Starting /dee2/code/volunteer_pipeline.sh SRR24040053 current disk space = 1548873879552 free memory = 1395084240 SRR24040053 SRAfilesize 4bb3e65df3f951f8d84ee97aa6c9a8ff SRR24040053.sra SRR24040053.sra file validated SRR24040053 is paired end SRR24040053 is conventional basespace SRR24040053 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040053_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 54 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.50825 37.0 37.0 37.0 37.0 37.0 2 36.4905 37.0 37.0 37.0 37.0 37.0 3 36.4405 37.0 37.0 37.0 37.0 37.0 4 36.713 37.0 37.0 37.0 37.0 37.0 5 36.632 37.0 37.0 37.0 37.0 37.0 6 31.9305 37.0 25.0 37.0 11.0 37.0 7 36.6435 37.0 37.0 37.0 37.0 37.0 8 36.696 37.0 37.0 37.0 37.0 37.0 9 27.836 37.0 11.0 37.0 11.0 37.0 10-14 36.582499999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.3995 37.0 37.0 37.0 37.0 37.0 20-24 36.2687 37.0 37.0 37.0 34.6 37.0 25-29 36.321999999999996 37.0 37.0 37.0 34.6 37.0 30-34 35.6892 37.0 37.0 37.0 31.8 37.0 35-39 36.4954 37.0 37.0 37.0 37.0 37.0 40-44 36.4208 37.0 37.0 37.0 37.0 37.0 45-49 36.08219999999999 37.0 37.0 37.0 34.6 37.0 50-54 36.3911 37.0 37.0 37.0 37.0 37.0 55-59 35.8361 37.0 37.0 37.0 34.6 37.0 60-64 35.79899999999999 37.0 37.0 37.0 34.6 37.0 65-69 36.3761 37.0 37.0 37.0 37.0 37.0 70-74 36.417 37.0 37.0 37.0 37.0 37.0 75-79 36.4969 37.0 37.0 37.0 37.0 37.0 80-84 35.6538 37.0 37.0 37.0 32.2 37.0 85-89 36.3096 37.0 37.0 37.0 37.0 37.0 90-94 36.44735000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.346000000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.2044 37.0 37.0 37.0 37.0 37.0 105-109 36.3101 37.0 37.0 37.0 37.0 37.0 110-114 36.16420000000001 37.0 37.0 37.0 37.0 37.0 115-119 35.85045 37.0 37.0 37.0 34.6 37.0 120-124 35.620050000000006 37.0 37.0 37.0 32.2 37.0 125-129 36.1924 37.0 37.0 37.0 37.0 37.0 130-134 35.4142 37.0 37.0 37.0 31.8 37.0 135-139 36.02485 37.0 37.0 37.0 37.0 37.0 140-144 35.73915 37.0 37.0 37.0 37.0 37.0 145-149 35.140750000000004 37.0 37.0 37.0 31.8 37.0 150 28.221 37.0 11.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 4.0 26 6.0 27 6.0 28 18.0 29 15.0 30 18.0 31 45.0 32 50.0 33 77.0 34 171.0 35 659.0 36 2887.0 37 42.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.89711417816813 11.869510664993726 6.248431618569636 35.9849435382685 2 25.0 11.625 30.925000000000004 32.45 3 22.975 14.6 23.225 39.2 4 28.299999999999997 23.275000000000002 20.05 28.375 5 28.000000000000004 27.150000000000002 21.575 23.275000000000002 6 23.825 31.474999999999998 20.599999999999998 24.099999999999998 7 19.85 20.5 37.824999999999996 21.825 8 20.4 17.8 31.15 30.65 9 22.900000000000002 23.075000000000003 27.375 26.650000000000002 10-14 25.09 23.635 23.400000000000002 27.875 15-19 25.724999999999998 21.485000000000003 24.205 28.585 20-24 24.990000000000002 23.455000000000002 23.724999999999998 27.83 25-29 25.165 21.89 24.445 28.499999999999996 30-34 25.31 22.175 24.19 28.325 35-39 25.21 21.87 23.87 29.049999999999997 40-44 26.27 21.57 23.51 28.65 45-49 25.14 22.14 24.19 28.53 50-54 24.145 22.13 24.555 29.17 55-59 25.185000000000002 21.634999999999998 23.78 29.4 60-64 24.635 21.505 24.825 29.035 65-69 24.815 22.065 24.26 28.860000000000003 70-74 25.874999999999996 21.8 23.919999999999998 28.405 75-79 26.68 21.705 22.82 28.794999999999998 80-84 25.655 21.915000000000003 23.535 28.895 85-89 26.155 21.584999999999997 23.005 29.255 90-94 26.32131606580329 22.146107305365266 23.121156057802892 28.41142057102855 95-99 24.905 22.345000000000002 23.61 29.14 100-104 26.595000000000002 21.94 22.235 29.23 105-109 26.179999999999996 23.435 22.33 28.055000000000003 110-114 25.75 23.635 22.6 28.015 115-119 26.976348817440872 23.021151057552878 21.83609180459023 28.16640832041602 120-124 26.256312815640783 23.481174058702937 22.33611680584029 27.92639631981599 125-129 26.86 23.3 21.875 27.965 130-134 27.18 22.825 21.85 28.144999999999996 135-139 27.13135656782839 23.101155057752887 22.196109805490273 27.571378568928445 140-144 27.801390069503473 22.86114305715286 21.901095054752737 27.43637181859093 145-149 27.85639281964098 22.13110655532777 22.4011200560028 27.611380569028455 150 27.55 25.55 20.9 26.0 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.5 25 0.5 26 0.5 27 1.0 28 1.5 29 2.5 30 2.0 31 2.5 32 4.5 33 6.5 34 6.5 35 8.5 36 18.5 37 20.0 38 17.5 39 33.0 40 45.5 41 56.5 42 69.5 43 79.5 44 96.0 45 103.5 46 139.0 47 168.0 48 174.5 49 192.5 50 196.5 51 187.0 52 175.0 53 179.5 54 162.0 55 148.5 56 156.0 57 140.0 58 121.5 59 108.0 60 105.5 61 102.0 62 86.0 63 93.0 64 102.0 65 92.0 66 83.5 67 74.5 68 75.5 69 66.0 70 48.5 71 55.0 72 55.0 73 38.0 74 25.5 75 25.5 76 22.0 77 11.5 78 7.0 79 3.5 80 1.5 81 0.5 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 1.0 99 1.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.375 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 0.005 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.005 120-124 0.005 125-129 0.0 130-134 0.0 135-139 0.005 140-144 0.005 145-149 0.005 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.325 #Duplication Level Percentage of deduplicated Percentage of total 1 88.24779836015792 72.65 2 7.197084725174613 11.85 3 2.247191011235955 5.55 4 1.0932280595201944 3.5999999999999996 5 0.5769814758578804 2.375 6 0.2733070148800486 1.35 7 0.18220467658669906 1.05 8 0.06073489219556636 0.4 9 0.03036744609778318 0.22499999999999998 >10 0.09110233829334953 0.95 >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 GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 15 0.375 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 12 0.3 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 11 0.27499999999999997 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 9 0.22499999999999998 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 8 0.2 No Hit GCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGC 8 0.2 No Hit CCCCGCTCAGGCATAGTTCACCATCTTTCGGGTCCCGACAGGCGTGCTCC 7 0.17500000000000002 No Hit GTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTC 7 0.17500000000000002 No Hit GTCGTCTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAG 7 0.17500000000000002 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 7 0.17500000000000002 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 7 0.17500000000000002 No Hit GGCAGAAATCACATTGCGTCAGCATCCGCGAGGACCATCGCAATGCTTTG 7 0.17500000000000002 No Hit ATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTCAGGC 6 0.15 No Hit CTCCTACTCATCGGGGCATGGCGCTCGCCCAGATGGCCGGGTGTGGGTCG 6 0.15 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 6 0.15 No Hit GTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTA 6 0.15 No Hit CCCGGATCGGCCCGGTCAGACCGGGCCTTGGAGCCAAAAGGAGGGGACTT 6 0.15 No Hit GTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACT 6 0.15 No Hit ATCCGTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCAC 6 0.15 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 6 0.15 No Hit GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 6 0.15 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit GTCAGTATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGC 5 0.125 No Hit CTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGAC 5 0.125 No Hit GTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGACGGAGTCTACCGC 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTAT 5 0.125 TruSeq Adapter, Index 7 (97% over 36bp) CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 5 0.125 No Hit CTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGG 5 0.125 No Hit GCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTA 5 0.125 No Hit GTTCCATTGGCCAGAGGCTGTTCACCTTGGAGACCTGATGCGGTTATGAG 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 5 0.125 No Hit GTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATCCAT 5 0.125 No Hit CCCGACTCGTTGACGGCGCCTCGTGGGGCGACAGGGTCCGGGCCGGACGG 5 0.125 No Hit GCCCACTTGGAGCTCCCGATTCCATGGCGCGGCTCACCGGAGCAGCCGCG 5 0.125 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 5 0.125 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 5 0.125 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 5 0.125 No Hit GCGGTTATGAGTACGACCGGGCGTGAACGGTACTCGGTCCTCCGGATTTT 5 0.125 No Hit GCGCAGTTGGGCACCGTAACCCGGCTTCCGGTTCATCCCGCATCGCCAGT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.07500000000000001 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.2 0.0 0.0 0.0 0.0 58-59 0.30000000000000004 0.0 0.0 0.0 0.0 60-61 0.3875 0.0 0.0 0.0 0.0 62-63 0.575 0.0 0.0 0.0 0.0 64-65 0.7375 0.0 0.0 0.0 0.0 66-67 0.875 0.0 0.0 0.0 0.0 68-69 1.0125 0.0 0.0 0.0 0.0 70-71 1.225 0.0 0.0 0.0 0.0 72-73 1.375 0.0 0.0 0.0 0.0 74-75 1.525 0.0 0.0 0.0 0.0 76-77 1.7 0.0 0.0 0.0 0.0 78-79 2.0375 0.0 0.0 0.0 0.0 80-81 2.375 0.0 0.0 0.0 0.0 82-83 2.6625 0.0 0.0 0.0 0.0 84-85 3.0375 0.0 0.0 0.0 0.0 86-87 3.475 0.0 0.0 0.0 0.0 88-89 3.9625000000000004 0.0 0.0 0.0 0.0 90-91 4.425000000000001 0.0 0.0 0.0 0.0 92-93 4.9 0.0 0.0 0.0 0.0 94-95 5.262499999999999 0.0 0.0 0.0 0.0 96-97 5.7875 0.0 0.0 0.0 0.0 98-99 6.3125 0.0 0.0 0.0 0.0 100-101 6.987500000000001 0.0 0.0 0.0 0.0 102-103 7.612500000000001 0.0 0.0 0.0 0.0 104-105 8.350000000000001 0.0 0.0 0.0 0.0 106-107 9.15 0.0 0.0 0.0 0.0 108-109 9.925 0.0 0.0 0.0 0.0 110-111 10.5625 0.0 0.0 0.0 0.0 112-113 11.3125 0.0 0.0 0.0 0.0 114-115 12.0125 0.0 0.0 0.0 0.0 116-117 12.7 0.0 0.0 0.0 0.0 118-119 13.537500000000001 0.0 0.0 0.0 0.0 120-121 14.462499999999999 0.0 0.0 0.0 0.0 122-123 15.5125 0.0 0.0 0.0 0.0 124-125 16.237499999999997 0.0 0.0 0.0 0.0 126-127 17.0625 0.0 0.0 0.0 0.0 128-129 18.1 0.0 0.0 0.0 0.0 130-131 19.0875 0.0 0.0 0.0 0.0 132-133 20.174999999999997 0.0 0.0 0.0 0.0 134-135 20.9875 0.0 0.0 0.0 0.0 136-137 21.875 0.0 0.0 0.0 0.0 138 22.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 20 0.006139246 28.8 140-144 >>END_MODULE SRR24040053 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040053_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 54 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.253 37.0 37.0 37.0 37.0 37.0 2 35.387 37.0 37.0 37.0 37.0 37.0 3 27.775 37.0 11.0 37.0 11.0 37.0 4 35.212 37.0 37.0 37.0 37.0 37.0 5 35.693 37.0 37.0 37.0 37.0 37.0 6 35.648 37.0 37.0 37.0 37.0 37.0 7 35.648 37.0 37.0 37.0 37.0 37.0 8 35.1565 37.0 37.0 37.0 37.0 37.0 9 32.4995 37.0 37.0 37.0 11.0 37.0 10-14 34.9494 37.0 37.0 37.0 29.8 37.0 15-19 34.206 37.0 34.6 37.0 27.0 37.0 20-24 33.955600000000004 37.0 34.6 37.0 31.8 37.0 25-29 34.7466 37.0 37.0 37.0 32.2 37.0 30-34 32.3865 34.6 29.4 37.0 26.6 37.0 35-39 35.1991 37.0 37.0 37.0 34.6 37.0 40-44 34.9618 37.0 37.0 37.0 34.6 37.0 45-49 35.209999999999994 37.0 37.0 37.0 37.0 37.0 50-54 35.2879 37.0 37.0 37.0 37.0 37.0 55-59 35.2225 37.0 37.0 37.0 37.0 37.0 60-64 35.108999999999995 37.0 37.0 37.0 37.0 37.0 65-69 34.8644 37.0 37.0 37.0 34.6 37.0 70-74 34.236000000000004 37.0 34.6 37.0 29.4 37.0 75-79 32.9414 34.6 31.8 37.0 29.4 37.0 80-84 34.4738 37.0 37.0 37.0 29.4 37.0 85-89 34.0148 37.0 37.0 37.0 21.8 37.0 90-94 33.463499999999996 37.0 31.8 37.0 27.0 37.0 95-99 34.83839999999999 37.0 37.0 37.0 29.8 37.0 100-104 33.824200000000005 37.0 34.6 37.0 24.6 37.0 105-109 34.7374 37.0 37.0 37.0 25.0 37.0 110-114 33.265 37.0 34.6 37.0 19.4 37.0 115-119 34.3651 37.0 37.0 37.0 25.0 37.0 120-124 33.63969999999999 37.0 37.0 37.0 19.4 37.0 125-129 33.8815 37.0 37.0 37.0 25.0 37.0 130-134 33.8305 37.0 37.0 37.0 25.0 37.0 135-139 33.558299999999996 37.0 37.0 37.0 11.0 37.0 140-144 33.443850000000005 37.0 37.0 37.0 13.8 37.0 145-149 33.0312 37.0 37.0 37.0 11.0 37.0 150 33.049 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 14.0 14 25.0 15 24.0 16 17.0 17 4.0 18 17.0 19 18.0 20 22.0 21 38.0 22 43.0 23 25.0 24 29.0 25 23.0 26 18.0 27 16.0 28 18.0 29 17.0 30 39.0 31 75.0 32 144.0 33 177.0 34 399.0 35 1192.0 36 1589.0 37 16.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.824999999999996 17.8 6.9750000000000005 30.4 2 35.8 20.200000000000003 23.575 20.424999999999997 3 26.224999999999998 27.224999999999998 22.275 24.275 4 32.6 30.025000000000002 17.025000000000002 20.349999999999998 5 33.300000000000004 31.674999999999997 15.7 19.325 6 30.2 32.15 15.55 22.1 7 28.1 18.825 28.125 24.95 8 27.975 20.1 22.05 29.875 9 27.6 23.375 23.974999999999998 25.05 10-14 30.31 24.555 19.580000000000002 25.555 15-19 30.54 24.125 20.330000000000002 25.005 20-24 29.744999999999997 25.435000000000002 20.035 24.785 25-29 28.915000000000003 25.130000000000003 20.635 25.319999999999997 30-34 28.189999999999998 26.900000000000002 19.79 25.119999999999997 35-39 28.444999999999997 25.965 19.96 25.629999999999995 40-44 29.555 25.195 20.169999999999998 25.080000000000002 45-49 28.87 25.55 20.565 25.014999999999997 50-54 28.665000000000003 25.69 19.830000000000002 25.814999999999998 55-59 28.754999999999995 25.285000000000004 20.979999999999997 24.98 60-64 29.409999999999997 25.27 19.755 25.564999999999998 65-69 28.99 25.735000000000003 20.03 25.245 70-74 28.7 25.669999999999998 19.79 25.840000000000003 75-79 28.76 26.1 20.25 24.89 80-84 29.085 25.455 20.71 24.75 85-89 29.18 25.525 20.580000000000002 24.715 90-94 28.665000000000003 26.435 20.285 24.615000000000002 95-99 30.615 25.575 19.61 24.2 100-104 29.975 25.935000000000002 20.615 23.474999999999998 105-109 30.445 25.629999999999995 20.8 23.125 110-114 31.31 26.729999999999997 18.375 23.585 115-119 31.95 25.89 19.12 23.04 120-124 32.37 25.855 19.465 22.31 125-129 33.839999999999996 25.515 18.73 21.915000000000003 130-134 34.92 25.415 18.715 20.95 135-139 35.96 25.319999999999997 18.315 20.405 140-144 37.001850092504625 24.7912395619781 17.83089154457723 20.376018800940045 145-149 38.055 24.26 17.835 19.85 150 39.925 24.05 18.099999999999998 17.925 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 1.5 3 3.5 4 2.0 5 0.0 6 2.0 7 5.0 8 3.5 9 2.0 10 4.5 11 3.0 12 1.5 13 2.5 14 3.5 15 4.5 16 3.0 17 4.0 18 3.5 19 1.0 20 1.5 21 3.5 22 4.0 23 3.5 24 3.0 25 2.5 26 2.0 27 2.5 28 5.0 29 7.0 30 8.0 31 7.0 32 6.0 33 8.5 34 10.0 35 12.5 36 17.0 37 21.5 38 22.0 39 33.5 40 48.5 41 52.0 42 60.0 43 76.0 44 96.0 45 104.0 46 111.5 47 145.5 48 157.5 49 138.5 50 143.0 51 165.5 52 169.0 53 178.5 54 179.5 55 153.0 56 145.5 57 133.0 58 117.5 59 114.0 60 108.0 61 100.5 62 93.0 63 83.5 64 85.5 65 90.5 66 81.5 67 89.0 68 99.5 69 78.0 70 69.0 71 63.0 72 39.0 73 26.0 74 24.0 75 29.0 76 24.5 77 17.0 78 14.5 79 8.0 80 2.0 81 1.5 82 2.5 83 1.5 84 1.0 85 2.5 86 2.5 87 0.5 88 0.0 89 0.0 90 1.0 91 3.0 92 3.0 93 1.5 94 1.5 95 1.0 96 2.0 97 4.5 98 5.5 99 6.5 100 9.0 >>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 0.005 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.4 #Duplication Level Percentage of deduplicated Percentage of total 1 92.08612975391499 82.325 2 5.732662192393736 10.25 3 1.45413870246085 3.9 4 0.33557046979865773 1.2 5 0.19574944071588368 0.8750000000000001 6 0.05592841163310962 0.3 7 0.08389261744966443 0.525 8 0.0 0.0 9 0.02796420581655481 0.22499999999999998 >10 0.02796420581655481 0.4 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 16 0.4 No Hit GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 9 0.22499999999999998 No Hit CTGAAACCTGGGATGCGCAAGGAAGCTGACGAGCGGGAGGCCCTCACGGG 7 0.17500000000000002 No Hit GGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCA 7 0.17500000000000002 No Hit GTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGT 7 0.17500000000000002 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAA 6 0.15 No Hit CCGGAAGCCGGGTTACGGTGCCCAACTGCGCGCTAACCTAGAACCCACAA 6 0.15 No Hit GTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAAT 5 0.125 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 5 0.125 No Hit CCAGCTTGAGAATCGGGCGGCCGTGCCGTCCGAATTGTAGTCTGGAGAGG 5 0.125 No Hit GTGAAATACCACTACTTTTAACGTTATTTTACTTATTCCGTGGGTCGGAA 5 0.125 No Hit CGACGGGTTCTGAAACCTGGGATGCGCAAGGAAGCTGACGAGCGGGAGGC 5 0.125 No Hit TGAAAATCCGGAGGACCGAGTACCGTTCACGCCCGGTCGTACTCATAACC 5 0.125 No Hit AGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.07500000000000001 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.2 0.0 0.0 0.0 0.0 58-59 0.30000000000000004 0.0 0.0 0.0 0.0 60-61 0.3875 0.0 0.0 0.0 0.0 62-63 0.55 0.0 0.0 0.0 0.0 64-65 0.6875 0.0 0.0 0.0 0.0 66-67 0.825 0.0 0.0 0.0 0.0 68-69 0.9624999999999999 0.0 0.0 0.0 0.0 70-71 1.125 0.0 0.0 0.0 0.0 72-73 1.275 0.0 0.0 0.0 0.0 74-75 1.4125 0.0 0.0 0.0 0.0 76-77 1.575 0.0 0.0 0.0 0.0 78-79 1.8875 0.0 0.0 0.0 0.0 80-81 2.175 0.0 0.0 0.0 0.0 82-83 2.4625 0.0 0.0 0.0 0.0 84-85 2.7875 0.0 0.0 0.0 0.0 86-87 3.1375 0.0 0.0 0.0 0.0 88-89 3.6 0.0 0.0 0.0 0.0 90-91 4.0375 0.0 0.0 0.0 0.0 92-93 4.4875 0.0 0.0 0.0 0.0 94-95 4.8375 0.0 0.0 0.0 0.0 96-97 5.3375 0.0 0.0 0.0 0.0 98-99 5.8375 0.0 0.0 0.0 0.0 100-101 6.512499999999999 0.0 0.0 0.0 0.0 102-103 7.112500000000001 0.0 0.0 0.0 0.0 104-105 7.862500000000001 0.0 0.0 0.0 0.0 106-107 8.6125 0.0 0.0 0.0 0.0 108-109 9.35 0.0 0.0 0.0 0.0 110-111 10.0 0.0 0.0 0.0 0.0 112-113 10.7875 0.0 0.0 0.0 0.0 114-115 11.524999999999999 0.0 0.0 0.0 0.0 116-117 12.2375 0.0 0.0 0.0 0.0 118-119 13.0625 0.0 0.0 0.0 0.0 120-121 14.025 0.0 0.0 0.0 0.0 122-123 15.037500000000001 0.0 0.0 0.0 0.0 124-125 15.825 0.0 0.0 0.0 0.0 126-127 16.675 0.0 0.0 0.0 0.0 128-129 17.7375 0.0 0.0 0.0 0.0 130-131 18.762500000000003 0.0 0.0 0.0 0.0 132-133 19.9125 0.0 0.0 0.0 0.0 134-135 20.8125 0.0 0.0 0.0 0.0 136-137 21.6875 0.0 0.0 0.0 0.0 138 22.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATGGAC 10 0.006973645 144.0 5 GAACAAT 10 0.006973645 144.0 2 >>END_MODULE Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra Read 4250000 spots for SRR24040053.sra Written 4250000 spots for SRR24040053.sra SRR ids: ['SRR24040053.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_n1l72zfz SRR24040053.sra spots: 85000000 blocks: [[1, 4250000], [4250001, 8500000], [8500001, 12750000], [12750001, 17000000], [17000001, 21250000], [21250001, 25500000], [25500001, 29750000], [29750001, 34000000], [34000001, 38250000], [38250001, 42500000], [42500001, 46750000], [46750001, 51000000], [51000001, 55250000], [55250001, 59500000], [59500001, 63750000], [63750001, 68000000], [68000001, 72250000], [72250001, 76500000], [76500001, 80750000], [80750001, 85000000]] SRR24040053 file size 28699002 SRR24040053 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 SRR24040053 SRR24040053_1.fastq SRR24040053_2.fastq Input file: SRR24040053_1.fastq Paired file: SRR24040053_2.fastq trimmed: SRR24040053-trimmed-pair1.fastq, SRR24040053-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 22:06:38 2024 >> started Fri Dec 6 22:08:32 2024 >> done (113.904s) 85000000 read pairs processed; of these: 7209 ( 0.01%) short read pairs filtered out after trimming by size control 78679 ( 0.09%) empty read pairs filtered out after trimming by size control 84914112 (99.90%) read pairs available; of these: 25725914 (30.30%) trimmed read pairs available after processing 59188198 (69.70%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 310 0.00% 19 270 0.00% 20 166 0.00% 21 231 0.00% 22 270 0.00% 23 217 0.00% 24 244 0.00% 25 273 0.00% 26 396 0.00% 27 472 0.00% 28 597 0.00% 29 658 0.00% 30 1231 0.00% 31 973 0.00% 32 1061 0.00% 33 1130 0.00% 34 1439 0.00% 35 1700 0.00% 36 1845 0.00% 37 2145 0.00% 38 2854 0.00% 39 3387 0.00% 40 3888 0.00% 41 4586 0.01% 42 4622 0.01% 43 5099 0.01% 44 5670 0.01% 45 6432 0.01% 46 7437 0.01% 47 9011 0.01% 48 11195 0.01% 49 12827 0.02% 50 14680 0.02% 51 16540 0.02% 52 17904 0.02% 53 19083 0.02% 54 20403 0.02% 55 21659 0.03% 56 23947 0.03% 57 27050 0.03% 58 32410 0.04% 59 35857 0.04% 60 40274 0.05% 61 44483 0.05% 62 48679 0.06% 63 51062 0.06% 64 52489 0.06% 65 53882 0.06% 66 57700 0.07% 67 62378 0.07% 68 67271 0.08% 69 72573 0.09% 70 76401 0.09% 71 83983 0.10% 72 93290 0.11% 73 101116 0.12% 74 103451 0.12% 75 106023 0.12% 76 109931 0.13% 77 113202 0.13% 78 121120 0.14% 79 131330 0.15% 80 141583 0.17% 81 151973 0.18% 82 161012 0.19% 83 165012 0.19% 84 174199 0.21% 85 183637 0.22% 86 197706 0.23% 87 200253 0.24% 88 199807 0.24% 89 205427 0.24% 90 213179 0.25% 91 218412 0.26% 92 236845 0.28% 93 252929 0.30% 94 252798 0.30% 95 270928 0.32% 96 272588 0.32% 97 278175 0.33% 98 292225 0.34% 99 289049 0.34% 100 301300 0.35% 101 300984 0.35% 102 303253 0.36% 103 320867 0.38% 104 317069 0.37% 105 311705 0.37% 106 323567 0.38% 107 331262 0.39% 108 319966 0.38% 109 328886 0.39% 110 327905 0.39% 111 353193 0.42% 112 359550 0.42% 113 350344 0.41% 114 366750 0.43% 115 374862 0.44% 116 386089 0.45% 117 371518 0.44% 118 362229 0.43% 119 378219 0.45% 120 395265 0.47% 121 390943 0.46% 122 404922 0.48% 123 414344 0.49% 124 422663 0.50% 125 417268 0.49% 126 425381 0.50% 127 417635 0.49% 128 407554 0.48% 129 424724 0.50% 130 397816 0.47% 131 409510 0.48% 132 405545 0.48% 133 423835 0.50% 134 426086 0.50% 135 427072 0.50% 136 432026 0.51% 137 431267 0.51% 138 426568 0.50% 139 424411 0.50% 140 418021 0.49% 141 425142 0.50% 142 444411 0.52% 143 429021 0.51% 144 455042 0.54% 145 437227 0.51% 146 438293 0.52% 147 443956 0.52% 148 429020 0.51% 149 420884 0.50% 150 59188198 69.70% 84914112 reads passed initial QC criterion=sequence-density sequence-density=1.59 sequence-density-rank=1 fanout-score=39.18 fanout-score-rank=1 prefix-density=1.69 prefix-fanout=37.0 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTATGCCGTCTTCTGCTTGAAAAGGGGG criterion=fanout-score sequence-density=1.59 sequence-density-rank=1 fanout-score=39.18 fanout-score-rank=1 prefix-density=1.69 prefix-fanout=37.0 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTATGCCGTCTTCTGCTTGAAAAGGGGG criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=2.35 fanout-score-rank=31 prefix-density=0.76 prefix-fanout=2.3 sequence=TTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCACACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGTGCCGGATTATGACTGAACGCCTCTAAGTCAGAATCCAAGCTAGCAAGCGGCGCCTGCGCCCGCCGCCTGCCCCGACCCACGTTAGGGGCGCTTGCGCCCCCAAGGGCACGTGCCATTGGCTAAGCCGTTCCGGCCGACGAGCCGCGTCCGGCCGCCTCGAAGCTCCCTTCCCCACGGGCGGCGGGCTGAATCCTTTGCAGACGACTTAAATACGCGACGGGGCATTGTAAGTGGCAGAGTGGCCTTGCTGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=47.71 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=3.5 sequence=AGCAGCAAGAACAGGGGCAGCAAGGTCAGATCCCTTCGCGCCGGTTCGGGGCCCAGTCACAGGAGTGCGGACAACAGGGTATCTTCTCGCCCCAGCTGCTAGCTCAGATACTACCGGCGATGTGCAATGTGTACCTCCCACCGTACTGCCGCGCCACCGCCGCTGATCAGCCATTCGGACCCGGTGGCTACTGATAAGACAAAGGGCTCTTGTAGTAGATAGATAGGGATCACCGCT SRR24040053 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:09:37 Started mapping on | Dec 06 22:09:37 Finished on | Dec 06 22:21:46 Mapping speed, Million of reads per hour | 419.33 Number of input reads | 84914112 Average input read length | 279 UNIQUE READS: Uniquely mapped reads number | 33785645 Uniquely mapped reads % | 39.79% Average mapped length | 278.67 Number of splices: Total | 25060300 Number of splices: Annotated (sjdb) | 23532858 Number of splices: GT/AG | 24603769 Number of splices: GC/AG | 282955 Number of splices: AT/AC | 14335 Number of splices: Non-canonical | 159241 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 | 2.65 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6347358 % of reads mapped to multiple loci | 7.48% Number of reads mapped to too many loci | 5961155 % of reads mapped to too many loci | 7.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.60% % of reads unmapped: other | 38.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 44781109 44781109 44781109 N_multimapping 6347358 6347358 6347358 N_noFeature 1846314 32918095 2059852 N_ambiguous 833810 1779 241734 UnstrandedReadsAssigned:31105521 PositiveStrandReadsAssigned:865771 NegativeStrandReadsAssigned:31484059 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=128 echo kmer=123 SRR24040053 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: SRR24040053-trimmed-pair1.fastq SRR24040053-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 84,914,112 reads, 38,134,501 reads pseudoaligned [quant] estimated average fragment length: 196.503 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,234 rounds 52973 SRR24040053.ke.tsv 35125 SRR24040053.se.tsv 88098 total ==> SRR24040053.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 740.74 201.156 7.95564 PNS24247 1044 848.497 33.398 1.15313 PNS24249 1928 1732.5 322.237 5.44893 PNS24246 1044 848.497 33.398 1.15313 PNS24248 1044 848.497 33.398 1.15313 PNS24244 1471 1275.5 54.4134 1.24978 PNS24243 293 124.626 0 0 KQK14069 1603 1407.5 8362.17 174.052 KQK14071 474 283.082 53.1499 5.50046 ==> SRR24040053.se.tsv <== BRADI_1g14170v3 7986 BRADI_1g53295v3 41 BRADI_1g59795v3 42 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 1267 BRADI_1g74790v3 66 BRADI_1g09890v3 26 BRADI_1g77505v3 542 BRADI_1g48960v3 15 SRR24040053 completed mapping pipeline successfully