Starting /dee2/code/volunteer_pipeline.sh SRR6127925 current disk space = 1526341709824 free memory = 1560016156 SRR6127925 SRAfilesize 87db65f113f0dee0b4dbd58b07e3c994 SRR6127925.sra SRR6127925.sra file validated SRR6127925 is paired end SRR6127925 is conventional basespace SRR6127925 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127925_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.2885 33.0 33.0 33.0 33.0 33.0 2 32.47125 33.0 33.0 33.0 33.0 33.0 3 32.71125 33.0 33.0 33.0 33.0 33.0 4 36.69 37.0 37.0 37.0 37.0 37.0 5 36.67275 37.0 37.0 37.0 37.0 37.0 6 36.6115 37.0 37.0 37.0 37.0 37.0 7 36.616 37.0 37.0 37.0 37.0 37.0 8 36.6585 37.0 37.0 37.0 37.0 37.0 9 36.638 37.0 37.0 37.0 37.0 37.0 10-11 36.634125 37.0 37.0 37.0 37.0 37.0 12-13 36.611125 37.0 37.0 37.0 37.0 37.0 14-15 38.9115 40.0 40.0 40.0 37.0 40.0 16-17 38.933875 40.0 40.0 40.0 37.0 40.0 18-19 38.839875 40.0 40.0 40.0 37.0 40.0 20-21 38.827875 40.0 40.0 40.0 37.0 40.0 22-23 38.656125 40.0 37.0 40.0 37.0 40.0 24-25 38.516999999999996 40.0 37.0 40.0 37.0 40.0 26-27 38.5055 40.0 37.0 40.0 37.0 40.0 28-29 38.4685 40.0 37.0 40.0 37.0 40.0 30-31 38.42 40.0 37.0 40.0 37.0 40.0 32-33 38.336625 40.0 37.0 40.0 37.0 40.0 34-35 38.236875 40.0 37.0 40.0 37.0 40.0 36-37 38.081375 40.0 37.0 40.0 37.0 40.0 38-39 37.923500000000004 40.0 37.0 40.0 35.0 40.0 40-41 37.834125 40.0 37.0 40.0 33.0 40.0 42-43 37.574625 40.0 37.0 40.0 33.0 40.0 44-45 37.418625 40.0 37.0 40.0 33.0 40.0 46-47 37.038875000000004 40.0 37.0 40.0 33.0 40.0 48-49 36.998875 40.0 37.0 40.0 33.0 40.0 50-51 36.73825 38.5 37.0 40.0 33.0 40.0 52-53 36.380375 37.0 37.0 40.0 33.0 40.0 54-55 35.973375000000004 37.0 37.0 40.0 33.0 40.0 56-57 35.783125 37.0 37.0 40.0 33.0 40.0 58-59 35.528999999999996 37.0 37.0 40.0 30.0 40.0 60-61 35.346375 37.0 37.0 40.0 30.0 40.0 62-63 35.086875 37.0 35.0 37.0 27.0 40.0 64-65 34.8365 37.0 33.0 37.0 27.0 40.0 66-67 34.345124999999996 37.0 33.0 37.0 27.0 40.0 68-69 34.18675 37.0 33.0 37.0 27.0 40.0 70-71 33.95725 37.0 33.0 37.0 27.0 37.0 72-73 33.64175 37.0 33.0 37.0 27.0 37.0 74-75 33.25 37.0 33.0 37.0 27.0 37.0 76-77 30.5855 33.0 30.0 35.0 22.0 37.0 78-79 32.40275 35.0 33.0 37.0 22.0 37.0 80-81 32.535624999999996 37.0 33.0 37.0 22.0 37.0 82-83 32.638875 37.0 33.0 37.0 22.0 37.0 84-85 32.56275 37.0 33.0 37.0 22.0 37.0 86-87 32.552375 37.0 33.0 37.0 22.0 37.0 88-89 32.213125000000005 37.0 33.0 37.0 22.0 37.0 90-91 32.265125 37.0 33.0 37.0 22.0 37.0 92-93 32.01825 37.0 33.0 37.0 22.0 37.0 94-95 31.8615 37.0 33.0 37.0 22.0 37.0 96-97 31.595125 37.0 33.0 37.0 15.0 37.0 98-99 31.132375 37.0 33.0 37.0 8.5 37.0 100 27.41575 33.0 27.0 33.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 1.0 9 7.0 10 4.0 11 5.0 12 2.0 13 4.0 14 12.0 15 9.0 16 11.0 17 13.0 18 12.0 19 8.0 20 17.0 21 21.0 22 18.0 23 23.0 24 23.0 25 22.0 26 25.0 27 38.0 28 48.0 29 66.0 30 45.0 31 100.0 32 105.0 33 134.0 34 171.0 35 274.0 36 559.0 37 1401.0 38 821.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.29071537290715 13.571790969051243 7.179096905124302 41.958396752917295 2 22.325 15.5 38.224999999999994 23.95 3 20.075000000000003 21.475 24.55 33.900000000000006 4 27.474999999999998 28.475 20.75 23.3 5 26.05 30.875000000000004 22.725 20.349999999999998 6 20.45 31.75 26.400000000000002 21.4 7 17.025000000000002 19.1 41.85 22.025 8 20.0 18.6 30.599999999999998 30.8 9 20.075000000000003 18.65 32.875 28.4 10-11 24.712500000000002 27.825 21.1125 26.35 12-13 24.3 21.4375 25.95 28.3125 14-15 22.900000000000002 23.962500000000002 27.474999999999998 25.662499999999998 16-17 23.1125 24.55 25.3125 27.025 18-19 23.6125 23.4875 25.85 27.05 20-21 24.6125 24.75 25.074999999999996 25.5625 22-23 24.275 24.2375 25.924999999999997 25.5625 24-25 23.075000000000003 24.375 25.4625 27.0875 26-27 22.9375 23.724999999999998 26.687499999999996 26.650000000000002 28-29 23.5125 23.1375 26.187500000000004 27.1625 30-31 23.1125 23.7875 25.637500000000003 27.462500000000002 32-33 22.912499999999998 24.3875 26.075 26.625 34-35 23.175 24.337500000000002 25.8125 26.674999999999997 36-37 23.6375 24.224999999999998 26.2625 25.874999999999996 38-39 22.787499999999998 24.05 25.2 27.962500000000002 40-41 23.674999999999997 24.5125 25.4375 26.375 42-43 23.9 24.525 25.674999999999997 25.900000000000002 44-45 24.1375 24.087500000000002 26.1 25.674999999999997 46-47 23.724999999999998 23.0875 26.3625 26.825 48-49 23.175 23.95 25.95 26.924999999999997 50-51 22.9375 24.625 25.7 26.737499999999997 52-53 23.65 23.275000000000002 25.6125 27.462500000000002 54-55 24.6125 23.1 24.975 27.3125 56-57 22.775000000000002 22.475 27.224999999999998 27.525 58-59 23.4625 23.400000000000002 25.474999999999998 27.6625 60-61 23.4375 23.674999999999997 25.162499999999998 27.725 62-63 24.075 23.275000000000002 25.8625 26.787499999999998 64-65 22.5125 23.425 26.6 27.462500000000002 66-67 22.325 24.474999999999998 25.6125 27.5875 68-69 22.625 24.962500000000002 25.174999999999997 27.237499999999997 70-71 24.9 24.05 24.8625 26.187500000000004 72-73 24.8625 24.275 24.212500000000002 26.650000000000002 74-75 24.0 23.7875 25.7125 26.5 76-77 24.2875 23.1625 25.85 26.700000000000003 78-79 23.1625 24.4 24.65 27.787499999999998 80-81 23.799999999999997 23.2625 26.150000000000002 26.787499999999998 82-83 25.424999999999997 23.425 24.725 26.424999999999997 84-85 23.8625 22.6875 25.112499999999997 28.3375 86-87 23.9375 22.75 26.337500000000002 26.974999999999998 88-89 23.575 24.15 25.474999999999998 26.8 90-91 23.5375 23.9125 25.15 27.400000000000002 92-93 24.3 22.8375 26.2125 26.650000000000002 94-95 23.825 23.6125 25.074999999999996 27.487499999999997 96-97 23.9875 23.724999999999998 25.2875 27.0 98-99 25.074999999999996 23.1 25.35 26.474999999999998 100 26.375 22.900000000000002 23.275000000000002 27.450000000000003 >>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 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.0 24 1.0 25 0.5 26 1.0 27 1.0 28 2.0 29 3.5 30 10.5 31 15.0 32 17.5 33 21.5 34 31.5 35 42.0 36 47.0 37 64.0 38 73.5 39 68.0 40 68.0 41 80.5 42 98.0 43 104.5 44 103.5 45 127.5 46 165.5 47 170.5 48 168.5 49 176.0 50 178.0 51 169.0 52 182.0 53 202.0 54 191.0 55 210.5 56 210.5 57 167.5 58 144.0 59 126.5 60 100.5 61 69.0 62 57.0 63 56.5 64 41.0 65 30.0 66 28.0 67 24.0 68 22.5 69 19.5 70 15.5 71 16.5 72 16.5 73 10.5 74 5.5 75 10.5 76 11.0 77 6.5 78 6.0 79 3.0 80 1.0 81 1.0 82 1.0 83 1.0 84 1.0 85 0.5 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 1.4500000000000002 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 84.82499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 88.56469201296787 75.125 2 7.427055702917771 12.6 3 2.564102564102564 6.525 4 0.8547008547008548 2.9000000000000004 5 0.3241968759210138 1.375 6 0.17683465959328026 0.8999999999999999 7 0.05894488653109342 0.35000000000000003 8 0.0 0.0 9 0.02947244326554671 0.22499999999999998 >10 0.0 0.0 >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 GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 9 0.22499999999999998 No Hit GTGGAAAGCTGTGTGTTGATTTCATGAATGCGATTTCTGATATGGCGGCG 7 0.17500000000000002 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 7 0.17500000000000002 No Hit ATCGGGTCCAGCGTGGCAAACAGGAGGTCTTCTTCATAGCTGTCAGCACT 6 0.15 No Hit CCTGACCCCGGGGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTA 6 0.15 No Hit CCACAACCCCGTTTTCACGGTTTAGGCTGCTCCCATTTCGCTCGCCGCTA 6 0.15 No Hit ATCGACTACGCCTTTCGGCCTGATCTTAGGCCCTGACTCACCCTCCGTGG 6 0.15 No Hit GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 6 0.15 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 6 0.15 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 5 0.125 No Hit CTTTCGGCTAACCTAGCCTCCTCCGTCCCTCCGTACCAACAAGGGGTAGT 5 0.125 No Hit CCTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAGT 5 0.125 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 5 0.125 No Hit GTCCAGCGTGGCAAACAGGAGGTCTTCTTCATAGCTGTCAGCACTCGTCA 5 0.125 No Hit CTTACAAGTCCGCTCCTCGGGGAGCTTGATTGATAATTCTGTATAAGGTG 5 0.125 No Hit CAATGACTTCAGCTGACTTGGCGACAGTTCATCATTAAAGATGAGGAGAT 5 0.125 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 5 0.125 No Hit GTCGGTTTCGGGTACAGGTACCCTTTTGTTGAAGGTCGTTCGAGCTTTTC 5 0.125 No Hit CGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTA 5 0.125 No Hit GGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATGG 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 0.0125 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.0625 0.0 0.0 0.0 0.0 56-57 0.0875 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.1875 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.30000000000000004 0.0 0.0 0.0 0.0 80-81 0.36250000000000004 0.0 0.0 0.0 0.0 82-83 0.5125 0.0 0.0 0.0 0.0 84-85 0.8500000000000001 0.0 0.0 0.0 0.0 86-87 1.1625 0.0 0.0 0.0 0.0 88 1.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6127925 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127925_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.7735 33.0 33.0 33.0 33.0 33.0 2 31.852 33.0 33.0 33.0 33.0 33.0 3 31.9835 33.0 33.0 33.0 33.0 33.0 4 35.53675 37.0 37.0 37.0 33.0 37.0 5 35.52325 37.0 37.0 37.0 33.0 37.0 6 35.50525 37.0 37.0 37.0 33.0 37.0 7 35.523 37.0 37.0 37.0 33.0 37.0 8 35.597 37.0 37.0 37.0 33.0 37.0 9 35.768 37.0 37.0 37.0 37.0 37.0 10-11 35.804375 37.0 37.0 37.0 37.0 37.0 12-13 35.754125 37.0 37.0 37.0 37.0 37.0 14-15 37.959125 40.0 37.0 40.0 37.0 40.0 16-17 37.948 40.0 37.0 40.0 37.0 40.0 18-19 38.01825 40.0 37.0 40.0 37.0 40.0 20-21 37.921625 40.0 37.0 40.0 37.0 40.0 22-23 37.216125 40.0 37.0 40.0 33.0 40.0 24-25 37.698125000000005 40.0 37.0 40.0 33.0 40.0 26-27 37.743750000000006 40.0 37.0 40.0 35.0 40.0 28-29 37.8 40.0 37.0 40.0 37.0 40.0 30-31 37.64525 40.0 37.0 40.0 35.0 40.0 32-33 37.52075 40.0 37.0 40.0 33.0 40.0 34-35 37.505125 40.0 37.0 40.0 33.0 40.0 36-37 37.344875 40.0 37.0 40.0 33.0 40.0 38-39 37.21525 40.0 37.0 40.0 33.0 40.0 40-41 37.1015 40.0 37.0 40.0 33.0 40.0 42-43 37.02075 40.0 37.0 40.0 33.0 40.0 44-45 36.835499999999996 40.0 37.0 40.0 33.0 40.0 46-47 36.575500000000005 40.0 37.0 40.0 33.0 40.0 48-49 36.405125 38.5 37.0 40.0 33.0 40.0 50-51 34.630875 37.0 35.0 38.5 30.0 38.5 52-53 34.940375 37.0 35.0 38.5 30.0 40.0 54-55 35.595375000000004 37.0 37.0 40.0 33.0 40.0 56-57 35.537875 37.0 37.0 40.0 33.0 40.0 58-59 35.337875 37.0 37.0 40.0 33.0 40.0 60-61 35.0205 37.0 37.0 37.0 33.0 40.0 62-63 34.894125 37.0 37.0 37.0 33.0 40.0 64-65 34.706125 37.0 35.0 37.0 30.0 40.0 66-67 34.589749999999995 37.0 33.0 37.0 30.0 40.0 68-69 34.285625 37.0 33.0 37.0 27.0 40.0 70-71 34.160375 37.0 33.0 37.0 27.0 37.0 72-73 33.901375 37.0 33.0 37.0 27.0 37.0 74-75 33.71475 37.0 33.0 37.0 27.0 37.0 76-77 33.539625 37.0 33.0 37.0 27.0 37.0 78-79 33.20075 37.0 33.0 37.0 27.0 37.0 80-81 33.009625 37.0 33.0 37.0 27.0 37.0 82-83 32.846875 37.0 33.0 37.0 24.5 37.0 84-85 32.953125 37.0 33.0 37.0 27.0 37.0 86-87 32.928125 37.0 33.0 37.0 27.0 37.0 88-89 32.82325 37.0 33.0 37.0 27.0 37.0 90-91 32.763625 37.0 33.0 37.0 27.0 37.0 92-93 32.581 37.0 33.0 37.0 24.5 37.0 94-95 32.4095 37.0 33.0 37.0 22.0 37.0 96-97 32.175875000000005 37.0 33.0 37.0 22.0 37.0 98-99 32.10075 37.0 33.0 37.0 22.0 37.0 100-101 30.362875000000003 35.0 30.0 37.0 8.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 61.0 3 11.0 4 4.0 5 3.0 6 1.0 7 7.0 8 4.0 9 4.0 10 4.0 11 4.0 12 7.0 13 13.0 14 2.0 15 9.0 16 3.0 17 4.0 18 4.0 19 9.0 20 13.0 21 12.0 22 8.0 23 8.0 24 22.0 25 21.0 26 21.0 27 28.0 28 39.0 29 45.0 30 44.0 31 64.0 32 90.0 33 134.0 34 156.0 35 254.0 36 576.0 37 1563.0 38 748.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.074999999999996 18.0 8.200000000000001 34.725 2 29.525000000000002 22.95 29.275000000000002 18.25 3 22.775000000000002 27.575 24.875 24.775 4 27.425 34.050000000000004 18.025 20.5 5 28.249999999999996 34.55 17.2 20.0 6 23.875 36.6 19.075 20.45 7 22.05 18.25 35.075 24.625 8 25.025 21.025 23.150000000000002 30.8 9 25.8 22.025 26.325 25.85 10-11 28.225 28.199999999999996 19.2125 24.3625 12-13 27.825 22.275 23.150000000000002 26.75 14-15 26.1 25.6 24.175 24.125 16-17 28.125 25.4625 22.25 24.1625 18-19 27.5125 25.7 22.8375 23.95 20-21 27.53532574715518 24.85932224584219 22.78354382893585 24.821808178066775 22-23 27.437499999999996 25.624999999999996 23.5875 23.35 24-25 26.644161040260066 26.344086021505376 23.380845211302827 23.63090772693173 26-27 27.212500000000002 25.112499999999997 23.1875 24.4875 28-29 27.3625 26.05 22.725 23.8625 30-31 27.437499999999996 26.7125 22.3375 23.5125 32-33 26.700000000000003 26.0 23.2375 24.0625 34-35 26.8125 26.55 22.725 23.9125 36-37 28.0625 25.7 22.4625 23.775 38-39 27.762500000000003 26.4625 22.2 23.575 40-41 27.8875 25.45 23.7125 22.95 42-43 27.0 26.137500000000003 23.225 23.6375 44-45 27.1125 24.762500000000003 24.05 24.075 46-47 26.775 26.5375 22.900000000000002 23.7875 48-49 27.987499999999997 25.525 22.5875 23.9 50-51 26.450000000000003 25.5125 24.0125 24.025 52-53 27.125 26.1625 23.200000000000003 23.5125 54-55 27.0625 26.137500000000003 23.1125 23.6875 56-57 27.1625 26.0625 23.5625 23.2125 58-59 27.437499999999996 25.2125 23.5625 23.7875 60-61 27.200000000000003 24.8125 23.8875 24.099999999999998 62-63 26.5 25.637500000000003 24.025 23.8375 64-65 27.150000000000002 26.700000000000003 22.5125 23.6375 66-67 26.900000000000002 26.187500000000004 22.8875 24.025 68-69 26.806701675418854 24.90622655663916 23.455863965991497 24.831207801950487 70-71 28.1875 24.8125 23.5125 23.4875 72-73 27.11927981995499 24.718679669917478 23.680920230057513 24.48112028007002 74-75 26.55 26.325 22.925 24.2 76-77 27.400000000000002 25.362499999999997 24.05 23.1875 78-79 27.51937984496124 24.718679669917478 23.280820205051263 24.48112028007002 80-81 27.6 25.5 22.8125 24.087500000000002 82-83 26.42240840315118 26.172314617981744 23.50881580592722 23.896461172939855 84-85 26.973601901663958 25.534842987614166 23.12023020142625 24.371324909295634 86-87 26.6816704176044 25.35633908477119 23.443360840210055 24.518629657414355 88-89 28.012500000000003 26.674999999999997 22.7375 22.575 90-91 25.825 27.425 23.3375 23.4125 92-93 28.3125 25.1 23.5125 23.075000000000003 94-95 27.6875 25.5125 23.6125 23.1875 96-97 28.425 26.0375 22.525000000000002 23.0125 98-99 27.2625 26.700000000000003 23.05 22.9875 100-101 29.512500000000003 25.924999999999997 22.237499999999997 22.325 >>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 0.5 17 0.5 18 0.0 19 0.0 20 0.5 21 1.0 22 0.5 23 0.0 24 0.0 25 0.5 26 0.5 27 1.5 28 3.5 29 5.5 30 8.5 31 13.5 32 15.5 33 19.5 34 29.0 35 35.0 36 45.0 37 55.0 38 66.5 39 73.5 40 73.0 41 80.0 42 87.5 43 96.0 44 113.0 45 126.5 46 135.0 47 151.0 48 171.5 49 176.0 50 168.5 51 161.5 52 163.0 53 194.0 54 217.0 55 224.0 56 207.5 57 162.0 58 150.5 59 135.0 60 94.0 61 76.0 62 70.5 63 56.0 64 39.5 65 30.0 66 29.5 67 38.0 68 34.5 69 29.0 70 26.0 71 21.5 72 19.5 73 15.5 74 11.5 75 9.0 76 7.5 77 5.5 78 4.5 79 3.0 80 2.5 81 2.0 82 1.5 83 1.0 84 0.5 85 1.0 86 1.0 87 0.0 88 0.0 89 0.5 90 0.5 91 0.0 92 0.5 93 0.5 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 0.0375 22-23 0.0 24-25 0.025 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 0.025 70-71 0.0 72-73 0.025 74-75 0.0 76-77 0.0 78-79 0.025 80-81 0.0 82-83 0.0375 84-85 0.08750000000000001 86-87 0.025 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 89.72524327418432 78.375 2 7.55580995993131 13.200000000000001 3 1.8030910131654265 4.725 4 0.5151688609044075 1.7999999999999998 5 0.28620492272467085 1.25 6 0.08586147681740126 0.44999999999999996 7 0.0 0.0 8 0.028620492272467084 0.2 9 0.0 0.0 >10 0.0 0.0 >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 GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 8 0.2 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 6 0.15 No Hit CATCCCTCCGCAGCTAGCTTCTTAGAGGGACTATCGCCGTTTAGGCGACG 6 0.15 No Hit CAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATTGGTTTATAC 6 0.15 No Hit CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 5 0.125 No Hit GTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGAAA 5 0.125 No Hit CGCATTTTGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCA 5 0.125 No Hit GAAAAACGGTGTGCTTCAAATTGCGCTTGTCGGCTATACAAACGCAGGGA 5 0.125 No Hit CTGGAATCGGTTCAGCCGGAGGTAGGGTCCAGTGGCCGGAAGAGCACCGC 5 0.125 No Hit ACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 5 0.125 No Hit GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 5 0.125 No Hit CTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAGGGGACTT 5 0.125 No Hit GGAACATCCTCGTGTTAGATATTGAGGCTGCTTCGTGTCGGCACGAAGTG 5 0.125 No Hit GCTAACTCCAAAAACCCGTCCTCAGTTCGGATTGCAGGCTGCAACTCGCC 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 0.0125 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.0625 0.0 0.0 0.0 0.0 56-57 0.0875 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.1875 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.30000000000000004 0.0 0.0 0.0 0.0 80-81 0.36250000000000004 0.0 0.0 0.0 0.0 82-83 0.55 0.0 0.0 0.0 0.0 84-85 0.8999999999999999 0.0 0.0 0.0 0.0 86-87 1.1749999999999998 0.0 0.0 0.0 0.0 88-89 1.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647113 spots for SRR6127925.sra Written 1647113 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra Read 1647097 spots for SRR6127925.sra Written 1647097 spots for SRR6127925.sra SRR ids: ['SRR6127925.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a6v3kkul SRR6127925.sra spots: 32941956 blocks: [[1, 1647097], [1647098, 3294194], [3294195, 4941291], [4941292, 6588388], [6588389, 8235485], [8235486, 9882582], [9882583, 11529679], [11529680, 13176776], [13176777, 14823873], [14823874, 16470970], [16470971, 18118067], [18118068, 19765164], [19765165, 21412261], [21412262, 23059358], [23059359, 24706455], [24706456, 26353552], [26353553, 28000649], [28000650, 29647746], [29647747, 31294843], [31294844, 32941956]] SRR6127925 file size 7859919 SRR6127925 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 SRR6127925 SRR6127925_1.fastq SRR6127925_2.fastq Input file: SRR6127925_1.fastq Paired file: SRR6127925_2.fastq trimmed: SRR6127925-trimmed-pair1.fastq, SRR6127925-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 Dec 10 04:19:30 2024 >> started Tue Dec 10 04:20:01 2024 >> done (30.778s) 32941956 read pairs processed; of these: 166290 ( 0.50%) short read pairs filtered out after trimming by size control 480579 ( 1.46%) empty read pairs filtered out after trimming by size control 32295087 (98.04%) read pairs available; of these: 6451043 (19.98%) trimmed read pairs available after processing 25844044 (80.02%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 26 0.00% 19 22 0.00% 20 52 0.00% 21 71 0.00% 22 138 0.00% 23 195 0.00% 24 270 0.00% 25 339 0.00% 26 438 0.00% 27 551 0.00% 28 669 0.00% 29 807 0.00% 30 966 0.00% 31 1136 0.00% 32 1284 0.00% 33 1616 0.01% 34 1725 0.01% 35 1981 0.01% 36 2244 0.01% 37 2481 0.01% 38 2854 0.01% 39 3151 0.01% 40 3462 0.01% 41 3859 0.01% 42 4238 0.01% 43 4567 0.01% 44 5239 0.02% 45 5617 0.02% 46 6274 0.02% 47 6593 0.02% 48 7410 0.02% 49 7713 0.02% 50 8300 0.03% 51 9001 0.03% 52 9483 0.03% 53 10366 0.03% 54 11208 0.03% 55 12436 0.04% 56 13167 0.04% 57 14395 0.04% 58 16021 0.05% 59 29937 0.09% 60 31997 0.10% 61 33216 0.10% 62 40070 0.12% 63 40930 0.13% 64 45449 0.14% 65 48288 0.15% 66 46948 0.15% 67 47830 0.15% 68 51397 0.16% 69 61426 0.19% 70 59572 0.18% 71 61845 0.19% 72 67224 0.21% 73 63971 0.20% 74 68917 0.21% 75 65699 0.20% 76 65758 0.20% 77 69189 0.21% 78 74726 0.23% 79 77774 0.24% 80 81690 0.25% 81 87866 0.27% 82 98539 0.31% 83 105188 0.33% 84 113160 0.35% 85 127231 0.39% 86 141045 0.44% 87 141009 0.44% 88 145859 0.45% 89 141679 0.44% 90 170432 0.53% 91 173046 0.54% 92 192009 0.59% 93 218187 0.68% 94 234672 0.73% 95 272198 0.84% 96 328379 1.02% 97 408217 1.26% 98 512403 1.59% 99 645919 2.00% 100 26621831 82.43% 32295087 reads passed initial QC criterion=sequence-density sequence-density=1.21 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=16 prefix-density=1.18 prefix-fanout=2.0 sequence=TTCGCTATCGGTC criterion=fanout-score sequence-density=0.50 sequence-density-rank=16 fanout-score=4.82 fanout-score-rank=1 prefix-density=1.21 prefix-fanout=2.0 sequence=ATTTAGCCTTGGACGGAGTCTACCGCCCGATTTGGGCTGCATTCCCAAACAACCCGACTCGTTGACGGCGCCTCGTGGGGCGACAGGGTCCGGGCCGGACGGGGCTCTCACCCTCCCAGGCGCCCCTTTCCAGGGGACTTGGGCCCGGTCCGTCGCTGAGGACGCCTCTCCAGACTACAATTCGGACGGCACGGCCGCCCGATTCTCAAGCTGGGCTGCTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTCTCCTCCGCTTATTTATATGCTTAAACTCAGCGGGTAGTCCCGCCTG criterion=sequence-density sequence-density=1.13 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=23 prefix-density=1.11 prefix-fanout=2.0 sequence=GGTGGTGCATGGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=9.64 fanout-score-rank=1 prefix-density=0.21 prefix-fanout=1.0 sequence=TAACTTCGGGAGAAGGGGTGCCCCCTCACAAAAGGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTCTCCGCAAAGTCGTAAGACCATGTATGGGGGCTGACGCCTGCCCAGTGCCGGAAGGTCAAGGAAGTTGGTGAACTGATGACAGGGAAGCCGGCGACCGAAGCCCCGGTGAACGGCGGCCGTAAC SRR6127925 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 04:20:49 Started mapping on | Dec 10 04:20:49 Finished on | Dec 10 04:38:09 Mapping speed, Million of reads per hour | 111.79 Number of input reads | 32295087 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 12210148 Uniquely mapped reads % | 37.81% Average mapped length | 196.57 Number of splices: Total | 5936117 Number of splices: Annotated (sjdb) | 5563164 Number of splices: GT/AG | 5844724 Number of splices: GC/AG | 71022 Number of splices: AT/AC | 2201 Number of splices: Non-canonical | 18170 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.32 Insertion rate per base | 0.02% Insertion average length | 1.96 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5101838 % of reads mapped to multiple loci | 15.80% Number of reads mapped to too many loci | 1098550 % of reads mapped to too many loci | 3.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 26.53% % of reads unmapped: other | 16.46% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 14996937 14996937 14996937 N_multimapping 5101838 5101838 5101838 N_noFeature 1994879 11873959 2090861 N_ambiguous 286636 1363 47755 UnstrandedReadsAssigned:9928633 PositiveStrandReadsAssigned:334826 NegativeStrandReadsAssigned:10071532 Dataset is classified negative stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR6127925 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: SRR6127925-trimmed-pair1.fastq SRR6127925-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,295,087 reads, 10,989,221 reads pseudoaligned [quant] estimated average fragment length: 168.342 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,132 rounds 52973 SRR6127925.ke.tsv 35125 SRR6127925.se.tsv 88098 total ==> SRR6127925.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 768.793 0 0 PNS24247 1044 876.658 14.8412 1.72292 PNS24249 1928 1760.66 10.4351 0.603178 PNS24246 1044 876.658 14.8412 1.72292 PNS24248 1044 876.658 14.8412 1.72292 PNS24244 1471 1303.66 106.041 8.27821 PNS24243 293 134.022 0 0 KQK14069 1603 1435.66 3165.12 224.37 KQK14071 474 308.167 105.39 34.8047 ==> SRR6127925.se.tsv <== BRADI_1g14170v3 3479 BRADI_1g53295v3 338 BRADI_1g59795v3 70 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 132 BRADI_1g74790v3 59 BRADI_1g09890v3 0 BRADI_1g77505v3 268 BRADI_1g48960v3 0 SRR6127925 completed mapping pipeline successfully