Starting /dee2/code/volunteer_pipeline.sh ERR5262795 current disk space = 1551415418880 free memory = 1341758896 ERR5262795 SRAfilesize f632295e24a49050d3190c194afc26ad ERR5262795.sra ERR5262795.sra file validated ERR5262795 is paired end ERR5262795 is conventional basespace ERR5262795 read1 length is 101-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5262795_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101-150 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.758 37.0 37.0 37.0 37.0 37.0 2 36.7395 37.0 37.0 37.0 37.0 37.0 3 36.7555 37.0 37.0 37.0 37.0 37.0 4 36.725 37.0 37.0 37.0 37.0 37.0 5 36.794 37.0 37.0 37.0 37.0 37.0 6 36.7495 37.0 37.0 37.0 37.0 37.0 7 36.7445 37.0 37.0 37.0 37.0 37.0 8 36.685 37.0 37.0 37.0 37.0 37.0 9 36.6985 37.0 37.0 37.0 37.0 37.0 10-14 36.68429999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.6536 37.0 37.0 37.0 37.0 37.0 20-24 36.671400000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.6134 37.0 37.0 37.0 37.0 37.0 30-34 36.644099999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.6396 37.0 37.0 37.0 37.0 37.0 40-44 36.608799999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.581 37.0 37.0 37.0 37.0 37.0 50-54 36.54709999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.5296 37.0 37.0 37.0 37.0 37.0 60-64 36.4927 37.0 37.0 37.0 37.0 37.0 65-69 36.4882 37.0 37.0 37.0 37.0 37.0 70-74 36.4585 37.0 37.0 37.0 37.0 37.0 75-79 36.507400000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.4195 37.0 37.0 37.0 37.0 37.0 85-89 36.4313 37.0 37.0 37.0 37.0 37.0 90-94 36.3932 37.0 37.0 37.0 37.0 37.0 95-99 36.402 37.0 37.0 37.0 37.0 37.0 100-104 36.46560846269404 37.0 37.0 37.0 37.0 37.0 105-109 36.55389344114045 37.0 37.0 37.0 37.0 37.0 110-114 36.50846714776892 37.0 37.0 37.0 37.0 37.0 115-119 36.5372721392556 37.0 37.0 37.0 37.0 37.0 120-124 36.46869353730092 37.0 37.0 37.0 37.0 37.0 125-129 36.23888010033077 37.0 37.0 37.0 37.0 37.0 130-134 36.32084881679608 37.0 37.0 37.0 37.0 37.0 135-139 36.25700125220486 37.0 37.0 37.0 37.0 37.0 140-144 36.3328963080971 37.0 37.0 37.0 37.0 37.0 145-149 36.4305167182967 37.0 37.0 37.0 37.0 37.0 150 36.3278463648834 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 27 4.0 28 1.0 29 5.0 30 8.0 31 27.0 32 29.0 33 37.0 34 89.0 35 236.0 36 2528.0 37 1036.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 10.85 12.775 0.7250000000000001 75.64999999999999 2 3.675 23.3 13.975000000000001 59.050000000000004 3 28.825 23.65 17.299999999999997 30.225 4 25.025 20.9 16.025 38.05 5 25.374999999999996 32.5 19.725 22.400000000000002 6 26.825 32.475 18.95 21.75 7 14.725 22.275 37.75 25.25 8 17.65 23.65 26.25 32.45 9 20.3 20.849999999999998 34.300000000000004 24.55 10-14 22.43 26.174999999999997 25.740000000000002 25.655 15-19 23.18 24.37 24.87 27.58 20-24 21.345 24.495 24.985 29.175 25-29 22.195 27.12 23.32 27.365000000000002 30-34 26.279999999999998 23.645 23.03 27.045 35-39 23.595 23.7 25.865 26.840000000000003 40-44 21.21 24.605 26.33 27.855 45-49 23.31 26.810000000000002 24.990000000000002 24.89 50-54 25.215 24.26 25.06 25.465 55-59 25.775 27.515 22.220000000000002 24.490000000000002 60-64 24.245 25.235000000000003 25.369999999999997 25.15 65-69 22.759999999999998 26.200000000000003 24.515 26.525 70-74 24.605 25.47 23.615 26.31 75-79 24.45 24.495 23.330000000000002 27.725 80-84 26.805 25.650000000000002 23.84 23.705000000000002 85-89 25.415 23.880000000000003 26.695 24.01 90-94 24.03 23.855 25.985000000000003 26.13 95-99 24.32 24.759999999999998 23.23 27.689999999999998 100-104 21.058953057751978 25.618056250625564 28.260434390951854 25.0625563006706 105-109 20.171137390635515 22.690125949427937 23.391981540236515 33.746755119700026 110-114 17.226680040120364 43.781344032096285 16.700100300902708 22.291875626880643 115-119 10.787025396027156 37.46542620065376 22.00150867488056 29.74603972843852 120-124 10.722433460076045 40.557667934093786 23.67553865652725 25.044359949302912 125-129 23.535510627268014 25.63504406428201 31.337480559875587 19.491964748574393 130-134 21.49191444966093 32.60302556077204 24.047991653625456 21.857068335941577 135-139 16.636149620716715 32.9322521579911 27.46534135495684 22.96625686633534 140-144 16.724092234296318 25.62947256824808 17.333686721441826 40.31274847601378 145-149 25.242980561555072 20.49136069114471 17.359611231101514 36.906047516198704 150 14.951989026063101 22.359396433470508 16.46090534979424 46.22770919067216 >>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 0.0 25 2.5 26 3.0 27 0.5 28 0.0 29 4.0 30 7.0 31 4.5 32 3.5 33 10.0 34 23.0 35 30.0 36 46.5 37 56.0 38 59.5 39 75.5 40 92.0 41 110.5 42 121.5 43 140.5 44 160.5 45 186.0 46 176.0 47 176.5 48 215.5 49 203.5 50 182.0 51 154.0 52 127.0 53 151.0 54 171.5 55 221.5 56 176.0 57 73.5 58 68.0 59 62.5 60 59.5 61 64.0 62 65.5 63 56.0 64 45.0 65 43.5 66 42.0 67 52.5 68 56.5 69 37.0 70 32.5 71 33.0 72 26.0 73 24.5 74 19.0 75 12.0 76 11.0 77 9.0 78 5.5 79 1.0 80 1.0 81 2.5 82 3.5 83 2.5 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 100-101 6.0 102-103 0.0 104-105 5.0 106-107 3190.0 108-109 1.0 110-111 0.0 112-113 2.0 114-115 0.0 116-117 1.0 118-119 3.0 120-121 1.0 122-123 8.0 124-125 10.0 126-127 5.0 128-129 0.0 130-131 1.0 132-133 1.0 134-135 1.0 136-137 0.0 138-139 4.0 140-141 7.0 142-143 4.0 144-145 5.0 146-147 8.0 148-149 8.0 150-151 729.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 62.575 #Duplication Level Percentage of deduplicated Percentage of total 1 71.8337994406712 44.95 2 19.137035557331203 23.95 3 5.19376747902517 9.75 4 1.5181781861765882 3.8 5 0.9188973232121453 2.875 6 0.3595685177786656 1.35 7 0.23971234518577705 1.05 8 0.07990411506192568 0.4 9 0.07990411506192568 0.44999999999999996 >10 0.5992808629644426 7.6499999999999995 >50 0.0 0.0 >100 0.03995205753096284 3.775 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GCCAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTT 151 3.775 No Hit CAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTTGC 44 1.0999999999999999 No Hit GCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTTGCTGA 37 0.9249999999999999 No Hit AGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTTGCT 33 0.8250000000000001 No Hit GGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTTGCTG 32 0.8 No Hit GTACAGTTTACAGTTATACACTAACTATGAAGAGATATGTGCTCGAATGA 31 0.775 No Hit CCAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTTG 17 0.42500000000000004 No Hit AGCCAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGT 16 0.4 No Hit CACACATACACCATCTTCGTTCCACAAAGTTGGTGTGCTAGGCCATACTA 14 0.35000000000000003 No Hit GTTCATCACACATACACCATCTTCGTTCCACAAAGTTGGTGTGCTAGGCC 13 0.325 No Hit GCCAAATAGAAGCACTCCCACCCTATGGGTTCTACTGACTGATCAGGCAG 13 0.325 No Hit GGGTTCTACTGACTGATCAGGCAGCTTCCTTGCTCCTCGCTTGTCGCACA 12 0.3 No Hit ATCACACATACACCATCTTCGTTCCACAAAGTTGGTGTGCTAGGCCATAC 12 0.3 No Hit GTCCAGCTTCTTTTGTGAGATTTCCATGTGACTCCTGAGAAAATGTGAGC 12 0.3 No Hit CCCCAAACCACCACTGGCAGCATGGGTGTAATGACCCAACGATGCTGCTT 10 0.25 No Hit GCCATACTAGCTCGTAGCGCGCCTAACCAGACACATAACCCACATTTTAT 10 0.25 No Hit ATACAGCCAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCA 9 0.22499999999999998 No Hit CCAGCTTCTTTTGTGAGATTTCCATGTGACTCCTGAGAAAATGTGAGCTT 9 0.22499999999999998 No Hit GGCCATACTAGCTCGTAGCGCGCCTAACCAGACACATAACCCACATTTTA 8 0.2 No Hit CCCCATCACAAAAACAAACTCAACCATTAGAACCACGGGATCTCTGCCGG 8 0.2 No Hit CTACTGACTGATCAGGCAGCTTCCTTGCTCCTCGCTTGTCGCACAAAAGT 7 0.17500000000000002 No Hit CACAGACACAGCAGCAGTAATCAAACACAGACCGAGACCTCTCTCTCCCT 7 0.17500000000000002 No Hit CCCAACGATGCTGCTTTGCTTCGGTGTATTGTACATGATTTACTTGCCAA 7 0.17500000000000002 No Hit CATCACACATACACCATCTTCGTTCCACAAAGTTGGTGTGCTAGGCCATA 7 0.17500000000000002 No Hit GTGAGATTTCCATGTGACTCCTGAGAAAATGTGAGCTTCGCACGAAGCGT 7 0.17500000000000002 No Hit GCTGCTTTGCTTCGGTGTATTGTACATGATTTACTTGCCAAATAGAAGCA 7 0.17500000000000002 No Hit CCATGGAAGAACACCAAGGTCGTCGAAGACGAAGAGGTTAAATCAGCAGT 6 0.15 No Hit CCACGCATCAACCTAAGGTAGGACATGCCACAATCCAAATCCACACATGG 6 0.15 No Hit CCGCACTTGCAGCCGGACCCGCACCCGCAGTTGCCGCCGCAGCACGACAT 6 0.15 No Hit GTTCCACAAAGTTGGTGTGCTAGGCCATACTAGCTCGTAGCGCGCCTAAC 6 0.15 No Hit GCGCGCCTAACCAGACACATAACCCACATTTTATGACTGGCAGTACACAT 6 0.15 No Hit CCACAAAGTTGGTGTGCTAGGCCATACTAGCTCGTAGCGCGCCTAACCAG 6 0.15 No Hit CCTATGTTCGATTGCATTGTCTAGATCGGCCTCAAAAGTTTCCTCTAATC 6 0.15 No Hit ACATGATTTACTTGCCAAATAGAAGCACTCCCACCCTATGGGTTCTACTG 6 0.15 No Hit GTCAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTT 6 0.15 No Hit CCTCAAACTCCTTGAGCTGGCCAATGGCATACTCATCAATGGCGTCAACC 5 0.125 No Hit CACGCCACCATCTGTAAGGTCAACTATGACCTGCTGGATTGGTTTGTCAT 5 0.125 No Hit GGCCAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGT 5 0.125 No Hit GGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTTGCT 5 0.125 No Hit CTGCTTTGCTTCGGTGTATTGTACATGATTTACTTGCCAAATAGAAGCAC 5 0.125 No Hit AAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAGTTGC 5 0.125 No Hit ATTGGATACTACACGGCGTCGCATTTTTTTCGCCAGCACAAAAAGATGGA 5 0.125 No Hit CAGCCAGGCCTTGTAGTTCCGGACCTTCCAAGCGCGGGTTCTTCTCAAAG 5 0.125 No Hit CCGGAAGCGGCGCGACAACCAACCGGCAACCAGTAGCCGGCCACACAGGA 5 0.125 No Hit CCAGCTCTGTAACAAAGGTTTTCGTTGTTATGATGTAATCCGGAGCAATG 5 0.125 No Hit CCGAGGTACTTACGGAGCAGCGAATGAAGGTACTTGCCATCGTACTTGGG 5 0.125 No Hit TTTTTTTTCGCAAAAAAAATATTGTATATATATAATGTATGTACAGTTTA 5 0.125 No Hit ATGGACTCTCACCTTTCCAGGAGATACAGTAATCATGGCACTGGAGACAT 5 0.125 No Hit CGCAAAAAAAATATTGTATATATATAATGTATGTACAGTTTACAGTTATA 5 0.125 No Hit GCCACTTTCAACCATGTCACGTAAAACATCACAACTGTGCTGCAACCAAT 5 0.125 No Hit CACCGCCAGAAGCGCCGCCAGACATGTGCTGCCCAATCTTTGAGACAGCC 5 0.125 No Hit GTGTATTGTACATGATTTACTTGCCAAATAGAAGCACTCCCACCCTATGG 5 0.125 No Hit CAGGTATCTCTGTCCTCTGGGAACATGACAGGAGAAGGTGGGATAATTAT 5 0.125 No Hit CAGGGTCATCTCTGTTGAGTATGCACTTCGTGACGATGATGAGAAAAGGA 5 0.125 No Hit CCATTACCAGAGTCACCCTTCGGAGCCTCCCTGATCTCCTCCGCAGTGTC 5 0.125 No Hit CCGTGATGATGTGCGCGCTGGCCGTCCAGAACGTGCCGGAGCGGCGTGGG 5 0.125 No Hit AAACCACCACTGGCAGCATGGGTGTAATGACCCAACGATGCTGCTTTGCT 5 0.125 No Hit GGTGTATTGTACATGATTTACTTGCCAAATAGAAGCACTCCCACCCTATG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCAGCT 20 5.7243105E-6 115.72 140-144 ACTTTGA 35 6.881237E-9 99.18857 120-124 GAGACTA 35 6.881237E-9 99.18857 125-129 TAGATAT 35 6.881237E-9 99.18857 130-134 CCAGCTC 25 1.7352235E-5 92.576004 140-144 CAGCTCC 20 8.752926E-4 86.79 140-144 ATCCCAG 40 1.740409E-8 86.79 135-139 AGCCAGC 40 1.740409E-8 86.79 140-144 CCAGAAA 45 5.9480953E-10 84.37917 105-109 AACATCA 45 5.9480953E-10 84.37917 110-114 TGAGACT 35 8.658626E-7 82.65714 125-129 AACTTTG 35 8.658626E-7 82.65714 120-124 TATCCCA 35 8.658626E-7 82.65714 135-139 CTAGATA 35 8.658626E-7 82.65714 130-134 AAACATC 40 2.7745045E-8 81.36562 110-114 TCAACAA 40 2.7745045E-8 81.36562 115-119 GCCAGGC 20 0.0011368612 81.36562 1 CAGGCCT 20 0.0011368612 81.36562 3 CCAGGCC 20 0.0011368612 81.36562 2 CAACAAC 50 1.369699E-9 75.94125 115-119 >>END_MODULE ERR5262795 read2 length is 85-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5262795_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 85-150 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.402 37.0 37.0 37.0 37.0 37.0 2 36.1625 37.0 37.0 37.0 37.0 37.0 3 36.2545 37.0 37.0 37.0 37.0 37.0 4 36.3315 37.0 37.0 37.0 37.0 37.0 5 36.4295 37.0 37.0 37.0 37.0 37.0 6 36.405 37.0 37.0 37.0 37.0 37.0 7 36.4595 37.0 37.0 37.0 37.0 37.0 8 36.538 37.0 37.0 37.0 37.0 37.0 9 36.4325 37.0 37.0 37.0 37.0 37.0 10-14 36.492399999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.468399999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.4576 37.0 37.0 37.0 37.0 37.0 25-29 36.420500000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.4178 37.0 37.0 37.0 37.0 37.0 35-39 36.428399999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.3949 37.0 37.0 37.0 37.0 37.0 45-49 36.405100000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.32 37.0 37.0 37.0 37.0 37.0 55-59 36.2855 37.0 37.0 37.0 37.0 37.0 60-64 36.2955 37.0 37.0 37.0 37.0 37.0 65-69 36.284499999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.207 37.0 37.0 37.0 37.0 37.0 75-79 36.210899999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.19070000000001 37.0 37.0 37.0 37.0 37.0 85-89 36.17905256469058 37.0 37.0 37.0 37.0 37.0 90-94 36.21500495089196 37.0 37.0 37.0 37.0 37.0 95-99 36.1610699682895 37.0 37.0 37.0 37.0 37.0 100-104 36.031818701787564 37.0 37.0 37.0 37.0 37.0 105-109 36.02457376148743 37.0 37.0 37.0 37.0 37.0 110-114 35.858967771186755 37.0 37.0 37.0 37.0 37.0 115-119 35.80845760464149 37.0 37.0 37.0 37.0 37.0 120-124 35.8683553195713 37.0 37.0 37.0 37.0 37.0 125-129 35.643051144837486 37.0 37.0 37.0 37.0 37.0 130-134 35.58992559711239 37.0 37.0 37.0 37.0 37.0 135-139 35.606357298564525 37.0 37.0 37.0 37.0 37.0 140-144 35.733616959001736 37.0 37.0 37.0 37.0 37.0 145-149 35.56357990101294 37.0 37.0 37.0 37.0 37.0 150 35.491083676268865 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 4.0 12 1.0 13 3.0 14 2.0 15 1.0 16 1.0 17 2.0 18 0.0 19 1.0 20 4.0 21 4.0 22 4.0 23 1.0 24 5.0 25 1.0 26 3.0 27 5.0 28 3.0 29 4.0 30 11.0 31 22.0 32 25.0 33 36.0 34 105.0 35 330.0 36 2613.0 37 809.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.325 20.9 8.35 24.425 2 28.449999999999996 23.150000000000002 26.224999999999998 22.175 3 23.9 26.075 28.65 21.375 4 26.724999999999998 30.3 20.575 22.400000000000002 5 25.15 32.550000000000004 19.8 22.5 6 24.0 35.05 20.549999999999997 20.4 7 24.65 17.8 34.625 22.925 8 20.474999999999998 23.125 26.900000000000002 29.5 9 24.325 21.925 26.700000000000003 27.05 10-14 27.169999999999998 25.369999999999997 23.585 23.875 15-19 25.874999999999996 23.705000000000002 26.165 24.255 20-24 25.8 24.665 25.275 24.26 25-29 26.08 24.44 25.165 24.315 30-34 26.795 24.709999999999997 24.985 23.51 35-39 25.775 24.62 25.28 24.325 40-44 25.985000000000003 24.39 26.419999999999998 23.205000000000002 45-49 26.290000000000003 24.12 26.22 23.369999999999997 50-54 26.685 24.91 25.085 23.32 55-59 25.83 24.255 25.89 24.025 60-64 26.465 24.725 25.224999999999998 23.585 65-69 26.924999999999997 24.465 25.585 23.025000000000002 70-74 27.665 23.494999999999997 26.215 22.625 75-79 25.924999999999997 25.135 25.595000000000002 23.345 80-84 26.169999999999998 24.9 25.71 23.22 85-89 26.589624293361346 24.203311821501828 25.889239081494825 23.317824803642004 90-94 26.997796915681953 24.749649509313038 25.66593230522732 22.586621269777687 95-99 27.533326651297983 24.476295479603085 26.120076175202968 21.87030169389596 100-104 25.364843710548907 23.223753976670203 27.26354592738474 24.147856385396153 105-109 55.46928079200233 13.646510725031543 22.39153644569543 8.492672037270697 110-114 24.899699097291876 24.924774322968908 28.25977933801404 21.915747241725175 115-119 26.151522778756608 23.936571860055373 27.384847722124338 22.52705763906368 120-124 26.294416243654823 24.238578680203045 26.42131979695431 23.045685279187815 125-129 23.054979253112034 28.319502074688796 25.38900414937759 23.236514522821576 130-134 26.395409494001044 26.734480959833075 24.90871152842984 21.961398017736045 135-139 28.145435521841485 22.887784462464033 27.779230970442057 21.187549045252418 140-144 26.848661542539094 25.31142327060694 25.152398621786375 22.687516565067586 145-149 26.13390928725702 24.487041036717063 25.296976241900648 24.08207343412527 150 21.947873799725652 32.23593964334705 22.633744855967077 23.18244170096022 >>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 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 1.5 19 1.5 20 1.0 21 0.5 22 0.0 23 0.0 24 0.5 25 0.5 26 1.0 27 1.5 28 1.0 29 1.5 30 2.0 31 3.0 32 4.5 33 11.0 34 25.5 35 37.5 36 46.5 37 66.0 38 78.0 39 96.5 40 136.0 41 146.5 42 142.0 43 177.0 44 197.5 45 182.0 46 183.5 47 196.0 48 207.5 49 214.0 50 199.0 51 167.0 52 132.0 53 102.0 54 100.0 55 97.5 56 76.5 57 70.5 58 72.0 59 78.0 60 75.5 61 73.5 62 78.5 63 62.5 64 46.5 65 46.0 66 43.0 67 51.0 68 49.0 69 35.0 70 40.0 71 37.5 72 24.5 73 18.5 74 15.0 75 12.5 76 11.5 77 5.5 78 3.5 79 3.5 80 3.0 81 2.0 82 1.0 83 1.0 84 0.5 85 0.5 86 0.5 87 0.0 88 0.0 89 0.5 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 84-85 2.0 86-87 1.0 88-89 1.0 90-91 1.0 92-93 2.0 94-95 2.0 96-97 1.0 98-99 1.0 100-101 44.0 102-103 0.0 104-105 5.0 106-107 3141.0 108-109 1.0 110-111 0.0 112-113 2.0 114-115 1.0 116-117 1.0 118-119 3.0 120-121 1.0 122-123 8.0 124-125 10.0 126-127 4.0 128-129 0.0 130-131 1.0 132-133 1.0 134-135 1.0 136-137 0.0 138-139 4.0 140-141 7.0 142-143 4.0 144-145 5.0 146-147 8.0 148-149 8.0 150-151 729.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 69.125 #Duplication Level Percentage of deduplicated Percentage of total 1 71.64556962025317 49.525000000000006 2 19.638336347197107 27.150000000000002 3 5.3164556962025316 11.025 4 1.5551537070524413 4.3 5 0.7956600361663654 2.75 6 0.5786618444846293 2.4 7 0.14466546112115733 0.7000000000000001 8 0.108499095840868 0.6 9 0.03616636528028933 0.22499999999999998 >10 0.18083182640144665 1.325 >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 ATTTGAAGAACCTAATTAGCTTGGACTTGTACAAGAACAATGTTTCGGGC 12 0.3 No Hit GCCAATTCCAAGGGAGCTGGCTGGGATATCTAGTCTCAAAGTTGTTGATG 11 0.27499999999999997 No Hit GTTTCGGGCACTATACCTCCAACACTTGGGAAGTTGAAGTCCCTTGTATT 10 0.25 No Hit GTTGAAGTCCCTTGTATTCCTGCGGCTCAATGGCAATCGTTTGACTGGGC 10 0.25 No Hit AATCGTTTGACTGGGCCAATTCCAAGGGAGCTGGCTGGGATATCTAGTCT 10 0.25 No Hit AATCTATCCTTGCTCTTCCTTAGCATGAGGCGTGTGTTCATGTGATTCCT 9 0.22499999999999998 No Hit GTTGTTGATGTTTCTGGTAATGATCTGTGCGGAACAATCCCTACCACTGG 8 0.2 No Hit ATAACATTCAAGGAACGATCCCTTCAGAACTTGGTGATTTGAAGAACCTA 8 0.2 No Hit GTTTGACTGGGCCAATTCCAAGGGAGCTGGCTGGGATATCTAGTCTCAAA 8 0.2 No Hit TGGCAATCTGAACCTATCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGG 7 0.17500000000000002 No Hit GCCGATCATGCTTGCATGCATGAGAGTGGCTGAACCTAGCTAATAATCAT 7 0.17500000000000002 No Hit GAACAATGTTTCGGGCACTATACCTCCAACACTTGGGAAGTTGAAGTCCC 7 0.17500000000000002 No Hit AGCAGATCCCAGTGACATACAGATCTGAGAGCCGCCTCTGATCTTCTTCC 7 0.17500000000000002 No Hit GCCAATGCGGGCAGCATCTCTACCCATGTGGCTTGCGTGCTCTGTTTGTA 6 0.15 No Hit CTTGTACAAGAACAATGTTTCGGGCACTATACCTCCAACACTTGGGAAGT 6 0.15 No Hit GGCTGGGATATCTAGTCTCAAAGTTGTTGATGTTTCTGGTAATGATCTGT 6 0.15 No Hit GCGCTCTCGGCGCTGCGGCGCAGCCTTCAGGACCCCGGCGGCGTGCTGCA 6 0.15 No Hit GAGAACTCCCCCTTCCTGGAGAGGCTGAAGAAGAAGGGCTATGAGGTTAT 6 0.15 No Hit GGCACTATACCTCCAACACTTGGGAAGTTGAAGTCCCTTGTATTCCTGCG 6 0.15 No Hit GGAGAATTTCCAGTCATGAACTACCGGATGACTCAGGAATTTAAGCCACC 6 0.15 No Hit GCCCAAGATCGCCAACAAAGATTTGCCTTTGAAACTGCCTAGCTTTCCTC 6 0.15 No Hit GAAGAACCTAATTAGCTTGGACTTGTACAAGAACAATGTTTCGGGCACTA 6 0.15 No Hit AAGAACTCTTACAGCTGATGTTAGCTATGCCTTACTATATTATGACTTGT 6 0.15 No Hit TCGGCGTTGGGATCGTACTGAAGAACAACTTTTCATTGAGGAAGAGAGGG 6 0.15 No Hit TGGATCATTTGCAATATCTGGAACTCTACAAAAATAACATTCAAGGAACG 6 0.15 No Hit GCCTCTTCTTCATCGGATCCCTTTTGTGCGTTCTTCTTCTTCTACATCGT 6 0.15 No Hit TATACCTCCAACACTTGGGAAGTTGAAGTCCCTTGTATTCCTGCGGCTCA 6 0.15 No Hit GAACGATCCCTTCAGAACTTGGTGATTTGAAGAACCTAATTAGCTTGGAC 6 0.15 No Hit TGGCAATCGTTTGACTGGGCCAATTCCAAGGGAGCTGGCTGGGATATCTA 6 0.15 No Hit ATTCCCAAAACAGCAACCTATCCTGACGTTGCAGAGTTCTCAGCACTGTA 5 0.125 No Hit ATGCAGGCCTCAAATATGTACGCGACATGCAATGCTCTGATTGTAACCTG 5 0.125 No Hit GTCCCTTCTGTCCGGAGATCTATCACGACCACCTCTCCTTTCTGGACTGT 5 0.125 No Hit GGATCATTTGCAATATCTGGAACTCTACAAAAATAACATTCAAGGAACGA 5 0.125 No Hit ATACCTCCAACACTTGGGAAGTTGAAGTCCCTTGTATTCCTGCGGCTCAA 5 0.125 No Hit GTTGCTGTTAAGAGGATTGCTGTTGGCAAATGGGGCTGTAACAATGGCCA 5 0.125 No Hit AAAGTTTGATGTTGCTAAGAACTTTGGGGTTACAGAATTTGTGAACCCAA 5 0.125 No Hit GAGATGGCCTCAGATGACATTGAGAAGATAAAGAACAAGATGGAAGCGGC 5 0.125 No Hit GGTGATTTGAAGAACCTAATTAGCTTGGACTTGTACAAGAACAATGTTTC 5 0.125 No Hit GCCGTCTGGGACTCTCTTTGCTCATTGATGTGGACAGCAGCTTACTAAAC 5 0.125 No Hit CCCTTCAGAACTTGGTGATTTGAAGAACCTAATTAGCTTGGACTTGTACA 5 0.125 No Hit CTGGTGCCTGAGCTTGGGAAATTGGATCATTTGCAATATCTGGAACTCTA 5 0.125 No Hit AGGAACGATCCCTTCAGAACTTGGTGATTTGAAGAACCTAATTAGCTTGG 5 0.125 No Hit CTCCAACACTTGGGAAGTTGAAGTCCCTTGTATTCCTGCGGCTCAATGGC 5 0.125 No Hit GTGTCAGTGGAGGCCGGGAACGCGGACCAGGCATCCTGGCTGGACGACGA 5 0.125 No Hit TGTTAACTCAAAGATTGCTGGGTTACATTTACAAAATAAAATCATGCATA 5 0.125 No Hit CAACACTTGGGAAGTTGAAGTCCCTTGTATTCCTGCGGCTCAATGGCAAT 5 0.125 No Hit GATGGAGAAAGCAGGGTGGCAAAAATATTCTCGTACAGCTCAGGGATCTT 5 0.125 No Hit AGAAGGCCCTGCCTGCGGCGACGATTGCGACCCCATCTTCCACTTCATGA 5 0.125 No Hit GTCTTCTAGTCATCTAGAATCCTCCGTTCTGCAGGCGATTGGGGTCGGTG 5 0.125 No Hit AGCATCTCTACCCATGTGGCTTGCGTGCTCTGTTTGTAACATGCAGGCCT 5 0.125 No Hit CACAGAAGAATGGGTTTTTCTCTAAGATCGGCACAGCCCTTAAGATGGTT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422519 spots for ERR5262795.sra Written 1422519 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra Read 1422501 spots for ERR5262795.sra Written 1422501 spots for ERR5262795.sra SRR ids: ['ERR5262795.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8ajxqyox ERR5262795.sra spots: 28450038 blocks: [[1, 1422501], [1422502, 2845002], [2845003, 4267503], [4267504, 5690004], [5690005, 7112505], [7112506, 8535006], [8535007, 9957507], [9957508, 11380008], [11380009, 12802509], [12802510, 14225010], [14225011, 15647511], [15647512, 17070012], [17070013, 18492513], [18492514, 19915014], [19915015, 21337515], [21337516, 22760016], [22760017, 24182517], [24182518, 25605018], [25605019, 27027519], [27027520, 28450038]] ERR5262795 file size 9343981 ERR5262795 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 ERR5262795 ERR5262795_1.fastq ERR5262795_2.fastq Input file: ERR5262795_1.fastq Paired file: ERR5262795_2.fastq trimmed: ERR5262795-trimmed-pair1.fastq, ERR5262795-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 11:55:10 2024 >> started Fri Dec 6 11:55:40 2024 >> done (29.759s) 28450038 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 28450038 (100.00%) read pairs available; of these: 7983 ( 0.03%) trimmed read pairs available after processing 28442055 (99.97%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 22 1 0.00% 23 1 0.00% 24 0 0.00% 25 1 0.00% 26 0 0.00% 27 3 0.00% 28 2 0.00% 29 1 0.00% 30 1 0.00% 31 0 0.00% 32 2 0.00% 33 1 0.00% 34 1 0.00% 35 2 0.00% 36 2 0.00% 37 2 0.00% 38 2 0.00% 39 4 0.00% 40 3 0.00% 41 1 0.00% 42 1 0.00% 43 0 0.00% 44 1 0.00% 45 2 0.00% 46 1 0.00% 47 2 0.00% 48 1 0.00% 49 264 0.00% 50 302 0.00% 51 330 0.00% 52 371 0.00% 53 394 0.00% 54 421 0.00% 55 500 0.00% 56 496 0.00% 57 602 0.00% 58 651 0.00% 59 777 0.00% 60 894 0.00% 61 1041 0.00% 62 1128 0.00% 63 1312 0.00% 64 1331 0.00% 65 1483 0.01% 66 1639 0.01% 67 1749 0.01% 68 2057 0.01% 69 2329 0.01% 70 2756 0.01% 71 3165 0.01% 72 3671 0.01% 73 4096 0.01% 74 4598 0.02% 75 4952 0.02% 76 5370 0.02% 77 5960 0.02% 78 6474 0.02% 79 7265 0.03% 80 8309 0.03% 81 9356 0.03% 82 10677 0.04% 83 12044 0.04% 84 12992 0.05% 85 14218 0.05% 86 15082 0.05% 87 16219 0.06% 88 17314 0.06% 89 18369 0.06% 90 19852 0.07% 91 21645 0.08% 92 23839 0.08% 93 25500 0.09% 94 27376 0.10% 95 29139 0.10% 96 30674 0.11% 97 31990 0.11% 98 33230 0.12% 99 34458 0.12% 100 36358 0.13% 101 38374 0.13% 102 40561 0.14% 103 43650 0.15% 104 45208 0.16% 105 47619 0.17% 106 48935 0.17% 107 49585 0.17% 108 51665 0.18% 109 53191 0.19% 110 54128 0.19% 111 56062 0.20% 112 58159 0.20% 113 60673 0.21% 114 63441 0.22% 115 66118 0.23% 116 67012 0.24% 117 67870 0.24% 118 69796 0.25% 119 69732 0.25% 120 70441 0.25% 121 72982 0.26% 122 74506 0.26% 123 76033 0.27% 124 79145 0.28% 125 81350 0.29% 126 82538 0.29% 127 83286 0.29% 128 84118 0.30% 129 85143 0.30% 130 85807 0.30% 131 85683 0.30% 132 87568 0.31% 133 89464 0.31% 134 92191 0.32% 135 93561 0.33% 136 96529 0.34% 137 95673 0.34% 138 96801 0.34% 139 99656 0.35% 140 101051 0.36% 141 104519 0.37% 142 106055 0.37% 143 107705 0.38% 144 111705 0.39% 145 109233 0.38% 146 115312 0.41% 147 244882 0.86% 148 103516 0.36% 149 102828 0.36% 150 23961921 84.22% 28450038 reads passed initial QC criterion=sequence-density sequence-density=1.79 sequence-density-rank=1 fanout-score=2.91 fanout-score-rank=24 prefix-density=2.11 prefix-fanout=2.5 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.04 sequence-density-rank=28 fanout-score=184.96 fanout-score-rank=1 prefix-density=1.10 prefix-fanout=6.4 sequence=CCGCCGCCGCCTCCTCCGCCACGACCGCCGCCGCCACCACGGGACTGCGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCCCTCGATGGCGTCGCGCATCGACTGCTCGCTGGCGAAGGTGACGAAGCCGAACCCGCGGGAACGGCCAGTCTCCCTGTCGTTGATGATCTTGGAGTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCGTCGGTAGCCCAGGCGAGGCCGCCCACGAAGCAACGGTACTCAACTTCCGCCATTCCTCCCACTAAACCCTAACGAACCGGAACC criterion=sequence-density sequence-density=5.34 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=5.31 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=164.12 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=1.7 sequence=GTGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCA Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GAACCGGAACCG -y CGGTTCCGGTTC -o ERR5262795 ERR5262795_1.fastq ERR5262795_2.fastq Input file: ERR5262795_1.fastq Paired file: ERR5262795_2.fastq trimmed: ERR5262795-trimmed-pair1.fastq, ERR5262795-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): GAACCGGAACCG -- paired 3' end adapter sequence (-y): CGGTTCCGGTTC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Fri Dec 6 12:00:17 2024 >> started Fri Dec 6 12:00:31 2024 >> done (13.871s) 14225019 read pairs processed; of these: 54 ( 0.00%) short read pairs filtered out after trimming by size control 227 ( 0.00%) empty read pairs filtered out after trimming by size control 14224738 (100.00%) read pairs available; of these: 93 ( 0.00%) trimmed read pairs available after processing 14224645 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 23 1 0.00% 24 0 0.00% 25 1 0.00% 26 0 0.00% 27 1 0.00% 28 1 0.00% 29 0 0.00% 30 0 0.00% 31 0 0.00% 32 2 0.00% 33 1 0.00% 34 1 0.00% 35 2 0.00% 36 1 0.00% 37 1 0.00% 38 1 0.00% 39 1 0.00% 40 1 0.00% 41 1 0.00% 42 1 0.00% 43 0 0.00% 44 0 0.00% 45 2 0.00% 46 0 0.00% 47 0 0.00% 48 1 0.00% 49 217 0.00% 50 234 0.00% 51 263 0.00% 52 225 0.00% 53 156 0.00% 54 192 0.00% 55 89 0.00% 56 109 0.00% 57 474 0.00% 58 538 0.00% 59 628 0.00% 60 739 0.01% 61 637 0.00% 62 232 0.00% 63 240 0.00% 64 295 0.00% 65 1147 0.01% 66 1308 0.01% 67 878 0.01% 68 294 0.00% 69 1211 0.01% 70 1511 0.01% 71 1979 0.01% 72 1784 0.01% 73 2079 0.01% 74 1924 0.01% 75 1591 0.01% 76 3362 0.02% 77 2599 0.02% 78 4041 0.03% 79 3626 0.03% 80 3355 0.02% 81 4886 0.03% 82 4026 0.03% 83 6937 0.05% 84 6657 0.05% 85 6966 0.05% 86 5910 0.04% 87 9436 0.07% 88 8319 0.06% 89 8288 0.06% 90 10356 0.07% 91 11067 0.08% 92 11110 0.08% 93 13744 0.10% 94 12617 0.09% 95 16264 0.11% 96 14009 0.10% 97 17151 0.12% 98 15750 0.11% 99 17903 0.13% 100 17994 0.13% 101 18391 0.13% 102 20389 0.14% 103 22572 0.16% 104 22445 0.16% 105 23299 0.16% 106 24661 0.17% 107 24642 0.17% 108 25499 0.18% 109 27555 0.19% 110 26461 0.19% 111 28375 0.20% 112 29908 0.21% 113 31785 0.22% 114 32096 0.23% 115 33401 0.23% 116 34160 0.24% 117 32993 0.23% 118 35331 0.25% 119 35306 0.25% 120 35031 0.25% 121 36063 0.25% 122 37448 0.26% 123 38364 0.27% 124 39378 0.28% 125 40685 0.29% 126 41271 0.29% 127 41614 0.29% 128 42166 0.30% 129 42863 0.30% 130 43499 0.31% 131 42960 0.30% 132 44130 0.31% 133 44825 0.32% 134 46992 0.33% 135 46926 0.33% 136 48577 0.34% 137 48176 0.34% 138 48257 0.34% 139 49891 0.35% 140 51202 0.36% 141 52257 0.37% 142 53126 0.37% 143 53768 0.38% 144 56087 0.39% 145 54540 0.38% 146 58054 0.41% 147 119919 0.84% 148 51896 0.36% 149 51566 0.36% 150 11976571 84.20% criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=4.06 fanout-score-rank=35 prefix-density=0.19 prefix-fanout=3.0 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.10 sequence-density-rank=8 fanout-score=161.92 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=23.0 sequence=AGCAGCAGCAGC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=35 prefix-density=0.67 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=11 fanout-score=212.52 fanout-score-rank=1 prefix-density=1.08 prefix-fanout=25.3 sequence=CGCCGCCGCCGC ERR5262795 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 12:02:08 Started mapping on | Dec 06 12:02:09 Finished on | Dec 06 12:04:03 Mapping speed, Million of reads per hour | 898.41 Number of input reads | 28449757 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 27377437 Uniquely mapped reads % | 96.23% Average mapped length | 291.32 Number of splices: Total | 25203797 Number of splices: Annotated (sjdb) | 23275095 Number of splices: GT/AG | 24837139 Number of splices: GC/AG | 321224 Number of splices: AT/AC | 16351 Number of splices: Non-canonical | 29083 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.52 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 255622 % of reads mapped to multiple loci | 0.90% Number of reads mapped to too many loci | 1187 % of reads mapped to too many loci | 0.00% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.84% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 816698 816698 816698 N_multimapping 255622 255622 255622 N_noFeature 1289193 26582795 1573881 N_ambiguous 593370 3902 83592 UnstrandedReadsAssigned:25494874 PositiveStrandReadsAssigned:790740 NegativeStrandReadsAssigned:25719964 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR5262795 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: ERR5262795-trimmed-pair1.fastq ERR5262795-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,449,757 reads, 26,146,781 reads pseudoaligned [quant] estimated average fragment length: 266.047 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,181 rounds 52973 ERR5262795.ke.tsv 35125 ERR5262795.se.tsv 88098 total ==> ERR5262795.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 671.534 0 0 PNS24247 1044 778.953 158.001 11.471 PNS24249 1928 1662.95 413.835 14.0734 PNS24246 1044 778.953 158.001 11.471 PNS24248 1044 778.953 158.001 11.471 PNS24244 1471 1205.95 211.162 9.90234 PNS24243 293 103.833 0 0 KQK14069 1603 1337.95 57431.7 2427.52 KQK14071 474 238.571 187.182 44.371 ==> ERR5262795.se.tsv <== BRADI_1g14170v3 57687 BRADI_1g53295v3 336 BRADI_1g59795v3 923 BRADI_1g07683v3 0 BRADI_1g00485v3 10 BRADI_1g20270v3 1037 BRADI_1g74790v3 2309 BRADI_1g09890v3 0 BRADI_1g77505v3 335 BRADI_1g48960v3 0 ERR5262795 completed mapping pipeline successfully