Starting /dee2/code/volunteer_pipeline.sh SRR6127949 current disk space = 1526180638720 free memory = 1595996316 SRR6127949 SRAfilesize 5327e300b7504ae5683acdd1c696fde1 SRR6127949.sra SRR6127949.sra file validated SRR6127949 is paired end SRR6127949 is conventional basespace SRR6127949 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127949_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.274 33.0 33.0 33.0 33.0 33.0 2 32.4885 33.0 33.0 33.0 33.0 33.0 3 32.75775 33.0 33.0 33.0 33.0 33.0 4 36.708 37.0 37.0 37.0 37.0 37.0 5 36.7175 37.0 37.0 37.0 37.0 37.0 6 36.63925 37.0 37.0 37.0 37.0 37.0 7 36.6755 37.0 37.0 37.0 37.0 37.0 8 36.67225 37.0 37.0 37.0 37.0 37.0 9 36.6805 37.0 37.0 37.0 37.0 37.0 10-11 36.68075 37.0 37.0 37.0 37.0 37.0 12-13 36.613625 37.0 37.0 37.0 37.0 37.0 14-15 38.965875 40.0 40.0 40.0 37.0 40.0 16-17 38.98525 40.0 40.0 40.0 37.0 40.0 18-19 38.9105 40.0 40.0 40.0 37.0 40.0 20-21 38.910875000000004 40.0 40.0 40.0 37.0 40.0 22-23 38.857875 40.0 40.0 40.0 37.0 40.0 24-25 38.748374999999996 40.0 40.0 40.0 37.0 40.0 26-27 38.731125000000006 40.0 40.0 40.0 37.0 40.0 28-29 38.624624999999995 40.0 38.5 40.0 37.0 40.0 30-31 38.660375 40.0 37.0 40.0 37.0 40.0 32-33 38.670375 40.0 37.0 40.0 37.0 40.0 34-35 38.54375 40.0 37.0 40.0 37.0 40.0 36-37 38.504 40.0 37.0 40.0 37.0 40.0 38-39 38.28212499999999 40.0 37.0 40.0 37.0 40.0 40-41 38.1605 40.0 37.0 40.0 37.0 40.0 42-43 37.905875 40.0 37.0 40.0 33.0 40.0 44-45 37.841625 40.0 37.0 40.0 33.0 40.0 46-47 37.61125 40.0 37.0 40.0 33.0 40.0 48-49 37.586625 40.0 37.0 40.0 33.0 40.0 50-51 37.43725 40.0 37.0 40.0 33.0 40.0 52-53 37.228875 40.0 37.0 40.0 33.0 40.0 54-55 36.693625 37.0 37.0 40.0 33.0 40.0 56-57 36.737125 37.0 37.0 40.0 33.0 40.0 58-59 36.503 37.0 37.0 40.0 33.0 40.0 60-61 36.30775 37.0 37.0 40.0 33.0 40.0 62-63 36.028000000000006 37.0 37.0 40.0 33.0 40.0 64-65 35.8375 37.0 37.0 40.0 33.0 40.0 66-67 35.461875 37.0 37.0 37.0 33.0 40.0 68-69 35.304 37.0 35.0 37.0 33.0 40.0 70-71 35.05525 37.0 33.0 37.0 30.0 40.0 72-73 34.808125000000004 37.0 33.0 37.0 30.0 40.0 74-75 34.4925 37.0 33.0 37.0 27.0 37.0 76-77 31.737000000000002 33.0 30.0 35.0 24.5 37.0 78-79 33.46775 37.0 33.0 37.0 27.0 37.0 80-81 33.5805 37.0 33.0 37.0 27.0 37.0 82-83 33.707625 37.0 33.0 37.0 27.0 37.0 84-85 33.62712500000001 37.0 33.0 37.0 27.0 37.0 86-87 33.651125 37.0 33.0 37.0 27.0 37.0 88-89 33.30525 37.0 33.0 37.0 27.0 37.0 90-91 33.3635 37.0 33.0 37.0 27.0 37.0 92-93 33.178124999999994 37.0 33.0 37.0 27.0 37.0 94-95 33.05375 37.0 33.0 37.0 27.0 37.0 96-97 32.727625 37.0 33.0 37.0 27.0 37.0 98-99 32.332625 37.0 33.0 37.0 24.5 37.0 100 28.87025 33.0 27.0 33.0 15.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 1.0 10 2.0 11 1.0 12 3.0 13 4.0 14 4.0 15 8.0 16 3.0 17 8.0 18 8.0 19 5.0 20 12.0 21 12.0 22 3.0 23 10.0 24 17.0 25 18.0 26 28.0 27 28.0 28 34.0 29 50.0 30 65.0 31 73.0 32 105.0 33 109.0 34 159.0 35 255.0 36 521.0 37 1375.0 38 1077.0 39 2.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.445262890525782 10.896621793243586 9.906019812039624 47.75209550419101 2 22.35 15.4 37.325 24.925 3 22.225 20.775 23.35 33.650000000000006 4 25.874999999999996 29.075 20.65 24.4 5 26.85 32.125 22.575 18.45 6 20.75 33.1 25.575 20.575 7 16.400000000000002 21.7 41.349999999999994 20.549999999999997 8 19.400000000000002 21.85 30.075000000000003 28.675 9 20.75 20.225 33.15 25.874999999999996 10-11 24.5 29.2 21.6125 24.6875 12-13 22.9875 22.6 27.275 27.1375 14-15 23.0375 25.362499999999997 27.150000000000002 24.45 16-17 24.5375 24.675 24.8625 25.924999999999997 18-19 23.1125 25.525 25.374999999999996 25.9875 20-21 23.8125 25.324999999999996 24.9875 25.874999999999996 22-23 23.5125 25.0375 25.7875 25.662499999999998 24-25 23.775 23.7625 26.325 26.137500000000003 26-27 24.0625 25.2875 26.75 23.9 28-29 23.45 25.8 25.775 24.975 30-31 23.599999999999998 25.4375 26.1 24.8625 32-33 22.375 26.1125 26.1125 25.4 34-35 23.400000000000002 24.9875 25.6 26.0125 36-37 24.25 25.637500000000003 24.6875 25.424999999999997 38-39 23.7875 25.687500000000004 25.1875 25.337500000000002 40-41 24.95 25.412499999999998 24.825 24.8125 42-43 24.4 25.0625 25.45 25.087500000000002 44-45 23.05 25.0625 26.575 25.3125 46-47 23.974999999999998 25.0375 25.2125 25.775 48-49 23.7875 24.775 25.974999999999998 25.4625 50-51 24.175 24.8 25.374999999999996 25.650000000000002 52-53 24.725 24.712500000000002 25.6125 24.95 54-55 23.8625 24.45 25.275 26.4125 56-57 23.6375 25.2 25.775 25.387500000000003 58-59 24.4125 24.9875 24.825 25.775 60-61 23.962500000000002 25.8125 25.0625 25.162499999999998 62-63 23.1875 26.474999999999998 25.1875 25.15 64-65 23.674999999999997 26.387500000000003 24.375 25.5625 66-67 23.7625 24.4125 26.1125 25.7125 68-69 23.6875 25.2 26.125 24.9875 70-71 24.2 24.7375 25.662499999999998 25.4 72-73 24.125 23.8125 26.2125 25.85 74-75 24.099999999999998 24.55 26.0125 25.337500000000002 76-77 23.674999999999997 25.474999999999998 25.837500000000002 25.0125 78-79 23.9 25.8 25.85 24.45 80-81 23.799999999999997 24.7375 25.837500000000002 25.624999999999996 82-83 24.1625 24.625 26.0375 25.174999999999997 84-85 23.925 24.8625 25.35 25.8625 86-87 23.3875 24.825 25.7375 26.05 88-89 24.925 24.762500000000003 24.975 25.337500000000002 90-91 24.462500000000002 24.5375 25.5375 25.4625 92-93 23.95 25.5375 26.2625 24.25 94-95 24.8 25.2 24.3875 25.6125 96-97 23.5 25.275 26.575 24.65 98-99 24.875 24.6625 25.7125 24.75 100 25.5 24.15 23.95 26.400000000000002 >>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 0.0 19 0.0 20 0.0 21 0.5 22 0.5 23 0.0 24 1.0 25 1.0 26 1.0 27 2.0 28 4.0 29 8.5 30 10.5 31 16.5 32 26.5 33 29.5 34 34.0 35 45.0 36 65.0 37 74.0 38 82.0 39 104.5 40 114.0 41 118.5 42 123.0 43 138.5 44 156.5 45 180.5 46 194.5 47 195.0 48 196.0 49 175.5 50 156.5 51 165.0 52 160.5 53 133.5 54 121.0 55 126.5 56 122.5 57 108.0 58 97.0 59 90.0 60 87.0 61 72.5 62 59.0 63 60.5 64 51.5 65 37.5 66 37.5 67 40.5 68 38.0 69 29.5 70 27.0 71 20.5 72 17.5 73 15.0 74 7.5 75 5.5 76 4.5 77 3.0 78 1.5 79 1.5 80 1.5 81 1.5 82 1.5 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 1.575 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 93.0 #Duplication Level Percentage of deduplicated Percentage of total 1 95.3225806451613 88.64999999999999 2 2.956989247311828 5.5 3 1.129032258064516 3.15 4 0.24193548387096775 0.8999999999999999 5 0.1881720430107527 0.8750000000000001 6 0.13440860215053765 0.75 7 0.026881720430107527 0.17500000000000002 8 0.0 0.0 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 GGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTAGCC 7 0.17500000000000002 No Hit GTTGATTTCATGAATGCGATTTCTGATATGGCGGCGGTCGGTTTCCAGTT 6 0.15 No Hit CATGACTGGACACTGCATCGGAAGACACTTCGTGCCGACACGAAGCAGCC 6 0.15 No Hit GGCAGTTTTTGATCACGTTTATTGTAAGCCGTCAGCATCGGGATATCATC 6 0.15 No Hit GCCATTCGGACCTACCGTAAGCCTATATTTCGTTTTTCTGAGACCTATCC 6 0.15 No Hit GCCTTCTCTCGTTCTCGCCCGCTTTGCAAAAATATCTAATATCAATTGCG 6 0.15 No Hit ATCACATCTAGGCATGGAATCTTATGCCAGCTAACGGAACAAGCTTTGTG 5 0.125 No Hit ATCGGGTCCAGCGTGGCAAACAGGAGGTCTTCTTCATAGCTGTCAGCACT 5 0.125 No Hit CTGCGATAGGCTAGTTCATAAACGAGGGGCGATGCCCGGGCTCAGAATCC 5 0.125 No Hit GTCGGTTTAGCTGAGATTGCACCGTTGTTATAATCGACCCGGGCTGCGAC 5 0.125 No Hit CCGATCTTTTCCCTATCTAATTCACCTCCTATTAGGAGCCGATCGTGCTT 5 0.125 No Hit CGACAAGCGCAATTTGAAGCACACCGTTTTTCTTTCTTCTTTCACGGTAT 5 0.125 No Hit CCGGGATCGGGCAAAGGGGCAACTCGAGCTAATCTCCCCAGCGGCTAGCA 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.0625 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.1875 0.0 0.0 0.0 0.0 68-69 0.2375 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.30000000000000004 0.0 0.0 0.0 0.0 74-75 0.3375 0.0 0.0 0.0 0.0 76-77 0.4 0.0 0.0 0.0 0.0 78-79 0.48750000000000004 0.0 0.0 0.0 0.0 80-81 0.5874999999999999 0.0 0.0 0.0 0.0 82-83 0.7 0.0 0.0 0.0 0.0 84-85 0.8375 0.0 0.0 0.0 0.0 86-87 1.0625 0.0 0.0 0.0 0.0 88 1.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6127949 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127949_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.091 33.0 33.0 33.0 33.0 33.0 2 32.29725 33.0 33.0 33.0 33.0 33.0 3 32.2595 33.0 33.0 33.0 33.0 33.0 4 35.92025 37.0 37.0 37.0 33.0 37.0 5 35.8585 37.0 37.0 37.0 37.0 37.0 6 35.83625 37.0 37.0 37.0 37.0 37.0 7 35.8635 37.0 37.0 37.0 33.0 37.0 8 35.899 37.0 37.0 37.0 37.0 37.0 9 36.17625 37.0 37.0 37.0 37.0 37.0 10-11 36.24425 37.0 37.0 37.0 37.0 37.0 12-13 36.22125 37.0 37.0 37.0 37.0 37.0 14-15 38.50275 40.0 40.0 40.0 37.0 40.0 16-17 38.46625 40.0 40.0 40.0 37.0 40.0 18-19 38.476124999999996 40.0 40.0 40.0 37.0 40.0 20-21 38.341375 40.0 40.0 40.0 37.0 40.0 22-23 37.747125 40.0 37.0 40.0 35.0 40.0 24-25 38.175 40.0 37.0 40.0 37.0 40.0 26-27 38.187875 40.0 37.0 40.0 37.0 40.0 28-29 38.28375 40.0 37.0 40.0 37.0 40.0 30-31 38.183875 40.0 37.0 40.0 37.0 40.0 32-33 38.025999999999996 40.0 37.0 40.0 37.0 40.0 34-35 38.07075 40.0 37.0 40.0 37.0 40.0 36-37 37.952375 40.0 37.0 40.0 37.0 40.0 38-39 37.792375 40.0 37.0 40.0 33.0 40.0 40-41 37.784125 40.0 37.0 40.0 33.0 40.0 42-43 37.608000000000004 40.0 37.0 40.0 33.0 40.0 44-45 37.497 40.0 37.0 40.0 33.0 40.0 46-47 37.378 40.0 37.0 40.0 33.0 40.0 48-49 37.187250000000006 40.0 37.0 40.0 33.0 40.0 50-51 35.51275 38.5 35.0 38.5 30.0 40.0 52-53 35.828375 37.0 37.0 38.5 33.0 40.0 54-55 36.539874999999995 37.0 37.0 40.0 33.0 40.0 56-57 36.52625 37.0 37.0 40.0 33.0 40.0 58-59 36.33 37.0 37.0 40.0 33.0 40.0 60-61 36.062875000000005 37.0 37.0 40.0 33.0 40.0 62-63 35.836375000000004 37.0 37.0 40.0 33.0 40.0 64-65 35.645250000000004 37.0 37.0 38.5 33.0 40.0 66-67 35.462125 37.0 37.0 37.0 33.0 40.0 68-69 35.1785 37.0 37.0 37.0 33.0 40.0 70-71 34.957375 37.0 37.0 37.0 33.0 40.0 72-73 34.726124999999996 37.0 35.0 37.0 33.0 38.5 74-75 34.640375 37.0 33.0 37.0 33.0 37.0 76-77 34.27975 37.0 33.0 37.0 27.0 37.0 78-79 33.905375 37.0 33.0 37.0 27.0 37.0 80-81 33.794125 37.0 33.0 37.0 27.0 37.0 82-83 33.703625 37.0 33.0 37.0 27.0 37.0 84-85 33.79075 37.0 33.0 37.0 27.0 37.0 86-87 33.6965 37.0 33.0 37.0 27.0 37.0 88-89 33.565625 37.0 33.0 37.0 27.0 37.0 90-91 33.580124999999995 37.0 33.0 37.0 27.0 37.0 92-93 33.432375 37.0 33.0 37.0 27.0 37.0 94-95 33.282125 37.0 33.0 37.0 27.0 37.0 96-97 33.000125 37.0 33.0 37.0 27.0 37.0 98-99 32.966375 37.0 33.0 37.0 27.0 37.0 100-101 31.38175 35.0 30.0 37.0 21.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 22.0 3 2.0 4 5.0 5 5.0 6 3.0 7 3.0 8 2.0 9 4.0 10 6.0 11 4.0 12 5.0 13 3.0 14 3.0 15 4.0 16 10.0 17 5.0 18 7.0 19 12.0 20 6.0 21 8.0 22 13.0 23 12.0 24 13.0 25 26.0 26 15.0 27 24.0 28 29.0 29 43.0 30 39.0 31 66.0 32 72.0 33 101.0 34 148.0 35 219.0 36 510.0 37 1427.0 38 1124.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.599999999999998 15.7 13.3 40.400000000000006 2 28.4 22.400000000000002 31.474999999999998 17.724999999999998 3 23.474999999999998 25.624999999999996 26.325 24.575 4 26.900000000000002 32.95 18.525 21.625 5 27.800000000000004 34.275 18.45 19.475 6 21.4 36.275 21.0 21.325 7 21.425 16.775000000000002 38.2 23.599999999999998 8 23.25 20.349999999999998 25.55 30.85 9 24.6 21.875 27.474999999999998 26.05 10-11 25.4375 29.362500000000004 20.2125 24.9875 12-13 25.7875 23.1125 24.5 26.6 14-15 24.0125 25.874999999999996 25.7375 24.375 16-17 25.10627656914228 25.09377344336084 24.3935983995999 25.406351587896975 18-19 25.703212901612705 26.153269158644832 24.878109763720467 23.265408176022003 20-21 25.859697386519947 25.772164561710643 24.134050268850817 24.234087782918596 22-23 25.62820352544068 26.053256657082137 24.32804100512564 23.990498812351543 24-25 25.922220832812304 26.147305239464803 23.533825184444165 24.39664874327873 26-27 25.637500000000003 25.4625 24.25 24.65 28-29 25.974999999999998 24.887500000000003 23.599999999999998 25.5375 30-31 24.9375 25.5625 24.9125 24.587500000000002 32-33 25.4 25.8625 23.9 24.837500000000002 34-35 23.8125 26.5 24.2875 25.4 36-37 26.4125 25.8 23.2375 24.55 38-39 25.4 25.474999999999998 24.5375 24.587500000000002 40-41 26.5625 25.3125 24.099999999999998 24.025 42-43 25.587500000000002 25.75 25.2875 23.375 44-45 25.775 25.587500000000002 24.775 23.8625 46-47 26.075 25.0375 23.974999999999998 24.9125 48-49 25.740717589698715 24.765595699462434 25.153144143017876 24.34054256782098 50-51 25.403175396924617 25.62820352544068 24.553069133641706 24.415551943992998 52-53 25.424999999999997 25.924999999999997 24.8125 23.8375 54-55 24.8906113264158 25.9407425928241 25.54069258657332 23.627953494186773 56-57 25.465683210401302 25.203150393799223 26.22827853481685 23.102887860982623 58-59 25.0125 25.974999999999998 25.074999999999996 23.9375 60-61 25.775 25.0375 25.05 24.1375 62-63 25.387500000000003 26.237500000000004 23.974999999999998 24.4 64-65 24.85310663832979 26.103262907863485 25.115639454931866 23.92799099887486 66-67 25.5125 25.4375 24.75 24.3 68-69 25.684631736901338 25.872202075778418 24.296611229210953 24.14655495810929 70-71 25.2375 24.75 25.5125 24.5 72-73 25.422033262473427 26.20982868575716 23.583843941478055 24.78429411029136 74-75 25.924999999999997 26.075 24.9375 23.0625 76-77 26.025 25.05 24.675 24.25 78-79 25.82218331874453 24.99687382768538 24.496686257346507 24.684256596223584 80-81 25.5125 26.187500000000004 24.5 23.799999999999997 82-83 25.25328330206379 25.67854909318324 24.30268918073796 24.765478424015008 84-85 25.538038038038035 26.013513513513516 25.175175175175173 23.273273273273272 86-87 26.3631815907954 24.912456228114056 25.56278139069535 23.1615807903952 88-89 25.937500000000004 25.924999999999997 24.9 23.2375 90-91 25.2125 26.687499999999996 24.762500000000003 23.3375 92-93 25.51887971992998 25.78144536134033 24.74368592148037 23.95598899724931 94-95 26.450000000000003 25.662499999999998 24.65 23.2375 96-97 26.05 25.7875 25.387500000000003 22.775000000000002 98-99 25.9625 26.275 24.65 23.1125 100-101 26.96587073384173 26.52831603950494 23.465433179147393 23.040380047505938 >>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 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 0.5 25 0.5 26 2.0 27 3.5 28 5.5 29 9.0 30 13.0 31 22.5 32 25.0 33 22.5 34 31.0 35 44.5 36 48.0 37 57.5 38 82.0 39 111.5 40 123.5 41 116.0 42 118.5 43 141.5 44 157.5 45 160.5 46 169.5 47 174.0 48 181.5 49 187.5 50 171.5 51 144.0 52 136.0 53 144.5 54 147.0 55 131.0 56 113.5 57 94.0 58 100.5 59 110.0 60 84.0 61 75.0 62 74.5 63 71.5 64 66.5 65 52.0 66 49.5 67 52.0 68 43.5 69 34.0 70 24.5 71 19.0 72 19.0 73 10.5 74 6.0 75 7.0 76 3.0 77 0.5 78 0.0 79 1.0 80 2.0 81 1.0 82 0.0 83 0.5 84 0.5 85 1.0 86 1.0 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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.025 18-19 0.0125 20-21 0.0375 22-23 0.0125 24-25 0.0375 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 0.0125 50-51 0.0125 52-53 0.0 54-55 0.0125 56-57 0.0125 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0125 66-67 0.0 68-69 0.0375 70-71 0.0 72-73 0.0375 74-75 0.0 76-77 0.0 78-79 0.0375 80-81 0.0 82-83 0.0625 84-85 0.1 86-87 0.05 88-89 0.0 90-91 0.0 92-93 0.025 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.15 #Duplication Level Percentage of deduplicated Percentage of total 1 95.03488996242619 88.52499999999999 2 3.676865271068169 6.8500000000000005 3 0.6709608158883521 1.875 4 0.3488996242619431 1.3 5 0.1610305958132045 0.75 6 0.026838432635534086 0.15 7 0.05367686527106817 0.35000000000000003 8 0.026838432635534086 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 GAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAA 8 0.2 No Hit CAGCAATTGAAGTGAAGATGATTGACCGCACGCAATTGATATTAGATATT 7 0.17500000000000002 No Hit TGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAA 7 0.17500000000000002 No Hit GCCTGACGAGTGCTGACAGCTATGAAGAAGACCTCCTGTTTGCCACGCTG 6 0.15 No Hit GTTTATTGGAAGCATCAACCTGCGCCGTCTTGTTAACTTGTCATATCGCG 5 0.125 No Hit CGCATTTTGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCA 5 0.125 No Hit CTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGA 5 0.125 No Hit GAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATTG 5 0.125 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 5 0.125 No Hit CGAATAGCTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAG 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.0625 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.1875 0.0 0.0 0.0 0.0 68-69 0.2375 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.30000000000000004 0.0 0.0 0.0 0.0 74-75 0.3375 0.0 0.0 0.0 0.0 76-77 0.4 0.0 0.0 0.0 0.0 78-79 0.48750000000000004 0.0 0.0 0.0 0.0 80-81 0.6125 0.0 0.0 0.0 0.0 82-83 0.7250000000000001 0.0 0.0 0.0 0.0 84-85 0.8625 0.0 0.0 0.0 0.0 86-87 1.0875 0.0 0.0 0.0 0.0 88-89 1.3875000000000002 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427019 spots for SRR6127949.sra Written 1427019 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra Read 1427008 spots for SRR6127949.sra Written 1427008 spots for SRR6127949.sra SRR ids: ['SRR6127949.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_h5__il93 SRR6127949.sra spots: 28540171 blocks: [[1, 1427008], [1427009, 2854016], [2854017, 4281024], [4281025, 5708032], [5708033, 7135040], [7135041, 8562048], [8562049, 9989056], [9989057, 11416064], [11416065, 12843072], [12843073, 14270080], [14270081, 15697088], [15697089, 17124096], [17124097, 18551104], [18551105, 19978112], [19978113, 21405120], [21405121, 22832128], [22832129, 24259136], [24259137, 25686144], [25686145, 27113152], [27113153, 28540171]] SRR6127949 file size 6806758 SRR6127949 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 SRR6127949 SRR6127949_1.fastq SRR6127949_2.fastq Input file: SRR6127949_1.fastq Paired file: SRR6127949_2.fastq trimmed: SRR6127949-trimmed-pair1.fastq, SRR6127949-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 04:59:39 2024 >> started Tue Dec 10 05:00:06 2024 >> done (26.553s) 28540171 read pairs processed; of these: 88061 ( 0.31%) short read pairs filtered out after trimming by size control 154509 ( 0.54%) empty read pairs filtered out after trimming by size control 28297601 (99.15%) read pairs available; of these: 4756954 (16.81%) trimmed read pairs available after processing 23540647 (83.19%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 25 0.00% 20 24 0.00% 21 52 0.00% 22 89 0.00% 23 128 0.00% 24 158 0.00% 25 243 0.00% 26 284 0.00% 27 312 0.00% 28 384 0.00% 29 478 0.00% 30 582 0.00% 31 670 0.00% 32 836 0.00% 33 903 0.00% 34 985 0.00% 35 1144 0.00% 36 1373 0.00% 37 1499 0.01% 38 1691 0.01% 39 1909 0.01% 40 2128 0.01% 41 2308 0.01% 42 2553 0.01% 43 2814 0.01% 44 3085 0.01% 45 3439 0.01% 46 3882 0.01% 47 4122 0.01% 48 4324 0.02% 49 4791 0.02% 50 5133 0.02% 51 5542 0.02% 52 5979 0.02% 53 6515 0.02% 54 6933 0.02% 55 7929 0.03% 56 8435 0.03% 57 9405 0.03% 58 10442 0.04% 59 18105 0.06% 60 19049 0.07% 61 20974 0.07% 62 23530 0.08% 63 25117 0.09% 64 27090 0.10% 65 29620 0.10% 66 29676 0.10% 67 31511 0.11% 68 32335 0.11% 69 34844 0.12% 70 35885 0.13% 71 38137 0.13% 72 39979 0.14% 73 42163 0.15% 74 44319 0.16% 75 41673 0.15% 76 41253 0.15% 77 45512 0.16% 78 49434 0.17% 79 52691 0.19% 80 56403 0.20% 81 61247 0.22% 82 65754 0.23% 83 73399 0.26% 84 82228 0.29% 85 90979 0.32% 86 107501 0.38% 87 108522 0.38% 88 105299 0.37% 89 106271 0.38% 90 118098 0.42% 91 128046 0.45% 92 141821 0.50% 93 157534 0.56% 94 181399 0.64% 95 211161 0.75% 96 252294 0.89% 97 317558 1.12% 98 402481 1.42% 99 511486 1.81% 100 24181680 85.45% 28297601 reads passed initial QC criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=2.70 fanout-score-rank=12 prefix-density=0.46 prefix-fanout=2.6 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=23 fanout-score=8.50 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=3.0 sequence=GCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAGCCTGGCGGGTGGCGCCCCATTCGGACTTCTTGGGAAGGAAAGACGATTTGAGGATAGTAGCCGAGGCCATTGTTTCTGGCTCCAAAGGCAAGAGGATCAGGTGCTACCCTCTTCTTTGACACAAGCTTG criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=3.54 fanout-score-rank=11 prefix-density=0.53 prefix-fanout=2.9 sequence=AAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=8.53 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=1.7 sequence=CGAGCTCGCATTTTGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAAAGTACTGACCAGCGTCACACAAAAACGGAACAGGGCTGACGCCGCTACATATATAGGAAAAGGGAAGGTAGAAGAGCTGAAGGCACTCGTGGAAGAGCTTGAAGCTGATCTCCTCATCTTTAATGATGAACTGTCGCCAAGTCAGCTGAAGTCATTGGCAACAGCAATTGAAGTGAAGATGATTGACCGCACGCAATTGATATTAGATATTTTTGCAAAGCGGGCGAGAACGAGAGAAGGCAAACTTCAAATTGAGCTGGCTCAGCTGCAATATGCACTGCCGCGTCTGACGGGACAAGGGATCAACCTTTCCCGGCAAGGCGGAGGAATTGGGGCAAGAGGTCCCGGGGAAACGAAACTGGAAACCGACCGCCGCCATATCAGAAATCGCATTCATGAAATCAACACACAGCTTTCCACTGTCATTCGCCATAGAAGCCGATACCG SRR6127949 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 05:00:59 Started mapping on | Dec 10 05:00:59 Finished on | Dec 10 05:15:05 Mapping speed, Million of reads per hour | 120.42 Number of input reads | 28297601 Average input read length | 197 UNIQUE READS: Uniquely mapped reads number | 19691450 Uniquely mapped reads % | 69.59% Average mapped length | 196.81 Number of splices: Total | 13289556 Number of splices: Annotated (sjdb) | 12570690 Number of splices: GT/AG | 13098285 Number of splices: GC/AG | 162209 Number of splices: AT/AC | 4838 Number of splices: Non-canonical | 24224 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.34 Insertion rate per base | 0.02% Insertion average length | 1.99 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 454062 % of reads mapped to multiple loci | 1.60% Number of reads mapped to too many loci | 69968 % of reads mapped to too many loci | 0.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 27.29% % of reads unmapped: other | 1.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8161827 8161827 8161827 N_multimapping 454062 454062 454062 N_noFeature 810294 19165014 963301 N_ambiguous 438673 2178 66069 UnstrandedReadsAssigned:18442483 PositiveStrandReadsAssigned:524258 NegativeStrandReadsAssigned:18662080 Dataset is classified negative stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR6127949 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: SRR6127949-trimmed-pair1.fastq SRR6127949-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,297,601 reads, 18,774,616 reads pseudoaligned [quant] estimated average fragment length: 165.054 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,114 rounds 52973 SRR6127949.ke.tsv 35125 SRR6127949.se.tsv 88098 total ==> SRR6127949.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 772.143 0 0 PNS24247 1044 879.946 39.2174 3.4792 PNS24249 1928 1763.95 52.7121 2.33282 PNS24246 1044 879.946 39.2174 3.4792 PNS24248 1044 879.946 39.2174 3.4792 PNS24244 1471 1306.95 109.636 6.54864 PNS24243 293 136.255 0 0 KQK14069 1603 1438.95 1873.14 101.621 KQK14071 474 311.656 77.9314 19.5207 ==> SRR6127949.se.tsv <== BRADI_1g14170v3 2205 BRADI_1g53295v3 618 BRADI_1g59795v3 163 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 269 BRADI_1g74790v3 147 BRADI_1g09890v3 0 BRADI_1g77505v3 482 BRADI_1g48960v3 0 SRR6127949 completed mapping pipeline successfully