Starting /dee2/code/volunteer_pipeline.sh ERR3450071 current disk space = 1543018139648 free memory = 1602283424 ERR3450071 SRAfilesize b8fc1e77daa4ea34ae31df06d9b1bc1d ERR3450071.sra ERR3450071.sra file validated ERR3450071 is paired end ERR3450071 is conventional basespace ERR3450071 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450071_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.0375 37.0 37.0 37.0 37.0 37.0 2 36.259 37.0 37.0 37.0 37.0 37.0 3 36.3285 37.0 37.0 37.0 37.0 37.0 4 36.5195 37.0 37.0 37.0 37.0 37.0 5 36.449 37.0 37.0 37.0 37.0 37.0 6 36.5125 37.0 37.0 37.0 37.0 37.0 7 36.4125 37.0 37.0 37.0 37.0 37.0 8 36.5345 37.0 37.0 37.0 37.0 37.0 9 36.444 37.0 37.0 37.0 37.0 37.0 10-11 36.435249999999996 37.0 37.0 37.0 37.0 37.0 12-13 36.475750000000005 37.0 37.0 37.0 37.0 37.0 14-15 36.50775 37.0 37.0 37.0 37.0 37.0 16-17 36.428250000000006 37.0 37.0 37.0 37.0 37.0 18-19 36.42975 37.0 37.0 37.0 37.0 37.0 20-21 36.403999999999996 37.0 37.0 37.0 37.0 37.0 22-23 36.4915 37.0 37.0 37.0 37.0 37.0 24-25 36.45975 37.0 37.0 37.0 37.0 37.0 26-27 36.369 37.0 37.0 37.0 37.0 37.0 28-29 36.3965 37.0 37.0 37.0 37.0 37.0 30-31 36.3615 37.0 37.0 37.0 37.0 37.0 32-33 36.422 37.0 37.0 37.0 37.0 37.0 34-35 36.32 37.0 37.0 37.0 37.0 37.0 36-37 36.3275 37.0 37.0 37.0 37.0 37.0 38-39 36.33175 37.0 37.0 37.0 37.0 37.0 40-41 36.31375 37.0 37.0 37.0 37.0 37.0 42-43 36.310500000000005 37.0 37.0 37.0 37.0 37.0 44-45 36.2195 37.0 37.0 37.0 37.0 37.0 46-47 36.233999999999995 37.0 37.0 37.0 37.0 37.0 48-49 36.217 37.0 37.0 37.0 37.0 37.0 50-51 36.199 37.0 37.0 37.0 37.0 37.0 52-53 36.174499999999995 37.0 37.0 37.0 37.0 37.0 54-55 36.219750000000005 37.0 37.0 37.0 37.0 37.0 56-57 36.1685 37.0 37.0 37.0 37.0 37.0 58-59 36.2025 37.0 37.0 37.0 37.0 37.0 60-61 36.086 37.0 37.0 37.0 37.0 37.0 62-63 36.129000000000005 37.0 37.0 37.0 37.0 37.0 64-65 35.950500000000005 37.0 37.0 37.0 37.0 37.0 66-67 36.12425 37.0 37.0 37.0 37.0 37.0 68-69 36.17475 37.0 37.0 37.0 37.0 37.0 70-71 36.136250000000004 37.0 37.0 37.0 37.0 37.0 72-73 36.0235 37.0 37.0 37.0 37.0 37.0 74-75 36.02525 37.0 37.0 37.0 37.0 37.0 76-77 36.09125 37.0 37.0 37.0 37.0 37.0 78-79 36.15375 37.0 37.0 37.0 37.0 37.0 80-81 36.12375 37.0 37.0 37.0 37.0 37.0 82-83 36.1695 37.0 37.0 37.0 37.0 37.0 84-85 36.0455 37.0 37.0 37.0 37.0 37.0 86-87 36.09425 37.0 37.0 37.0 37.0 37.0 88-89 36.056 37.0 37.0 37.0 37.0 37.0 90-91 36.024 37.0 37.0 37.0 37.0 37.0 92-93 36.028999999999996 37.0 37.0 37.0 37.0 37.0 94-95 35.9355 37.0 37.0 37.0 37.0 37.0 96-97 36.0255 37.0 37.0 37.0 37.0 37.0 98-99 35.94925 37.0 37.0 37.0 37.0 37.0 100-101 35.89075 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 2.0 24 3.0 25 5.0 26 9.0 27 21.0 28 20.0 29 31.0 30 44.0 31 50.0 32 71.0 33 75.0 34 116.0 35 204.0 36 1679.0 37 1666.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.30908178625188 10.888108379327646 11.51530356246864 39.287506271951834 2 20.875 13.450000000000001 29.875 35.8 3 21.775 18.875 23.825 35.525 4 27.650000000000002 22.900000000000002 18.45 31.0 5 26.900000000000002 26.224999999999998 21.85 25.025 6 22.575 32.0 22.975 22.45 7 20.025000000000002 23.275000000000002 37.625 19.075 8 21.4 21.525 29.175 27.900000000000002 9 22.575 21.175 30.975 25.275 10-11 23.9125 28.5875 22.6 24.9 12-13 24.275 22.650000000000002 25.837500000000002 27.237499999999997 14-15 23.5 23.875 26.150000000000002 26.474999999999998 16-17 22.9875 23.599999999999998 26.187500000000004 27.224999999999998 18-19 24.3875 23.8875 25.874999999999996 25.85 20-21 24.0 24.0375 25.3125 26.650000000000002 22-23 25.0375 23.4875 24.3125 27.1625 24-25 24.2875 24.099999999999998 24.962500000000002 26.650000000000002 26-27 24.4125 24.85 23.849999999999998 26.887499999999996 28-29 24.8125 23.400000000000002 23.8875 27.900000000000002 30-31 23.400000000000002 23.575 25.162499999999998 27.8625 32-33 24.125 23.7125 24.075 28.0875 34-35 25.25 23.025000000000002 23.8625 27.8625 36-37 24.65 23.2625 24.6625 27.425 38-39 24.762500000000003 23.375 25.2125 26.650000000000002 40-41 24.474999999999998 23.2375 24.05 28.237499999999997 42-43 25.374999999999996 23.6625 24.575 26.387500000000003 44-45 24.3125 23.4375 24.45 27.800000000000004 46-47 23.625 24.2625 24.6625 27.450000000000003 48-49 24.087500000000002 23.9 24.55 27.462500000000002 50-51 24.675 23.5875 24.9125 26.825 52-53 24.5 23.375 24.087500000000002 28.037499999999998 54-55 25.0125 24.05 23.65 27.287499999999998 56-57 25.1 23.3 24.65 26.950000000000003 58-59 24.8125 24.087500000000002 22.975 28.125 60-61 24.7375 23.674999999999997 24.15 27.437499999999996 62-63 24.5125 22.625 24.65 28.212500000000002 64-65 25.7375 22.6375 24.2375 27.3875 66-67 24.75 23.674999999999997 23.925 27.650000000000002 68-69 24.975 23.35 24.525 27.150000000000002 70-71 24.0375 22.925 24.2375 28.799999999999997 72-73 25.2125 23.925 24.224999999999998 26.637499999999996 74-75 25.8625 24.087500000000002 22.787499999999998 27.2625 76-77 25.174999999999997 24.55 23.150000000000002 27.125 78-79 24.762500000000003 24.962500000000002 23.025000000000002 27.250000000000004 80-81 24.8125 23.75 23.6625 27.775 82-83 24.337500000000002 23.962500000000002 23.6875 28.012500000000003 84-85 25.687500000000004 24.175 22.5625 27.575 86-87 24.762500000000003 24.375 24.0375 26.825 88-89 25.087500000000002 23.9125 24.462500000000002 26.5375 90-91 25.2375 23.65 22.675 28.4375 92-93 25.025 24.425 23.7125 26.8375 94-95 25.362499999999997 24.2375 23.1625 27.237499999999997 96-97 23.4875 24.55 23.4375 28.525 98-99 24.375 24.1625 24.025 27.437499999999996 100-101 25.174999999999997 23.9875 24.087500000000002 26.75 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 10.0 1 7.0 2 2.0 3 0.5 4 0.5 5 0.0 6 1.5 7 2.5 8 2.0 9 1.0 10 0.0 11 0.5 12 1.0 13 1.0 14 0.5 15 1.0 16 1.0 17 0.0 18 1.0 19 1.0 20 0.5 21 0.5 22 0.5 23 1.5 24 2.0 25 1.0 26 1.0 27 1.0 28 1.0 29 1.5 30 1.0 31 2.5 32 4.0 33 3.5 34 7.0 35 17.0 36 26.0 37 35.5 38 42.0 39 66.0 40 91.5 41 96.5 42 109.5 43 127.0 44 148.5 45 172.0 46 181.0 47 171.0 48 165.5 49 167.0 50 161.0 51 149.0 52 150.5 53 161.5 54 152.0 55 157.0 56 149.0 57 117.0 58 100.0 59 92.5 60 93.0 61 86.5 62 74.0 63 58.0 64 57.5 65 66.0 66 62.5 67 54.0 68 51.0 69 50.5 70 46.5 71 41.5 72 32.5 73 29.5 74 28.0 75 25.0 76 22.0 77 18.0 78 14.0 79 9.0 80 7.0 81 4.5 82 2.0 83 1.0 84 0.5 85 0.5 86 0.5 87 0.0 88 0.5 89 1.0 90 0.5 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 0.35000000000000003 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 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.375 #Duplication Level Percentage of deduplicated Percentage of total 1 89.72818311874106 78.4 2 7.954220314735336 13.900000000000002 3 1.3447782546494993 3.5249999999999995 4 0.5722460658082975 2.0 5 0.2575107296137339 1.125 6 0.028612303290414882 0.15 7 0.057224606580829764 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.057224606580829764 0.5499999999999999 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 11 0.27499999999999997 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 7 0.17500000000000002 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 7 0.17500000000000002 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 6 0.15 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 5 0.125 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 5 0.125 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 5 0.125 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 5 0.125 No Hit ATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATT 5 0.125 No Hit CTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGG 5 0.125 No Hit GTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGA 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 0.0125 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.3375 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.4125 0.0 0.0 0.0 0.0 56-57 0.4625 0.0 0.0 0.0 0.0 58-59 0.5125 0.0 0.0 0.0 0.0 60-61 0.6125 0.0 0.0 0.0 0.0 62-63 0.7749999999999999 0.0 0.0 0.0 0.0 64-65 0.975 0.0 0.0 0.0 0.0 66-67 1.1625 0.0 0.0 0.0 0.0 68-69 1.45 0.0 0.0 0.0 0.0 70-71 1.6625 0.0 0.0 0.0 0.0 72-73 1.8625 0.0 0.0 0.0 0.0 74-75 2.175 0.0 0.0 0.0 0.0 76-77 2.4125 0.0 0.0 0.0 0.0 78-79 2.6500000000000004 0.0 0.0 0.0 0.0 80-81 2.9375 0.0 0.0 0.0 0.0 82-83 3.3625 0.0 0.0 0.0 0.0 84-85 3.7 0.0 0.0 0.0 0.0 86-87 4.05 0.0 0.0 0.0 0.0 88-89 4.3875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450071 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450071_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.0025 37.0 37.0 37.0 37.0 37.0 2 35.9665 37.0 37.0 37.0 37.0 37.0 3 35.8115 37.0 37.0 37.0 37.0 37.0 4 36.094 37.0 37.0 37.0 37.0 37.0 5 36.1975 37.0 37.0 37.0 37.0 37.0 6 36.091 37.0 37.0 37.0 37.0 37.0 7 36.19 37.0 37.0 37.0 37.0 37.0 8 36.0765 37.0 37.0 37.0 37.0 37.0 9 36.2 37.0 37.0 37.0 37.0 37.0 10-11 36.122749999999996 37.0 37.0 37.0 37.0 37.0 12-13 36.095749999999995 37.0 37.0 37.0 37.0 37.0 14-15 36.092 37.0 37.0 37.0 37.0 37.0 16-17 36.098749999999995 37.0 37.0 37.0 37.0 37.0 18-19 36.20725 37.0 37.0 37.0 37.0 37.0 20-21 36.132000000000005 37.0 37.0 37.0 37.0 37.0 22-23 36.161 37.0 37.0 37.0 37.0 37.0 24-25 36.1025 37.0 37.0 37.0 37.0 37.0 26-27 36.045249999999996 37.0 37.0 37.0 37.0 37.0 28-29 36.0655 37.0 37.0 37.0 37.0 37.0 30-31 36.05775 37.0 37.0 37.0 37.0 37.0 32-33 35.98925 37.0 37.0 37.0 37.0 37.0 34-35 35.95925 37.0 37.0 37.0 37.0 37.0 36-37 35.952 37.0 37.0 37.0 37.0 37.0 38-39 35.99925 37.0 37.0 37.0 37.0 37.0 40-41 35.942 37.0 37.0 37.0 37.0 37.0 42-43 35.91225 37.0 37.0 37.0 37.0 37.0 44-45 35.84725 37.0 37.0 37.0 37.0 37.0 46-47 35.9295 37.0 37.0 37.0 37.0 37.0 48-49 35.897999999999996 37.0 37.0 37.0 37.0 37.0 50-51 35.953500000000005 37.0 37.0 37.0 37.0 37.0 52-53 35.929249999999996 37.0 37.0 37.0 37.0 37.0 54-55 35.868 37.0 37.0 37.0 37.0 37.0 56-57 35.897000000000006 37.0 37.0 37.0 37.0 37.0 58-59 35.82375 37.0 37.0 37.0 37.0 37.0 60-61 35.782 37.0 37.0 37.0 37.0 37.0 62-63 35.8565 37.0 37.0 37.0 37.0 37.0 64-65 35.747 37.0 37.0 37.0 37.0 37.0 66-67 35.8275 37.0 37.0 37.0 37.0 37.0 68-69 35.74325 37.0 37.0 37.0 37.0 37.0 70-71 35.6325 37.0 37.0 37.0 37.0 37.0 72-73 35.705 37.0 37.0 37.0 37.0 37.0 74-75 35.7295 37.0 37.0 37.0 37.0 37.0 76-77 35.82125 37.0 37.0 37.0 37.0 37.0 78-79 35.752250000000004 37.0 37.0 37.0 37.0 37.0 80-81 35.768 37.0 37.0 37.0 37.0 37.0 82-83 35.74025 37.0 37.0 37.0 37.0 37.0 84-85 35.69425 37.0 37.0 37.0 37.0 37.0 86-87 35.86150000000001 37.0 37.0 37.0 37.0 37.0 88-89 35.83625 37.0 37.0 37.0 37.0 37.0 90-91 35.82725000000001 37.0 37.0 37.0 37.0 37.0 92-93 35.7965 37.0 37.0 37.0 37.0 37.0 94-95 35.85375 37.0 37.0 37.0 37.0 37.0 96-97 35.766 37.0 37.0 37.0 37.0 37.0 98-99 35.78675 37.0 37.0 37.0 37.0 37.0 100-101 35.68925 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 3.0 16 2.0 17 3.0 18 1.0 19 2.0 20 7.0 21 8.0 22 15.0 23 12.0 24 15.0 25 17.0 26 13.0 27 13.0 28 27.0 29 30.0 30 39.0 31 46.0 32 54.0 33 76.0 34 121.0 35 265.0 36 2118.0 37 1112.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.949999999999996 17.0 11.899999999999999 29.15 2 27.3 21.9 27.0 23.799999999999997 3 25.374999999999996 22.95 27.3 24.375 4 30.425 27.450000000000003 17.349999999999998 24.775 5 29.099999999999998 30.25 18.45 22.2 6 24.275 33.15 20.474999999999998 22.1 7 25.75 18.5 30.075000000000003 25.674999999999997 8 25.55 21.425 22.975 30.049999999999997 9 24.875 22.375 25.7 27.05 10-11 27.3 26.6625 20.4125 25.624999999999996 12-13 29.5875 21.512500000000003 21.9375 26.9625 14-15 26.174999999999997 24.625 23.599999999999998 25.6 16-17 27.487499999999997 24.4125 22.35 25.75 18-19 29.037499999999998 24.712500000000002 21.925 24.325 20-21 27.3375 25.1 22.425 25.137500000000003 22-23 27.9375 24.7375 22.275 25.05 24-25 27.700000000000003 24.6 21.925 25.775 26-27 27.35 25.6125 22.175 24.8625 28-29 27.375 24.95 22.275 25.4 30-31 27.3375 23.1625 22.7125 26.787499999999998 32-33 27.5625 24.587500000000002 22.9875 24.8625 34-35 27.787499999999998 24.925 22.412499999999998 24.875 36-37 28.025 25.55 20.837500000000002 25.587500000000002 38-39 26.937499999999996 24.5125 22.975 25.575 40-41 27.9375 25.0 21.775 25.2875 42-43 27.6 24.712500000000002 22.85 24.837500000000002 44-45 26.674999999999997 24.7875 22.8 25.7375 46-47 27.8125 23.7625 22.8625 25.5625 48-49 27.462500000000002 23.525 22.35 26.6625 50-51 27.325 25.2375 22.1875 25.25 52-53 28.1375 23.8375 23.6375 24.3875 54-55 27.500000000000004 23.799999999999997 22.85 25.85 56-57 26.3 24.45 23.9 25.35 58-59 26.700000000000003 24.6125 23.4375 25.25 60-61 28.799999999999997 24.65 21.837500000000002 24.712500000000002 62-63 28.125 24.6625 22.275 24.9375 64-65 27.3875 24.3625 22.7 25.55 66-67 27.8625 24.725 22.125 25.2875 68-69 26.8125 25.724999999999998 22.650000000000002 24.8125 70-71 27.125 24.875 23.0875 24.9125 72-73 27.8375 25.112499999999997 22.237499999999997 24.8125 74-75 27.6 23.962500000000002 23.375 25.0625 76-77 27.650000000000002 24.8 23.150000000000002 24.4 78-79 27.975 24.575 22.0125 25.4375 80-81 26.825 25.5375 22.650000000000002 24.9875 82-83 27.675 24.4 23.325000000000003 24.6 84-85 28.125 24.0625 23.2125 24.6 86-87 28.1125 24.0375 22.575 25.275 88-89 28.65 24.5375 22.275 24.5375 90-91 28.462500000000002 24.2625 22.925 24.349999999999998 92-93 28.975 25.362499999999997 21.9 23.7625 94-95 28.975 25.575 22.4625 22.9875 96-97 29.1625 24.762500000000003 22.425 23.65 98-99 28.787499999999998 24.7 22.5125 24.0 100-101 28.65 25.8625 22.0875 23.400000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 1.5 6 1.5 7 0.5 8 0.5 9 1.0 10 3.0 11 2.0 12 1.5 13 1.5 14 1.5 15 3.5 16 2.0 17 1.5 18 2.0 19 1.5 20 1.0 21 0.0 22 1.0 23 1.0 24 0.5 25 2.0 26 2.5 27 3.0 28 2.5 29 1.0 30 2.0 31 5.0 32 5.5 33 5.0 34 10.0 35 16.5 36 20.0 37 18.0 38 32.5 39 67.0 40 79.5 41 89.5 42 109.0 43 129.0 44 154.0 45 150.5 46 153.5 47 171.5 48 168.0 49 162.0 50 155.0 51 157.0 52 151.0 53 160.0 54 159.0 55 143.5 56 129.0 57 103.0 58 97.5 59 86.0 60 79.5 61 75.0 62 67.5 63 73.0 64 79.0 65 70.5 66 69.0 67 69.5 68 65.5 69 71.5 70 60.5 71 48.5 72 48.5 73 40.0 74 35.5 75 30.0 76 25.0 77 19.0 78 11.5 79 8.5 80 4.0 81 3.0 82 3.0 83 3.0 84 1.5 85 1.0 86 1.5 87 1.0 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 2.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.675 #Duplication Level Percentage of deduplicated Percentage of total 1 90.49901325063433 80.25 2 7.499295179024528 13.3 3 1.3532562729066817 3.5999999999999996 4 0.39469974626444887 1.4000000000000001 5 0.140964195094446 0.625 6 0.0 0.0 7 0.028192839018889203 0.17500000000000002 8 0.028192839018889203 0.2 9 0.05638567803777841 0.44999999999999996 >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 CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 9 0.22499999999999998 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 9 0.22499999999999998 No Hit GGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAAC 8 0.2 No Hit GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 7 0.17500000000000002 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 5 0.125 No Hit GATTAAGCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGC 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit CGGGGAGGTAGTGACAATAAATAACAATACCGGGCACATTAGTGTCTGGT 5 0.125 No Hit GTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCA 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 0.0125 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.175 0.0 0.0 0.0 0.0 50-51 0.3125 0.0 0.0 0.0 0.0 52-53 0.3625 0.0 0.0 0.0 0.0 54-55 0.3875 0.0 0.0 0.0 0.0 56-57 0.4375 0.0 0.0 0.0 0.0 58-59 0.475 0.0 0.0 0.0 0.0 60-61 0.5625 0.0 0.0 0.0 0.0 62-63 0.7250000000000001 0.0 0.0 0.0 0.0 64-65 0.925 0.0 0.0 0.0 0.0 66-67 1.1124999999999998 0.0 0.0 0.0 0.0 68-69 1.4 0.0 0.0 0.0 0.0 70-71 1.6125 0.0 0.0 0.0 0.0 72-73 1.8125 0.0 0.0 0.0 0.0 74-75 2.125 0.0 0.0 0.0 0.0 76-77 2.375 0.0 0.0 0.0 0.0 78-79 2.625 0.0 0.0 0.0 0.0 80-81 2.9124999999999996 0.0 0.0 0.0 0.0 82-83 3.3375000000000004 0.0 0.0 0.0 0.0 84-85 3.675 0.0 0.0 0.0 0.0 86-87 4.0 0.0 0.0 0.0 0.0 88-89 4.3625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414536 spots for ERR3450071.sra Written 1414536 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra Read 1414532 spots for ERR3450071.sra Written 1414532 spots for ERR3450071.sra SRR ids: ['ERR3450071.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7ykhc2j6 ERR3450071.sra spots: 28290644 blocks: [[1, 1414532], [1414533, 2829064], [2829065, 4243596], [4243597, 5658128], [5658129, 7072660], [7072661, 8487192], [8487193, 9901724], [9901725, 11316256], [11316257, 12730788], [12730789, 14145320], [14145321, 15559852], [15559853, 16974384], [16974385, 18388916], [18388917, 19803448], [19803449, 21217980], [21217981, 22632512], [22632513, 24047044], [24047045, 25461576], [25461577, 26876108], [26876109, 28290644]] ERR3450071 file size 6802312 ERR3450071 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 ERR3450071 ERR3450071_1.fastq ERR3450071_2.fastq Input file: ERR3450071_1.fastq Paired file: ERR3450071_2.fastq trimmed: ERR3450071-trimmed-pair1.fastq, ERR3450071-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 Sat Dec 7 14:34:56 2024 >> started Sat Dec 7 14:35:23 2024 >> done (26.496s) 28290644 read pairs processed; of these: 168 ( 0.00%) short read pairs filtered out after trimming by size control 27741 ( 0.10%) empty read pairs filtered out after trimming by size control 28262735 (99.90%) read pairs available; of these: 2389384 ( 8.45%) trimmed read pairs available after processing 25873351 (91.55%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 26 0.00% 19 40 0.00% 20 150 0.00% 21 370 0.00% 22 463 0.00% 23 248 0.00% 24 212 0.00% 25 321 0.00% 26 466 0.00% 27 709 0.00% 28 934 0.00% 29 1257 0.00% 30 1673 0.01% 31 1907 0.01% 32 1916 0.01% 33 1840 0.01% 34 1820 0.01% 35 1949 0.01% 36 2133 0.01% 37 2417 0.01% 38 2777 0.01% 39 3223 0.01% 40 3910 0.01% 41 4435 0.02% 42 4890 0.02% 43 5269 0.02% 44 4839 0.02% 45 4807 0.02% 46 5114 0.02% 47 5601 0.02% 48 6237 0.02% 49 6975 0.02% 50 7669 0.03% 51 8845 0.03% 52 9538 0.03% 53 10276 0.04% 54 10570 0.04% 55 11172 0.04% 56 11506 0.04% 57 12198 0.04% 58 13446 0.05% 59 14647 0.05% 60 15580 0.06% 61 17571 0.06% 62 19211 0.07% 63 20616 0.07% 64 21616 0.08% 65 22500 0.08% 66 23232 0.08% 67 25019 0.09% 68 26256 0.09% 69 27055 0.10% 70 28932 0.10% 71 31583 0.11% 72 34243 0.12% 73 35889 0.13% 74 37614 0.13% 75 39387 0.14% 76 40578 0.14% 77 41694 0.15% 78 44323 0.16% 79 46925 0.17% 80 48475 0.17% 81 50735 0.18% 82 54159 0.19% 83 56297 0.20% 84 58800 0.21% 85 61579 0.22% 86 63200 0.22% 87 66204 0.23% 88 68922 0.24% 89 71860 0.25% 90 73603 0.26% 91 78279 0.28% 92 82216 0.29% 93 84829 0.30% 94 87657 0.31% 95 90917 0.32% 96 93101 0.33% 97 96311 0.34% 98 97408 0.34% 99 100129 0.35% 100 116084 0.41% 101 25873351 91.55% 28262735 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=2.47 fanout-score-rank=30 prefix-density=0.22 prefix-fanout=2.5 sequence=GTCAAATTAAGCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATAAGCAACATCCGCCGATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAGCGCATCGCCGGCTGAAGGGTCGAGTA criterion=fanout-score sequence-density=0.07 sequence-density-rank=28 fanout-score=181.96 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=21.9 sequence=CCGCCGCCGCCG criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=4.04 fanout-score-rank=21 prefix-density=0.25 prefix-fanout=3.4 sequence=AAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.08 sequence-density-rank=27 fanout-score=216.11 fanout-score-rank=1 prefix-density=1.43 prefix-fanout=12.1 sequence=CGCCGCCGCCGG ERR3450071 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:36:04 Started mapping on | Dec 07 14:36:04 Finished on | Dec 07 14:38:16 Mapping speed, Million of reads per hour | 770.80 Number of input reads | 28262735 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 20321449 Uniquely mapped reads % | 71.90% Average mapped length | 198.48 Number of splices: Total | 13167026 Number of splices: Annotated (sjdb) | 12511865 Number of splices: GT/AG | 12992742 Number of splices: GC/AG | 150136 Number of splices: AT/AC | 8644 Number of splices: Non-canonical | 15504 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.10 Insertion rate per base | 0.01% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1459628 % of reads mapped to multiple loci | 5.16% Number of reads mapped to too many loci | 1086422 % of reads mapped to too many loci | 3.84% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.10% % of reads unmapped: other | 15.99% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6481658 6481658 6481658 N_multimapping 1459628 1459628 1459628 N_noFeature 619589 19624654 1023296 N_ambiguous 361576 3131 72904 UnstrandedReadsAssigned:19340284 PositiveStrandReadsAssigned:693664 NegativeStrandReadsAssigned:19225249 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450071 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: ERR3450071-trimmed-pair1.fastq ERR3450071-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,262,735 reads, 20,363,004 reads pseudoaligned [quant] estimated average fragment length: 190.235 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,225 rounds 52973 ERR3450071.ke.tsv 35125 ERR3450071.se.tsv 88098 total ==> ERR3450071.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 746.933 0 0 PNS24247 1044 854.765 28.1027 2.33029 PNS24249 1928 1738.77 269.92 11.0028 PNS24246 1044 854.765 28.1027 2.33029 PNS24248 1044 854.765 28.1027 2.33029 PNS24244 1471 1281.77 34.7716 1.92276 PNS24243 293 127.541 0 0 KQK14069 1603 1413.77 1304.83 65.4159 KQK14071 474 288.939 36.609 8.98028 ==> ERR3450071.se.tsv <== BRADI_1g14170v3 1344 BRADI_1g53295v3 7 BRADI_1g59795v3 165 BRADI_1g07683v3 0 BRADI_1g00485v3 59 BRADI_1g20270v3 5075 BRADI_1g74790v3 230 BRADI_1g09890v3 33 BRADI_1g77505v3 335 BRADI_1g48960v3 1 ERR3450071 completed mapping pipeline successfully