Starting /dee2/code/volunteer_pipeline.sh ERR6133527 current disk space = 1544514519040 free memory = 1600921300 ERR6133527 SRAfilesize 39fea85f016c71c1d14a69f91251a889 ERR6133527.sra ERR6133527.sra file validated ERR6133527 is single end ERR6133527 is conventional basespace ERR6133527 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133527_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.63275 37.0 37.0 37.0 37.0 37.0 2 36.83925 37.0 37.0 37.0 37.0 37.0 3 36.5575 37.0 37.0 37.0 37.0 37.0 4 35.87525 37.0 37.0 37.0 33.0 37.0 5 36.072 37.0 37.0 37.0 33.0 37.0 6 36.34 37.0 37.0 37.0 33.0 37.0 7 38.259 40.0 37.0 40.0 37.0 40.0 8 38.285 40.0 37.0 40.0 37.0 40.0 9 38.3435 40.0 37.0 40.0 37.0 40.0 10-11 38.31375 40.0 37.0 40.0 37.0 40.0 12-13 38.258375 40.0 37.0 40.0 37.0 40.0 14-15 38.2675 40.0 37.0 40.0 37.0 40.0 16-17 38.164625 40.0 37.0 40.0 37.0 40.0 18-19 38.10725 40.0 37.0 40.0 37.0 40.0 20-21 38.080875 40.0 37.0 40.0 37.0 40.0 22-23 38.217 40.0 37.0 40.0 37.0 40.0 24-25 38.164500000000004 40.0 37.0 40.0 37.0 40.0 26-27 38.0775 40.0 37.0 40.0 37.0 40.0 28-29 38.00512500000001 40.0 37.0 40.0 37.0 40.0 30-31 38.043625 40.0 37.0 40.0 37.0 40.0 32-33 38.123125 40.0 37.0 40.0 37.0 40.0 34-35 38.009625 38.5 37.0 40.0 37.0 40.0 36-37 37.985749999999996 37.0 37.0 40.0 37.0 40.0 38-39 37.877375 37.0 37.0 40.0 37.0 40.0 40-41 37.660125 37.0 37.0 40.0 37.0 40.0 42-43 37.574375 37.0 37.0 40.0 37.0 40.0 44-45 37.367 37.0 37.0 40.0 35.0 40.0 46-47 37.25075 37.0 37.0 40.0 33.0 40.0 48-49 37.110875 37.0 37.0 38.5 33.0 40.0 50-51 36.898250000000004 37.0 37.0 37.0 33.0 40.0 52-53 36.43537499999999 37.0 37.0 37.0 33.0 40.0 54-55 36.422125 37.0 37.0 37.0 33.0 40.0 56-57 36.307125 37.0 37.0 37.0 33.0 38.5 58-59 35.989125 37.0 37.0 37.0 33.0 37.0 60-61 36.1215 37.0 37.0 37.0 33.0 37.0 62-63 35.990375 37.0 37.0 37.0 33.0 37.0 64-65 35.8955 37.0 37.0 37.0 33.0 37.0 66-67 35.8475 37.0 37.0 37.0 33.0 37.0 68-69 34.9425 35.0 35.0 37.0 33.0 37.0 70-71 35.142222764838465 37.0 33.0 37.0 33.0 37.0 72-73 35.66290371905859 37.0 35.0 37.0 33.0 37.0 74-75 35.650358011658035 37.0 35.0 37.0 33.0 37.0 76-77 35.61303149201909 37.0 33.0 37.0 33.0 37.0 78-79 35.51134939262843 37.0 33.0 37.0 33.0 37.0 80-81 35.366511206418394 37.0 33.0 37.0 33.0 37.0 82-83 35.33300789610461 37.0 33.0 37.0 33.0 37.0 84-85 35.17057692622415 37.0 33.0 37.0 33.0 37.0 86-87 35.119679453494484 37.0 33.0 37.0 33.0 37.0 88-89 35.08959537572254 37.0 33.0 37.0 33.0 37.0 90-91 35.029558591697324 37.0 33.0 37.0 33.0 37.0 92-93 34.992380451918024 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 3.0 22 2.0 23 3.0 24 6.0 25 10.0 26 6.0 27 10.0 28 15.0 29 20.0 30 23.0 31 29.0 32 51.0 33 60.0 34 108.0 35 292.0 36 1118.0 37 1428.0 38 797.0 39 17.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.025 2.35 3.1 5.525 2 74.3 15.45 6.1 4.15 3 36.375 39.025 13.175 11.425 4 32.5 29.325000000000003 17.974999999999998 20.200000000000003 5 27.725 28.95 25.95 17.375 6 20.474999999999998 40.125 24.275 15.125 7 37.475 27.875 19.25 15.4 8 29.525000000000002 30.049999999999997 24.325 16.1 9 25.974999999999998 29.849999999999998 26.75 17.424999999999997 10-11 25.137500000000003 28.5625 29.299999999999997 17.0 12-13 27.037499999999998 27.025 28.3125 17.625 14-15 21.9375 33.637499999999996 27.6375 16.7875 16-17 23.7375 31.424999999999997 25.2375 19.6 18-19 24.025 26.6125 28.725 20.6375 20-21 25.456364091022753 25.64391097774444 29.607401850462615 19.292323080770192 22-23 28.575 22.05 28.3625 21.0125 24-25 25.525 25.624999999999996 27.8625 20.9875 26-27 26.6625 25.4875 29.5875 18.2625 28-29 25.137500000000003 27.6875 27.712500000000002 19.4625 30-31 27.8625 25.687500000000004 27.462500000000002 18.987499999999997 32-33 24.65 27.8875 26.525 20.9375 34-35 23.9125 28.475 27.375 20.2375 36-37 24.7375 26.6125 27.5625 21.087500000000002 38-39 28.575 25.25 28.5875 17.5875 40-41 27.019254813703427 24.968742185546386 28.219554888722183 19.79244811202801 42-43 24.90311288911114 29.5286910863858 25.928241030128767 19.6399549943743 44-45 23.6125 26.825 29.975 19.5875 46-47 23.9 24.3125 28.975 22.8125 48-49 24.762500000000003 25.124999999999996 29.7125 20.4 50-51 23.8404800600075 27.465933241655204 28.691086385798226 20.002500312539066 52-53 24.908793558938232 27.714177884010567 26.116492640583722 21.26053591646748 54-55 23.6963861448043 29.035888458171815 28.160560210078778 19.107165186945103 56-57 25.7125 27.375 27.1125 19.8 58-59 23.4625 25.924999999999997 28.962500000000002 21.65 60-61 24.9 26.55 29.4 19.15 62-63 23.0125 27.037499999999998 31.225 18.725 64-65 22.9875 30.725 27.5875 18.7 66-67 24.4 29.025000000000002 28.3625 18.212500000000002 68-69 22.45 26.9125 28.275 22.3625 70-71 23.920930814462654 27.248842737395222 27.386463155260856 21.443763292881272 72-73 25.865324103209563 25.2863436123348 29.1881686595343 19.660163624921335 74-75 22.877388333544225 29.78615715551057 28.3436669619132 18.992787549032013 76-77 22.370766488413548 25.65571683218742 28.15126050420168 23.82225617519735 78-79 24.62130937098845 25.09627727856226 28.806161745827985 21.47625160462131 80-81 23.13953488372093 31.343669250645995 28.281653746770026 17.23514211886305 82-83 23.690027304641788 25.06826160447276 29.371993238850603 21.869717852034846 84-85 23.3774747607185 23.993706568768847 31.30982037498361 21.318998295529042 86-87 20.58591697320021 27.771939043615347 30.898581187598527 20.74356279558592 88-89 21.00630583289543 28.770362585391485 30.057803468208093 20.16552811350499 90-91 25.853914871255913 29.072517078297427 27.088807146610616 17.984760903836047 92-93 21.74198633736206 30.307409353652126 28.80977404098791 19.1408302679979 >>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 1.0 17 4.5 18 3.5 19 0.0 20 0.5 21 1.0 22 2.5 23 5.0 24 6.0 25 5.5 26 5.5 27 7.5 28 15.5 29 21.0 30 31.0 31 34.5 32 36.5 33 50.5 34 59.0 35 75.5 36 116.0 37 147.0 38 178.5 39 187.5 40 189.5 41 207.0 42 228.0 43 250.5 44 223.5 45 211.0 46 236.5 47 220.0 48 172.0 49 163.0 50 185.0 51 182.0 52 152.0 53 148.5 54 164.5 55 115.5 56 57.0 57 52.5 58 47.0 59 36.0 60 24.5 61 19.0 62 14.5 63 10.5 64 11.0 65 11.0 66 7.5 67 4.0 68 7.5 69 7.5 70 4.0 71 4.0 72 2.5 73 1.5 74 1.0 75 1.0 76 1.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.025 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 0.025 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0125 52-53 0.6375 54-55 0.0375 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 7.0 71 14.0 72 13.0 73 7.0 74 15.0 75 12.0 76 10.0 77 18.0 78 18.0 79 7.0 80 18.0 81 7.0 82 17.0 83 16.0 84 15.0 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 3806.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.775 #Duplication Level Percentage of deduplicated Percentage of total 1 91.6081578067536 68.5 2 4.847876964226011 7.249999999999999 3 1.170177198261451 2.625 4 0.3343363423604146 1.0 5 0.7689735874289535 2.875 6 0.2340354396522902 1.05 7 0.1671681711802073 0.8750000000000001 8 0.10030090270812438 0.6 9 0.10030090270812438 0.675 >10 0.6018054162487462 10.725 >50 0.06686726847208291 3.8249999999999997 >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 fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 99 2.475 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 54 1.35 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 46 1.15 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 36 0.8999999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 34 0.8500000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 33 0.8250000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 32 0.8 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 31 0.775 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 26 0.65 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 23 0.575 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 22 0.5499999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 21 0.525 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 21 0.525 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 21 0.525 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 19 0.475 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 18 0.44999999999999996 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 9 0.22499999999999998 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 8 0.2 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 8 0.2 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 8 0.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 7 0.17500000000000002 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 6 0.15 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 6 0.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit TAATTAAGAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAA 5 0.125 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 5 0.125 No Hit GGATCCGTGATTTTTGGCATGGAGAACAAGTCACGGGAACATCAATGGAA 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 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.037500000000000006 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.0625 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61186 READS because READLEN < 1 Read 61186 spots for ERR6133527.sra Written 61186 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra Rejected 61167 READS because READLEN < 1 Read 61167 spots for ERR6133527.sra Written 61167 spots for ERR6133527.sra SRR ids: ['ERR6133527.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_orbtg2l1 ERR6133527.sra spots: 1223359 blocks: [[1, 61167], [61168, 122334], [122335, 183501], [183502, 244668], [244669, 305835], [305836, 367002], [367003, 428169], [428170, 489336], [489337, 550503], [550504, 611670], [611671, 672837], [672838, 734004], [734005, 795171], [795172, 856338], [856339, 917505], [917506, 978672], [978673, 1039839], [1039840, 1101006], [1101007, 1162173], [1162174, 1223359]] ERR6133527 file size 268278 ERR6133527 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 ERR6133527 ERR6133527_1.fastq Input file: ERR6133527_1.fastq trimmed: ERR6133527-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 07:59:05 2024 >> started Sat Dec 7 07:59:06 2024 >> done (0.963s) 1223359 reads processed; of these: 229 ( 0.02%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 1223123 (99.98%) reads available; of these: 5855 ( 0.48%) trimmed reads available after processing 1217268 (99.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 33 0.00% 19 68 0.01% 20 18 0.00% 21 19 0.00% 22 17 0.00% 23 4 0.00% 24 9 0.00% 25 7 0.00% 26 7 0.00% 27 15 0.00% 28 15 0.00% 29 15 0.00% 30 17 0.00% 31 12 0.00% 32 20 0.00% 33 13 0.00% 34 11 0.00% 35 118 0.01% 36 194 0.02% 37 12 0.00% 38 23 0.00% 39 91 0.01% 40 84 0.01% 41 30 0.00% 42 7 0.00% 43 6 0.00% 44 12 0.00% 45 8 0.00% 46 2 0.00% 47 7 0.00% 48 5 0.00% 49 5 0.00% 50 5 0.00% 51 53 0.00% 52 12 0.00% 53 3 0.00% 54 3 0.00% 55 1 0.00% 56 4 0.00% 57 8 0.00% 58 6 0.00% 59 4 0.00% 60 13 0.00% 61 6 0.00% 62 3 0.00% 63 1 0.00% 64 1 0.00% 65 0 0.00% 66 5 0.00% 67 5 0.00% 68 5 0.00% 69 27 0.00% 70 4416 0.36% 71 3970 0.32% 72 4055 0.33% 73 3973 0.32% 74 3761 0.31% 75 3703 0.30% 76 3389 0.28% 77 3520 0.29% 78 4088 0.33% 79 4399 0.36% 80 4016 0.33% 81 5006 0.41% 82 5639 0.46% 83 4646 0.38% 84 4401 0.36% 85 13 0.00% 86 26 0.00% 87 46 0.00% 88 93 0.01% 89 165 0.01% 90 324 0.03% 91 788 0.06% 92 3096 0.25% 93 1154521 94.39% 1223123 reads passed initial QC criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=4.91 fanout-score-rank=15 prefix-density=1.09 prefix-fanout=1.9 sequence=AGGCTAAATACAGGCGAGAGACCGATAGCG criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=48.10 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=5.5 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGC Started job on | Dec 07 07:59:17 Started mapping on | Dec 07 07:59:17 Finished on | Dec 07 07:59:20 Mapping speed, Million of reads per hour | 1467.75 Number of input reads | 1223123 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 794056 Uniquely mapped reads % | 64.92% Average mapped length | 91.69 Number of splices: Total | 52781 Number of splices: Annotated (sjdb) | 44957 Number of splices: GT/AG | 51246 Number of splices: GC/AG | 858 Number of splices: AT/AC | 20 Number of splices: Non-canonical | 657 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.04% Deletion average length | 1.88 Insertion rate per base | 0.02% Insertion average length | 1.99 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 395983 % of reads mapped to multiple loci | 32.37% Number of reads mapped to too many loci | 12378 % of reads mapped to too many loci | 1.01% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.65% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 33084 33084 33084 N_multimapping 395983 395983 395983 N_noFeature 56973 64656 760305 N_ambiguous 30333 4218 157 UnstrandedReadsAssigned:706750 PositiveStrandReadsAssigned:725182 NegativeStrandReadsAssigned:33594 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133527 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: ERR6133527-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,223,123 reads, 986,497 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 917 rounds 52973 ERR6133527.ke.tsv 35125 ERR6133527.se.tsv 88098 total ==> ERR6133527.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 30 29.2841 PNS24243 293 194 0 0 KQK14069 1603 1504 21 18.6998 KQK14071 474 375 0 0 ==> ERR6133527.se.tsv <== BRADI_1g14170v3 21 BRADI_1g53295v3 10 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 8 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 25 BRADI_1g48960v3 0 ERR6133527 completed mapping pipeline successfully