.35000000000000003 No Hit GGAGTACATTGTTATTAAAATAGAGATTATACACTCGACATGTTCTAACA 14 0.35000000000000003 No Hit ATGCAATCTCGTCGCAAGCTTGTCTTCGGTTGGCAAGGAACATATGGGAT 13 0.325 No Hit CTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACTTACTC 12 0.3 No Hit TGTATGTTCAGTAGCAGCACTTACTCCTCGTCATCATCGTCGTCGCTGTC 11 0.27499999999999997 No Hit GTTATTAAAATAGAGATTATACACTCGACATGTTCTAACATTGCTGGTTG 10 0.25 No Hit CCCACCAAGAAAAACAAAACATCTTTATCCTTGCACACCAAATGAACCCC 10 0.25 No Hit ATTGGGAGTACATTGTTATTAAAATAGAGATTATACACTCGACATGTTCT 10 0.25 No Hit GGTTGTTCAAGCTAAAAGTTGCAGCCCACCAAGAAAAACAAAACATCTTT 10 0.25 No Hit TGGTTGTTCAAGCTAAAAGTTGCAGCCCACCAAGAAAAACAAAACATCTT 10 0.25 No Hit CGACATGTTCTAACATTGCTGGTTGTTCAAGCTAAAAGTTGCAGCCCACC 10 0.25 No Hit CATGTTCTAACATTGCTGGTTGTTCAAGCTAAAAGTTGCAGCCCACCAAG 9 0.22499999999999998 No Hit CATCTTTATCCTTGCACACCAAATGAACCCCAGTTTCTACAGCACGGACA 9 0.22499999999999998 No Hit CCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACTTACTCCTCGTCATC 9 0.22499999999999998 No Hit ACTCGACATGTTCTAACATTGCTGGTTGTTCAAGCTAAAAGTTGCAGCCC 8 0.2 No Hit GGGAGTACATTGTTATTAAAATAGAGATTATACACTCGACATGTTCTAAC 8 0.2 No Hit CTGGTTGTTCAAGCTAAAAGTTGCAGCCCACCAAGAAAAACAAAACATCT 8 0.2 No Hit ATGTTCAGTAGCAGCACTTACTCCTCGTCATCATCGTCGTCGCTGTCCTT 8 0.2 No Hit CCACTTGCAGCATCCTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCA 7 0.17500000000000002 No Hit CTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACTTACTCCTCGTC 7 0.17500000000000002 No Hit ATCCATTCGATGGATCTACACCACTAACGGCTGGACCCATTTGTTCCTTT 7 0.17500000000000002 No Hit GCTTAACTATCCTGTATGTTCAGTAGCAGCACTTACTCCTCGTCATCATC 7 0.17500000000000002 No Hit AGGAACACACGACAGGTAGCATCACGGACAAACACCTAATGGTAACCCTT 7 0.17500000000000002 No Hit GGGTGATACAAGTGTGTTTGCATATTGTGATGGGACTTCAGGTGAAATAT 7 0.17500000000000002 No Hit CAAACAGAAGTGATCTTGAGCAAAGTCCAGTGATCTAGGACGTGCCCACC 6 0.15 No Hit ATGTAATCCGACGCGGTGTCGCCGCCGCCGCCGTAGGAGCCCCTGGTGAT 6 0.15 No Hit GCAAACAGAAGTGATCTTGAGCAAAGTCCAGTGATCTAGGACGTGCCCAC 6 0.15 No Hit CCTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACTTA 6 0.15 No Hit CTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACTTAC 6 0.15 No Hit ACCCAATGTTGCCATAACCAAACATCTCCAGTAGCAGCAAACACAACTCC 6 0.15 No Hit GTTTGCATATTGTGATGGGACTTCAAGTGAAATATCAAGGCATCCATTCG 6 0.15 No Hit ACCAAGAAAAACAAAACATCTTTATCCTTGCACACCAAATGAACCCCAGT 6 0.15 No Hit ACCTCAAGTACGCTACTGTCCTCGATAAGTACCATAGCTGCTCATAAGCA 6 0.15 No Hit ACCTTATTGGGAGTACATTGTTATTAAAATAGAGATTATACACTCGACAT 6 0.15 No Hit CATCCATTCGATGGATCTACACCACTAACGGCTGGACCCATTTGTTCCTT 6 0.15 No Hit AGCACATTTAATTATTAATAGATGCAACGGGAATTTATGAGTTGAACTGT 6 0.15 No Hit ATCCTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGCACT 6 0.15 No Hit ACATGTTCTAACATTGCTGGTTGTTCAAGCTAAAAGTTGCAGCCCACCAA 6 0.15 No Hit GTGAAATATCAAGGCATCCATTCGATGGATCTACACCACTAACGGCTGGA 6 0.15 No Hit CTTGCAGCATCCTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTA 6 0.15 No Hit CTCGACATGTTCTAACATTGCTGGTTGTTCAAGCTAAAAGTTGCAGCCCA 6 0.15 No Hit ATCACGAGCACGAGTGAAGAAACAAGTTCCGAACGACCCCAATCCAGCAT 5 0.125 No Hit CCAAGAAAAACAAAACATCTTTATCCTTGCACACCAAATGAACCCCAGTT 5 0.125 No Hit AGATTTTACATCCCATTGGAAACGAAGATTTCATTCCTCCACTGACTAAT 5 0.125 No Hit AGAAAAACAAAACATCTTTATCCTTGCACACCAAATGAACCCCAGTTTCT 5 0.125 No Hit ACGAAGAAGGAGAGGAAGAAGAAGAAGAGGAACAGACGAAGGATTTGGGG 5 0.125 No Hit AGCATCCTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCAGC 5 0.125 No Hit ATAGAATTGGGCATGGACAGGGAACAGCTTGCGGATCCAGTCAAGCATCC 5 0.125 No Hit GTGATCTTGAGCAAAGTCCAGTGATCTAGGACGTGCCCACCACATGATGC 5 0.125 No Hit AGCGACGTCTATCTCACCAAGCAAAGCAGAACCATCAGTGGTGTTAAATG 5 0.125 No Hit ATCTTTATCCTTGCACACCAAATGAACCCCAGTTTCTACAGCACGGACAA 5 0.125 No Hit ATCACAACAAGATACAACATTACTGTGTTTAGCATAATACATGGTACAGT 5 0.125 No Hit CACCACTAACGGCTGGACCCATTTGTTCCTTTTTCTGTAAAGGCCTTTCA 5 0.125 No Hit GCATCCATTCGATGGATCTACACCACTAACGGCTGGACCCATTTGTTCCT 5 0.125 No Hit ACCTGCATTACTTTTACGTTTGCTTTTGACATTGGTGGAGGAAGATGGGT 5 0.125 No Hit AGTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCG 5 0.125 No Hit GCCACCAAGAAAAACAAAACATCTTTATCCTTGCACACCAAATGAACCCC 5 0.125 No Hit AGGAGCTAAAGTTCCAGATAAATTCAGCTGTAGAAGCTGCAGTTCTTGCA 5 0.125 No Hit GCAGCATCCTCTCCGGCTCCCTGCTTAACTATCCTGTATGTTCAGTAGCA 5 0.125 No Hit CTTATTGGGAGTACATTGTTATTAAAATAGAGATTATACACTCGACATGT 5 0.125 No Hit ATCTTGACATACACTTCCTCTTCATCAAATTCGCCTGTGCCTGATGAAAA 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 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.05 0.0 80-81 0.0 0.0 0.0 0.05 0.0 82-83 0.0 0.0 0.0 0.05 0.0 84-85 0.0 0.0 0.0 0.05 0.0 86-87 0.0 0.0 0.0 0.05 0.0 88-89 0.0 0.0 0.0 0.05 0.0 90-91 0.0 0.0 0.0 0.05 0.0 92-93 0.0 0.0 0.0 0.05 0.0 94-95 0.0 0.0 0.0 0.05 0.0 96-97 0.0 0.0 0.0 0.05 0.0 98-99 0.0 0.0 0.0 0.05 0.0 100-101 0.0 0.0 0.0 0.05 0.0 102-103 0.0 0.0 0.0 0.05 0.0 104-105 0.0 0.0 0.0 0.05 0.0 106-107 0.0 0.0 0.0 0.05 0.0 108-109 0.0 0.0 0.0 0.05 0.0 110-111 0.0 0.0 0.0 0.05 0.0 112-113 0.0 0.0 0.0 0.05 0.0 114-115 0.0 0.0 0.0 0.05 0.0 116-117 0.0 0.0 0.0 0.05 0.0 118-119 0.0 0.0 0.0 0.05 0.0 120-121 0.0 0.0 0.0 0.05 0.0 122-123 0.0 0.0 0.0 0.05 0.0 124-125 0.0 0.0 0.0 0.05 0.0 126-127 0.0 0.0 0.0 0.05 0.0 128-129 0.0 0.0 0.0 0.05 0.0 130-131 0.0 0.0 0.0 0.05 0.0 132-133 0.0 0.0 0.0 0.05 0.0 134-135 0.0 0.0 0.0 0.05 0.0 136-137 0.0 0.0 0.0 0.05 0.0 138 0.0 0.0 0.0 0.05 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR5262814 read2 length is 88-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5262814_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 88-150 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.367 37.0 37.0 37.0 37.0 37.0 2 36.1915 37.0 37.0 37.0 37.0 37.0 3 36.299 37.0 37.0 37.0 37.0 37.0 4 36.3265 37.0 37.0 37.0 37.0 37.0 5 36.455 37.0 37.0 37.0 37.0 37.0 6 36.3885 37.0 37.0 37.0 37.0 37.0 7 36.387 37.0 37.0 37.0 37.0 37.0 8 36.591 37.0 37.0 37.0 37.0 37.0 9 36.539 37.0 37.0 37.0 37.0 37.0 10-14 36.5505 37.0 37.0 37.0 37.0 37.0 15-19 36.554100000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.4962 37.0 37.0 37.0 37.0 37.0 25-29 36.5168 37.0 37.0 37.0 37.0 37.0 30-34 36.4503 37.0 37.0 37.0 37.0 37.0 35-39 36.4722 37.0 37.0 37.0 37.0 37.0 40-44 36.4223 37.0 37.0 37.0 37.0 37.0 45-49 36.42809999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.375800000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.3078 37.0 37.0 37.0 37.0 37.0 60-64 36.3454 37.0 37.0 37.0 37.0 37.0 65-69 36.3806 37.0 37.0 37.0 37.0 37.0 70-74 36.3189 37.0 37.0 37.0 37.0 37.0 75-79 36.2913 37.0 37.0 37.0 37.0 37.0 80-84 36.2993 37.0 37.0 37.0 37.0 37.0 85-89 36.32843676838419 37.0 37.0 37.0 37.0 37.0 90-94 36.30035115130745 37.0 37.0 37.0 37.0 37.0 95-99 36.263211076980966 37.0 37.0 37.0 37.0 37.0 100-104 36.251185256292786 37.0 37.0 37.0 37.0 37.0 105-109 36.01972935006575 37.0 37.0 37.0 37.0 37.0 110-114 35.890088018270696 37.0 37.0 37.0 37.0 37.0 115-119 35.83127102950562 37.0 37.0 37.0 37.0 37.0 120-124 35.824699872286075 37.0 37.0 37.0 37.0 37.0 125-129 35.845313059055826 37.0 37.0 37.0 37.0 37.0 130-134 35.93284932916646 37.0 37.0 37.0 37.0 37.0 135-139 35.829617660754835 37.0 37.0 37.0 37.0 37.0 140-144 35.81042591296221 37.0 37.0 37.0 37.0 37.0 145-149 35.81588038649107 37.0 37.0 37.0 37.0 37.0 150 35.48870056497175 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 2.0 13 2.0 14 1.0 15 0.0 16 0.0 17 1.0 18 1.0 19 2.0 20 2.0 21 2.0 22 5.0 23 5.0 24 2.0 25 0.0 26 1.0 27 6.0 28 5.0 29 9.0 30 10.0 31 9.0 32 23.0 33 48.0 34 79.0 35 306.0 36 2574.0 37 904.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.699999999999996 23.525 8.075000000000001 26.700000000000003 2 31.075000000000003 22.575 27.6 18.75 3 22.75 27.125 29.7 20.424999999999997 4 23.225 30.275000000000002 24.125 22.375 5 27.474999999999998 33.775 18.275 20.474999999999998 6 23.45 36.75 18.5 21.3 7 21.475 20.825 37.45 20.25 8 24.075 21.6 25.0 29.325000000000003 9 23.325000000000003 23.275000000000002 26.674999999999997 26.724999999999998 10-14 26.275 26.3 23.74 23.685000000000002 15-19 25.169999999999998 25.4 25.39 24.04 20-24 26.064999999999998 25.369999999999997 25.25 23.315 25-29 25.259999999999998 25.295 25.430000000000003 24.015 30-34 24.965 25.34 25.66 24.035 35-39 26.534999999999997 25.55 24.875 23.04 40-44 25.69 24.495 25.34 24.474999999999998 45-49 25.445 25.09 26.179999999999996 23.285 50-54 25.990000000000002 26.924999999999997 24.355 22.73 55-59 25.629999999999995 25.16 25.36 23.849999999999998 60-64 25.7 25.14 26.669999999999998 22.49 65-69 25.345000000000002 24.7 26.155 23.799999999999997 70-74 26.06 24.905 25.525 23.51 75-79 25.8 25.52 25.585 23.095 80-84 26.145000000000003 24.73 25.485000000000003 23.64 85-89 25.237523752375235 25.007500750075007 26.552655265526553 23.2023202320232 90-94 26.44719067393806 25.571621554010104 25.72171911742633 22.259468654625504 95-99 27.49799759711654 25.185222266720064 25.02503003604325 22.291750100120144 100-104 29.319686935580975 22.285771623519967 26.189042745334135 22.20549869556492 105-109 18.217802664607067 24.097316084186136 40.2587372079552 17.426144043251593 110-114 25.34039334341906 26.903681290973275 25.239536056480084 22.516389309127586 115-119 27.279635258358663 29.027355623100306 24.34143870314083 19.3515704154002 120-124 30.08192524321557 26.13927291346646 25.371223758320532 18.40757808499744 125-129 28.328611898016998 29.0754571207829 22.328096832346127 20.26783414885398 130-134 26.422018348623855 26.422018348623855 27.208387942332894 19.947575360419396 135-139 27.745202558635395 25.0 26.732409381663114 20.522388059701495 140-144 26.352813852813856 26.16341991341991 26.10930735930736 21.374458874458874 145-149 27.461283185840706 27.682522123893804 24.80641592920354 20.049778761061948 150 25.423728813559322 28.8135593220339 25.70621468926554 20.056497175141246 >>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 0.0 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 0.5 19 1.0 20 0.5 21 0.0 22 0.5 23 1.0 24 1.0 25 0.5 26 1.0 27 1.0 28 1.0 29 3.0 30 2.5 31 5.0 32 6.5 33 14.0 34 26.5 35 34.0 36 50.5 37 64.5 38 82.5 39 104.5 40 134.5 41 173.5 42 188.5 43 178.5 44 189.5 45 195.0 46 212.5 47 235.5 48 201.5 49 169.0 50 153.0 51 147.5 52 133.5 53 117.0 54 139.5 55 124.0 56 83.0 57 86.0 58 84.0 59 71.0 60 58.5 61 51.5 62 55.5 63 51.0 64 42.0 65 39.0 66 40.0 67 43.0 68 37.5 69 28.5 70 28.0 71 27.0 72 20.0 73 14.0 74 9.0 75 5.0 76 9.5 77 11.0 78 5.0 79 3.0 80 1.5 81 0.5 82 1.0 83 1.0 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 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 88-89 2.0 90-91 1.0 92-93 0.0 94-95 1.0 96-97 1.0 98-99 1.0 100-101 12.0 102-103 0.0 104-105 1.0 106-107 3181.0 108-109 6.0 110-111 1.0 112-113 0.0 114-115 2.0 116-117 4.0 118-119 4.0 120-121 3.0 122-123 0.0 124-125 0.0 126-127 5.0 128-129 7.0 130-131 7.0 132-133 3.0 134-135 7.0 136-137 2.0 138-139 8.0 140-141 2.0 142-143 1.0 144-145 12.0 146-147 6.0 148-149 12.0 150-151 708.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 67.025 #Duplication Level Percentage of deduplicated Percentage of total 1 69.37709809772473 46.5 2 20.738530399104814 27.800000000000004 3 5.632226781051846 11.325000000000001 4 2.3871689668034315 6.4 5 1.1189854531891086 3.75 6 0.26109660574412535 1.05 7 0.11189854531891084 0.525 8 0.11189854531891084 0.6 9 0.03729951510630362 0.22499999999999998 >10 0.2237970906378217 1.825 >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 warn #Sequence Count Percentage Possible Source GGAATGTTTAAAATCTGGCATCCATGTTAGCAGAGGACTTGTCCGTGCTG 16 0.4 No Hit GGGGCACTGGGTACACTATCAAGGGCAAGATCGATGTCGATACGCCCTTT 13 0.325 No Hit GGTGAAGGCAAGGAAATGTATTATTGTATACGTGTGTGTGCATGATATTA 13 0.325 No Hit GTTTAAAATCTGGCATCCATGTTAGCAGAGGACTTGTCCGTGCTGTAGAA 11 0.27499999999999997 No Hit ATGACATCGGTCACAGAAGGCATTGATGCAATTGCAACTACTCGAGTAGT 10 0.25 No Hit ATCAAGGGCAAGATCGATGTCGATACGCCCTTTGGGAACATGAAGCTGCC 10 0.25 No Hit CGGGAAAGTGCCGATTCCTTACAAGCCTGACGTTGATGTGGATAAGATCA 9 0.22499999999999998 No Hit GCTCATTCAGCCAATGCCCCTCAAAAGATAATTGTTAGATCAGAGCAGCA 8 0.2 No Hit GAACTGTTCAAACGGCAGAGTGAGTCTTGATATTGTCGGCTCATCACATC 8 0.2 No Hit CCAAGATCGACAAGCAAGGGATCACCAAGATGCAGATCCCATTCACCTTC 8 0.2 No Hit AGTGAGTCTTGATATTGTCGGCTCATCACATCCGCGGAGAAGGAATGTTT 7 0.17500000000000002 No Hit TGATCAGGGGCAGGGGCACTGGGTACACTATCAAGGGCAAGATCGATGTC 7 0.17500000000000002 No Hit GGGAAAAATGCTGACTTCATGTATGTTAGAGCAGTTGATGCTCATTCAGC 7 0.17500000000000002 No Hit GTTATCGCTCCCGAGTATCCTAGATCTCGCTCCATCGCGTAGGGTTTGAG 6 0.15 No Hit GGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAA 6 0.15 No Hit GTGACAGTAAATCCATACAAAAATAGTAAATTCTGAAGGCATCACGTATA 6 0.15 No Hit GAGAAGGAATGTTTAAAATCTGGCATCCATGTTAGCAGAGGACTTGTCCG 6 0.15 No Hit AAATGGTCTCGCACCGCTAGCATCGGAGCGGCCCGTACTTGATAATACAT 6 0.15 No Hit CGGAGTTCGAGGGCGCTGGCAGGGGCGCGCCCGCGCACCCCTACAGCGAC 6 0.15 No Hit CAAATCTAAACCGGTCCTCACAGAAAGAGGTGAAAGTGCTGATATGTCAG 6 0.15 No Hit GCTTACCTGAGTGCCCTGAACAAGATGTCCAGTTATGTTGGTGCCGTAAA 5 0.125 No Hit AGAAACTGGGGTTCATTTGGTGTGCAAGGATAAAGATGTTTTGTTTTTCT 5 0.125 No Hit CTTGATATTGTCGGCTCATCACATCCGCGGAGAAGGAATGTTTAAAATCT 5 0.125 No Hit GGATATGTTTCGTGGGATTCTGATGCTTAATTTCTGGTAGCACGGTGTGG 5 0.125 No Hit GCAGTTTTATTTTCCTTGTATATCACACAGTGCATGCAATGAAATGCAGT 5 0.125 No Hit CCTGAACAAGATGTCCAGTTATGTTGGTGCCGTAAAAGCCAGCAGCGAAG 5 0.125 No Hit GCTAAAGCAGATCAACAACTGGTTCATCAATCAAAGAAAAAGGAACTGGC 5 0.125 No Hit GCTTGATTGCAGAACCGTTGCGAGAAACCATTTACAAAAAGTCTGCCGAG 5 0.125 No Hit CTATCAAGGGCAAGATCGATGTCGATACGCCCTTTGGGAACATGAAGCTG 5 0.125 No Hit GCACTCAAGGACTACTGGAGAGGTCCTATGAAAAGAAAACTGGATTCATA 5 0.125 No Hit CACCAAGATGCAGATCCCATTCACCTTCAGGCCCAAGGATCTGGGCTCTG 5 0.125 No Hit AGGATCTGGGCTCTGCTGTCTGGGACATGATCAGGGGCAGGGGCACTGGG 5 0.125 No Hit GGAATGGCGGAAGTTGAGTACCGTTGCTTCGTGGGCGGCCTCGCCTGGGC 5 0.125 No Hit GTTCAAACGGCAGAGTGAGTCTTGATATTGTCGGCTCATCACATCCGCGG 5 0.125 No Hit TGTTATTGCAGTTTGTTTATCTGTATCGGGAGTTAACCATCCTTCAGATC 5 0.125 No Hit GGGATCACCAAGATGCAGATCCCATTCACCTTCAGGCCCAAGGATCTGGG 5 0.125 No Hit ACATGCTGAATGAGTGCCGTCGTGGAGGAGCCGGTTCAACTCTTTAAGCT 5 0.125 No Hit CCAAGATGCAGATCCCATTCACCTTCAGGCCCAAGGATCTGGGCTCTGCT 5 0.125 No Hit CACCAAGATCGACAAGCAAGGGATCACCAAGATGCAGATCCCATTCACCT 5 0.125 No Hit AAATTGGTCCCGTGTTATCTGTTACAATGCAACAGCAAGCGATGGATACT 5 0.125 No Hit CCTCAATTTGCTCCAGTATGAGATGTGGCTTGGGGATGATAGGGTGGCTG 5 0.125 No Hit GTCTGTTCCACAGAACAGTGATTCGGATATTCTGAACGAGACTGAAGGTT 5 0.125 No Hit GTGGAAGGCAAGGAAGGTATCCTGCTTTTGCCTTTTTGTGCAGGCGCCAA 5 0.125 No Hit GAATGACTGGGTTTGCTTTTCTACTCAAGGTCAGATGTAGGTCATGTAAC 5 0.125 No Hit GCGAAGCCAATCCAATTCTCATTCTCGCGTCCAGCCGCGAACCCGAAAGC 5 0.125 No Hit GTTCTCTCGATGGGGACGATTGCACACAAACAACGGTCTCAATGTTGGTT 5 0.125 No Hit CGTAAAAGCCAGCAGCGAAGCACCCGAAAGCATAAGAACTGTTCAAACGG 5 0.125 No Hit TTTTATGCCAGCTCAGTGGTATTTGGTCAGAAGTGAGATCTGCAATTACA 5 0.125 No Hit TCCTAGATCTCGCTCCATCGCGTAGGGTTTGAGATGTTTAAGGGTTACCA 5 0.125 No Hit GAGTCTTGATATTGTCGGCTCATCACATCCGCGGAGAAGGAATGTTTAAA 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 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra Read 1294425 spots for ERR5262814.sra Written 1294425 spots for ERR5262814.sra Read 1294412 spots for ERR5262814.sra Written 1294412 spots for ERR5262814.sra SRR ids: ['ERR5262814.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_y49cmne3 ERR5262814.sra spots: 25888253 blocks: [[1, 1294412], [1294413, 2588824], [2588825, 3883236], [3883237, 5177648], [5177649, 6472060], [6472061, 7766472], [7766473, 9060884], [9060885, 10355296], [10355297, 11649708], [11649709, 12944120], [12944121, 14238532], [14238533, 15532944], [15532945, 16827356], [16827357, 18121768], [18121769, 19416180], [19416181, 20710592], [20710593, 22005004], [22005005, 23299416], [23299417, 24593828], [24593829, 25888253]] ERR5262814 file size 8428013 ERR5262814 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 ERR5262814 ERR5262814_1.fastq ERR5262814_2.fastq Input file: ERR5262814_1.fastq Paired file: ERR5262814_2.fastq trimmed: ERR5262814-trimmed-pair1.fastq, ERR5262814-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 Fri Dec 6 12:35:02 2024 >> started Fri Dec 6 12:35:26 2024 >> done (24.279s) 25888253 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 25888253 (100.00%) read pairs available; of these: 7509 ( 0.03%) trimmed read pairs available after processing 25880744 (99.97%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 21 1 0.00% 22 0 0.00% 23 0 0.00% 24 1 0.00% 25 0 0.00% 26 3 0.00% 27 1 0.00% 28 2 0.00% 29 1 0.00% 30 3 0.00% 31 2 0.00% 32 2 0.00% 33 0 0.00% 34 7 0.00% 35 1 0.00% 36 4 0.00% 37 1 0.00% 38 4 0.00% 39 4 0.00% 40 2 0.00% 41 1 0.00% 42 3 0.00% 43 2 0.00% 44 1 0.00% 45 2 0.00% 46 3 0.00% 47 2 0.00% 48 2 0.00% 49 439 0.00% 50 443 0.00% 51 576 0.00% 52 611 0.00% 53 633 0.00% 54 678 0.00% 55 710 0.00% 56 885 0.00% 57 929 0.00% 58 1113 0.00% 59 1313 0.01% 60 1386 0.01% 61 1609 0.01% 62 1767 0.01% 63 2075 0.01% 64 2311 0.01% 65 2445 0.01% 66 2760 0.01% 67 3017 0.01% 68 3415 0.01% 69 3922 0.02% 70 4566 0.02% 71 5330 0.02% 72 5888 0.02% 73 6645 0.03% 74 7260 0.03% 75 7994 0.03% 76 8959 0.03% 77 9572 0.04% 78 10576 0.04% 79 11582 0.04% 80 12839 0.05% 81 14327 0.06% 82 16269 0.06% 83 18186 0.07% 84 19727 0.08% 85 21480 0.08% 86 22492 0.09% 87 23940 0.09% 88 25204 0.10% 89 26950 0.10% 90 28985 0.11% 91 31379 0.12% 92 33820 0.13% 93 36030 0.14% 94 38628 0.15% 95 40736 0.16% 96 42071 0.16% 97 43896 0.17% 98 45304 0.17% 99 46828 0.18% 100 48993 0.19% 101 50738 0.20% 102 53044 0.20% 103 56065 0.22% 104 57553 0.22% 105 60683 0.23% 106 62228 0.24% 107 62857 0.24% 108 63892 0.25% 109 65118 0.25% 110 66702 0.26% 111 68639 0.27% 112 71602 0.28% 113 72709 0.28% 114 75561 0.29% 115 76577 0.30% 116 78525 0.30% 117 79867 0.31% 118 81215 0.31% 119 80881 0.31% 120 81265 0.31% 121 82981 0.32% 122 84162 0.33% 123 85710 0.33% 124 88908 0.34% 125 89395 0.35% 126 89796 0.35% 127 91452 0.35% 128 91860 0.35% 129 92626 0.36% 130 92229 0.36% 131 93737 0.36% 132 94228 0.36% 133 95727 0.37% 134 97921 0.38% 135 98999 0.38% 136 99772 0.39% 137 100067 0.39% 138 99998 0.39% 139 101815 0.39% 140 101235 0.39% 141 102310 0.40% 142 103570 0.40% 143 104096 0.40% 144 105559 0.41% 145 106121 0.41% 146 109770 0.42% 147 208877 0.81% 148 102518 0.40% 149 101469 0.39% 150 20856076 80.56% 25888253 reads passed initial QC criterion=sequence-density sequence-density=1.35 sequence-density-rank=1 fanout-score=3.62 fanout-score-rank=22 prefix-density=1.75 prefix-fanout=2.8 sequence=CGCTGCTGGTCCGGGGGGATGCCCTCCTTGTCCTGGATCTT criterion=fanout-score sequence-density=0.05 sequence-density-rank=26 fanout-score=208.21 fanout-score-rank=1 prefix-density=1.46 prefix-fanout=7.2 sequence=CCGCCGCCGCCTCCTCCGCCACGACCGCCGCCGCCACCACGGGACTGCGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCCCTCGATGGCGTCGCGCATCGACTGCTCGCTGGCGAAGGTGACGAAGCCGAACCCGCGGGAACGGCCAGTCTCCCTGTCGTTGATGATCTTGGAGTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCGTCGGTAGCCCAGGCGAGGCCGCCCACGAAGCAACGGTACTCAACTTCCGCCATTCCTCCCACTAAACCCTAACGAACCGGAACC criterion=sequence-density sequence-density=6.47 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=21 prefix-density=6.43 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.22 sequence-density-rank=19 fanout-score=63.60 fanout-score-rank=1 prefix-density=6.66 prefix-fanout=2.1 sequence=GTTCCGGTTCGCGGCTAGCAGTAGTTGTTGTAGTAGCAGCTAGGGTTTCCGGTAGGGTTCCGTCGAGATCGCCATGGATGAGTACCGCTGCTTCGTGGG 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 CGCTGCTGGTCCGGGGGGATGCCCTCCTTGTCCTGGATCTT -y CGGTTCCGGTTC -o ERR5262814 ERR5262814_1.fastq ERR5262814_2.fastq Input file: ERR5262814_1.fastq Paired file: ERR5262814_2.fastq trimmed: ERR5262814-trimmed-pair1.fastq, ERR5262814-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): CGCTGCTGGTCCGGGGGGATGCCCTCCTTGTCCTGGATCTT -- paired 3' end adapter sequence (-y): CGGTTCCGGTTC -- 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 Fri Dec 6 12:37:55 2024 >> started Fri Dec 6 12:38:11 2024 >> done (15.202s) 15532952 read pairs processed; of these: 269 ( 0.00%) short read pairs filtered out after trimming by size control 1664 ( 0.01%) empty read pairs filtered out after trimming by size control 15531019 (99.99%) read pairs available; of these: 156 ( 0.00%) trimmed read pairs available after processing 15530863 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 21 1 0.00% 22 0 0.00% 23 0 0.00% 24 1 0.00% 25 0 0.00% 26 1 0.00% 27 1 0.00% 28 1 0.00% 29 1 0.00% 30 2 0.00% 31 2 0.00% 32 2 0.00% 33 0 0.00% 34 4 0.00% 35 0 0.00% 36 1 0.00% 37 1 0.00% 38 2 0.00% 39 2 0.00% 40 0 0.00% 41 1 0.00% 42 2 0.00% 43 3 0.00% 44 1 0.00% 45 2 0.00% 46 2 0.00% 47 1 0.00% 48 1 0.00% 49 385 0.00% 50 399 0.00% 51 516 0.00% 52 549 0.00% 53 558 0.00% 54 462 0.00% 55 340 0.00% 56 121 0.00% 57 226 0.00% 58 714 0.00% 59 1189 0.01% 60 1278 0.01% 61 512 0.00% 62 558 0.00% 63 1909 0.01% 64 764 0.00% 65 1600 0.01% 66 2084 0.01% 67 1172 0.01% 68 2728 0.02% 69 2648 0.02% 70 2214 0.01% 71 3090 0.02% 72 3118 0.02% 73 3980 0.03% 74 5159 0.03% 75 5214 0.03% 76 4059 0.03% 77 6609 0.04% 78 6438 0.04% 79 6507 0.04% 80 7914 0.05% 81 8044 0.05% 82 10171 0.07% 83 11283 0.07% 84 11153 0.07% 85 13140 0.08% 86 13000 0.08% 87 14329 0.09% 88 15292 0.10% 89 17236 0.11% 90 17113 0.11% 91 18710 0.12% 92 19851 0.13% 93 22402 0.14% 94 22509 0.14% 95 24648 0.16% 96 25345 0.16% 97 26351 0.17% 98 27244 0.18% 99 26986 0.17% 100 30211 0.19% 101 30315 0.20% 102 32076 0.21% 103 32921 0.21% 104 34797 0.22% 105 35498 0.23% 106 38411 0.25% 107 36084 0.23% 108 38567 0.25% 109 38622 0.25% 110 40381 0.26% 111 40752 0.26% 112 43062 0.28% 113 43891 0.28% 114 45071 0.29% 115 46359 0.30% 116 46085 0.30% 117 48222 0.31% 118 48124 0.31% 119 49155 0.32% 120 46874 0.30% 121 50169 0.32% 122 49339 0.32% 123 50936 0.33% 124 52516 0.34% 125 53455 0.34% 126 53523 0.34% 127 54745 0.35% 128 55061 0.35% 129 55200 0.36% 130 54684 0.35% 131 56239 0.36% 132 56369 0.36% 133 57254 0.37% 134 58402 0.38% 135 59032 0.38% 136 60081 0.39% 137 60046 0.39% 138 59888 0.39% 139 61138 0.39% 140 60667 0.39% 141 61329 0.39% 142 61765 0.40% 143 62549 0.40% 144 63680 0.41% 145 63496 0.41% 146 65669 0.42% 147 125333 0.81% 148 61568 0.40% 149 60683 0.39% 150 12520869 80.62% criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=4.29 fanout-score-rank=33 prefix-density=0.29 prefix-fanout=3.1 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.06 sequence-density-rank=26 fanout-score=234.34 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=22.3 sequence=CGCCGCCGCCACCACGGGACTGCGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCCCTCGATGGCGTCGCGCATCGACTGCTCGCTGGCGAAGGTGACGAAGCCGAACCCGCGGGAACGGCCAGTCTCCCTGTCGTTGATGATCTTGGAGTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCGTCGGTAGCCCAGGCGAGGCCGCCCACGAAGCAACGGTACTCAACTTCCGCCATTCCTCCCACTAAACCCTAACGAACCGGAACC criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=37 prefix-density=0.79 prefix-fanout=2.1 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.10 sequence-density-rank=24 fanout-score=273.96 fanout-score-rank=1 prefix-density=1.13 prefix-fanout=23.5 sequence=CGCCGCCGCCGG ERR5262814 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 12:39:27 Started mapping on | Dec 06 12:39:27 Finished on | Dec 06 12:41:12 Mapping speed, Million of reads per hour | 887.53 Number of input reads | 25886320 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 21536059 Uniquely mapped reads % | 83.19% Average mapped length | 288.99 Number of splices: Total | 20672172 Number of splices: Annotated (sjdb) | 19265231 Number of splices: GT/AG | 20390490 Number of splices: GC/AG | 232145 Number of splices: AT/AC | 12822 Number of splices: Non-canonical | 36715 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 2.40 Insertion rate per base | 0.01% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 224424 % of reads mapped to multiple loci | 0.87% Number of reads mapped to too many loci | 625 % of reads mapped to too many loci | 0.00% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 15.93% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4125837 4125837 4125837 N_multimapping 224424 224424 224424 N_noFeature 794650 20970692 965451 N_ambiguous 521482 3923 127801 UnstrandedReadsAssigned:20219927 PositiveStrandReadsAssigned:561444 NegativeStrandReadsAssigned:20442807 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR5262814 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: ERR5262814-trimmed-pair1.fastq ERR5262814-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,886,320 reads, 23,972,613 reads pseudoaligned [quant] estimated average fragment length: 251.038 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,376 rounds 52973 ERR5262814.ke.tsv 35125 ERR5262814.se.tsv 88098 total ==> ERR5262814.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 686.725 0 0 PNS24247 1044 793.962 115.128 8.88591 PNS24249 1928 1677.96 316.964 11.5758 PNS24246 1044 793.962 115.128 8.88591 PNS24248 1044 793.962 115.128 8.88591 PNS24244 1471 1220.96 199.652 10.0206 PNS24243 293 113.505 0 0 KQK14069 1603 1352.96 22291.5 1009.66 KQK14071 474 251.18 652.978 159.307 ==> ERR5262814.se.tsv <== BRADI_1g14170v3 20962 BRADI_1g53295v3 164 BRADI_1g59795v3 510 BRADI_1g07683v3 0 BRADI_1g00485v3 13 BRADI_1g20270v3 786 BRADI_1g74790v3 2128 BRADI_1g09890v3 0 BRADI_1g77505v3 188 BRADI_1g48960v3 0 ERR5262814 completed mapping pipeline successfully