Starting /dee2/code/volunteer_pipeline.sh ERR6133472 current disk space = 1545013964800 free memory = 1488750012 ERR6133472 SRAfilesize 812db88c1a9e57b6ba421b7b6c5c5ee0 ERR6133472.sra ERR6133472.sra file validated ERR6133472 is single end ERR6133472 is conventional basespace ERR6133472 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133472_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 34.722 37.0 33.0 37.0 33.0 37.0 2 36.0345 37.0 37.0 37.0 33.0 37.0 3 35.36 37.0 33.0 37.0 33.0 37.0 4 35.10675 37.0 37.0 37.0 33.0 37.0 5 34.964 37.0 37.0 37.0 33.0 37.0 6 35.4235 37.0 37.0 37.0 33.0 37.0 7 36.79125 37.0 37.0 40.0 33.0 40.0 8 36.8705 37.0 37.0 40.0 33.0 40.0 9 37.08375 37.0 37.0 40.0 33.0 40.0 10-11 36.954375 37.0 37.0 40.0 33.0 40.0 12-13 36.919375 37.0 37.0 40.0 33.0 40.0 14-15 36.895250000000004 37.0 37.0 40.0 33.0 40.0 16-17 36.763374999999996 37.0 37.0 40.0 33.0 40.0 18-19 36.364000000000004 37.0 37.0 40.0 33.0 40.0 20-21 36.177 37.0 37.0 40.0 33.0 40.0 22-23 35.945875 37.0 35.0 40.0 33.0 40.0 24-25 36.041875000000005 37.0 37.0 40.0 33.0 40.0 26-27 36.2145 37.0 37.0 40.0 33.0 40.0 28-29 36.17075 37.0 37.0 40.0 33.0 40.0 30-31 36.327625 37.0 37.0 40.0 33.0 40.0 32-33 36.2155 37.0 37.0 40.0 33.0 40.0 34-35 36.2025 37.0 37.0 40.0 33.0 40.0 36-37 36.16275 37.0 35.0 40.0 33.0 40.0 38-39 36.013875 37.0 35.0 40.0 33.0 40.0 40-41 35.863 37.0 33.0 40.0 33.0 40.0 42-43 35.902875 37.0 33.0 40.0 33.0 40.0 44-45 35.56325 37.0 33.0 40.0 30.0 40.0 46-47 35.429875 37.0 33.0 37.0 30.0 40.0 48-49 35.51375 37.0 33.0 37.0 30.0 40.0 50-51 35.27375 37.0 33.0 37.0 33.0 40.0 52-53 35.07275 37.0 33.0 37.0 27.0 40.0 54-55 34.988875 37.0 33.0 37.0 33.0 40.0 56-57 34.873125 37.0 33.0 37.0 30.0 40.0 58-59 34.121625 37.0 33.0 37.0 27.0 37.0 60-61 34.35825 37.0 33.0 37.0 27.0 37.0 62-63 34.312749999999994 37.0 33.0 37.0 27.0 37.0 64-65 34.07875 37.0 33.0 37.0 27.0 37.0 66-67 33.910624999999996 37.0 33.0 37.0 27.0 37.0 68-69 33.089625 35.0 33.0 37.0 27.0 37.0 70-71 33.25447891075457 33.0 33.0 37.0 27.0 37.0 72-73 33.66089430217697 37.0 33.0 37.0 27.0 37.0 74-75 33.706160952476324 37.0 33.0 37.0 27.0 37.0 76-77 33.69773948778678 37.0 33.0 37.0 27.0 37.0 78-79 33.56954576370292 37.0 33.0 37.0 27.0 37.0 80-81 33.64879551713833 37.0 33.0 37.0 27.0 37.0 82-83 33.445846962065005 37.0 33.0 37.0 27.0 37.0 84-85 33.19303856024952 33.0 33.0 37.0 27.0 37.0 86-87 33.05854304635761 33.0 33.0 37.0 27.0 37.0 88-89 33.25761589403974 33.0 33.0 37.0 27.0 37.0 90-91 32.9164238410596 33.0 33.0 37.0 27.0 37.0 92-93 32.98039735099338 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 16.0 21 13.0 22 12.0 23 26.0 24 29.0 25 26.0 26 55.0 27 42.0 28 65.0 29 101.0 30 122.0 31 139.0 32 164.0 33 198.0 34 306.0 35 516.0 36 811.0 37 886.0 38 465.0 39 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.95 3.375 3.5749999999999997 8.1 2 65.725 18.825 9.85 5.6000000000000005 3 33.675 39.85 14.325 12.15 4 33.125 27.675 19.85 19.35 5 24.224999999999998 29.599999999999998 26.8 19.375 6 19.75 36.6 25.974999999999998 17.675 7 34.5 31.5 18.625 15.375 8 29.725 30.425 23.65 16.2 9 25.85 28.675 28.1 17.375 10-11 25.1875 27.1625 28.487499999999997 19.162499999999998 12-13 27.425 27.275 27.275 18.025 14-15 22.537499999999998 29.5375 29.275000000000002 18.65 16-17 23.8625 31.5375 25.837500000000002 18.7625 18-19 23.3375 27.5625 28.5875 20.5125 20-21 24.965620702587824 25.928241030128767 28.653581697712216 20.452556569571197 22-23 26.7625 23.799999999999997 28.6625 20.775 24-25 25.362499999999997 24.6625 29.075 20.9 26-27 23.75 25.45 31.15 19.650000000000002 28-29 25.2375 26.450000000000003 28.4125 19.900000000000002 30-31 25.6125 25.9875 27.525 20.875 32-33 23.7875 26.2625 29.975 19.975 34-35 24.375 26.737499999999997 27.6875 21.2 36-37 25.275 25.8125 28.225 20.6875 38-39 25.5625 25.4375 29.9 19.1 40-41 26.05 24.1625 27.85 21.9375 42-43 24.518629657414355 27.494373593398347 28.307076769192296 19.679919979995 44-45 23.0 25.162499999999998 30.15 21.6875 46-47 23.7875 25.324999999999996 28.95 21.9375 48-49 23.75 25.15 31.0125 20.0875 50-51 23.674999999999997 26.35 29.625 20.349999999999998 52-53 24.812218327491237 26.877816725087634 27.72909364046069 20.58087130696044 54-55 23.793448362090523 28.40710177544386 29.332333083270818 18.467116779194797 56-57 25.8 26.0125 28.1625 20.025000000000002 58-59 24.6875 25.412499999999998 28.537499999999998 21.3625 60-61 24.025 25.587500000000002 30.1375 20.25 62-63 21.7875 28.65 31.337500000000002 18.224999999999998 64-65 23.45 27.2625 30.2625 19.025 66-67 22.8 27.200000000000003 29.3375 20.6625 68-69 21.842960740185045 27.644411102775695 28.457114278569644 22.05551387846962 70-71 23.857804481161597 27.26248591813744 27.663036675428714 21.21667292527225 72-73 25.147966251101877 25.286487847878103 28.32137010452084 21.24417579649918 74-75 22.86546744362807 27.742589308335447 30.098809222194074 19.293134025842413 76-77 23.072012257405518 25.893769152196118 29.59652706843718 21.437691521961185 78-79 22.737789203084834 25.16709511568123 31.902313624678662 20.19280205655527 80-81 22.731985484707103 29.328667703473304 29.40642820114049 18.532918610679108 82-83 22.671376242804815 26.62218733647305 30.167451596023025 20.53898482469911 84-85 23.80007933359778 23.694301203226235 31.429326986645513 21.07629247653048 86-87 22.19867549668874 26.384105960264904 32.09271523178808 19.32450331125828 88-89 20.821192052980134 28.26490066225166 30.834437086092713 20.079470198675498 90-91 25.03311258278146 26.87417218543046 29.046357615894042 19.04635761589404 92-93 21.748344370860927 30.066225165562916 28.47682119205298 19.708609271523176 >>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 5.5 18 7.5 19 2.5 20 2.5 21 3.5 22 3.0 23 5.0 24 6.0 25 4.5 26 9.0 27 16.0 28 22.0 29 27.0 30 35.0 31 38.0 32 47.0 33 75.0 34 87.0 35 101.5 36 131.5 37 171.0 38 210.0 39 200.0 40 191.0 41 201.0 42 213.5 43 230.0 44 218.0 45 199.5 46 201.0 47 171.0 48 142.0 49 157.5 50 158.0 51 134.5 52 121.0 53 128.5 54 122.5 55 96.5 56 66.0 57 51.5 58 49.0 59 41.5 60 34.0 61 29.0 62 27.5 63 26.0 64 23.0 65 23.0 66 17.5 67 15.0 68 15.5 69 11.5 70 9.5 71 8.0 72 4.0 73 1.0 74 3.0 75 3.5 76 2.5 77 1.5 78 0.5 79 0.0 80 0.0 81 0.5 82 0.5 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 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 0.0125 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 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.15 54-55 0.025 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.025 70-71 0.0 72-73 0.0 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 11.0 71 12.0 72 13.0 73 10.0 74 14.0 75 18.0 76 12.0 77 12.0 78 16.0 79 14.0 80 20.0 81 18.0 82 16.0 83 26.0 84 13.0 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 3775.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.6 #Duplication Level Percentage of deduplicated Percentage of total 1 93.75 76.5 2 3.278186274509804 5.35 3 0.9191176470588236 2.25 4 0.6740196078431373 2.1999999999999997 5 0.428921568627451 1.7500000000000002 6 0.061274509803921566 0.3 7 0.061274509803921566 0.35000000000000003 8 0.12254901960784313 0.8 9 0.12254901960784313 0.8999999999999999 >10 0.5514705882352942 8.175 >50 0.030637254901960783 1.425 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 57 1.425 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 34 0.8500000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 29 0.7250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 27 0.675 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 26 0.65 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 26 0.65 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 21 0.525 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 19 0.475 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 16 0.4 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 15 0.375 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 11 0.27499999999999997 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 9 0.22499999999999998 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 9 0.22499999999999998 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 8 0.2 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 8 0.2 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCC 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit GGATCCGTTGAAGCGTGCGGCGTCTCTGTCTATGTATTACTGTTTTATGC 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 5 0.125 No Hit GGCTAATTAAGAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACA 5 0.125 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 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 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.037500000000000006 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 0.0875 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCAATT 25 0.00696801 51.5025 4 AATTTCA 25 0.00696801 51.5025 7 CAATTTC 25 0.00696801 51.5025 6 GGATTCA 25 0.00696801 51.5025 1 TCAATTT 25 0.00696801 51.5025 5 >>END_MODULE Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119784 READS because READLEN < 1 Read 119784 spots for ERR6133472.sra Written 119784 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra Rejected 119770 READS because READLEN < 1 Read 119770 spots for ERR6133472.sra Written 119770 spots for ERR6133472.sra SRR ids: ['ERR6133472.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_q8wreri_ ERR6133472.sra spots: 2395414 blocks: [[1, 119770], [119771, 239540], [239541, 359310], [359311, 479080], [479081, 598850], [598851, 718620], [718621, 838390], [838391, 958160], [958161, 1077930], [1077931, 1197700], [1197701, 1317470], [1317471, 1437240], [1437241, 1557010], [1557011, 1676780], [1676781, 1796550], [1796551, 1916320], [1916321, 2036090], [2036091, 2155860], [2155861, 2275630], [2275631, 2395414]] ERR6133472 file size 526936 ERR6133472 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 ERR6133472 ERR6133472_1.fastq Input file: ERR6133472_1.fastq trimmed: ERR6133472-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 06:46:28 2024 >> started Sat Dec 7 06:46:30 2024 >> done (1.829s) 2395414 reads processed; of these: 136 ( 0.01%) short reads filtered out after trimming by size control 19 ( 0.00%) empty reads filtered out after trimming by size control 2395259 (99.99%) reads available; of these: 38645 ( 1.61%) trimmed reads available after processing 2356614 (98.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 25 0.00% 19 43 0.00% 20 19 0.00% 21 27 0.00% 22 24 0.00% 23 3 0.00% 24 4 0.00% 25 5 0.00% 26 6 0.00% 27 6 0.00% 28 12 0.00% 29 14 0.00% 30 12 0.00% 31 18 0.00% 32 18 0.00% 33 10 0.00% 34 19 0.00% 35 77 0.00% 36 501 0.02% 37 21 0.00% 38 33 0.00% 39 85 0.00% 40 75 0.00% 41 36 0.00% 42 8 0.00% 43 9 0.00% 44 12 0.00% 45 14 0.00% 46 10 0.00% 47 12 0.00% 48 7 0.00% 49 10 0.00% 50 11 0.00% 51 32 0.00% 52 6 0.00% 53 8 0.00% 54 5 0.00% 55 6 0.00% 56 7 0.00% 57 6 0.00% 58 16 0.00% 59 11 0.00% 60 19 0.00% 61 13 0.00% 62 0 0.00% 63 3 0.00% 64 4 0.00% 65 1 0.00% 66 7 0.00% 67 15 0.00% 68 25 0.00% 69 113 0.00% 70 9329 0.39% 71 8659 0.36% 72 9291 0.39% 73 8455 0.35% 74 8806 0.37% 75 8495 0.35% 76 7577 0.32% 77 7992 0.33% 78 9118 0.38% 79 9631 0.40% 80 8772 0.37% 81 9752 0.41% 82 11168 0.47% 83 11577 0.48% 84 9710 0.41% 85 84 0.00% 86 186 0.01% 87 273 0.01% 88 501 0.02% 89 959 0.04% 90 2113 0.09% 91 6655 0.28% 92 24791 1.04% 93 2219882 92.68% 2395259 reads passed initial QC criterion=sequence-density sequence-density=0.69 sequence-density-rank=1 fanout-score=1.93 fanout-score-rank=36 prefix-density=0.69 prefix-fanout=1.9 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=105.45 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=8.7 sequence=AGGAAGAGGAGGATGCAGTCAGGGCTCACAAACAACCTGCCACTGCCGCCATTGGCCTTCTAAAACAGGAGAGGAGGGGTTAGATAGTTTCGATCTGCAAGGGGGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACAGTAGCGTACTTGAGGTGTTGTATTTTTATTTATTTTCTTGTTTTTGAATGTCCGATCTGTTTGAGCCTTTGGTGACCGAAGAAAATAAAGCTG Started job on | Dec 07 06:46:50 Started mapping on | Dec 07 06:46:50 Finished on | Dec 07 06:46:56 Mapping speed, Million of reads per hour | 1437.16 Number of input reads | 2395259 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1661520 Uniquely mapped reads % | 69.37% Average mapped length | 91.52 Number of splices: Total | 73657 Number of splices: Annotated (sjdb) | 61100 Number of splices: GT/AG | 70897 Number of splices: GC/AG | 1404 Number of splices: AT/AC | 34 Number of splices: Non-canonical | 1322 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.04% Deletion average length | 1.88 Insertion rate per base | 0.02% Insertion average length | 1.86 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 667886 % of reads mapped to multiple loci | 27.88% Number of reads mapped to too many loci | 26734 % of reads mapped to too many loci | 1.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.54% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 65853 65853 65853 N_multimapping 667886 667886 667886 N_noFeature 124913 141447 1589842 N_ambiguous 62467 7243 247 UnstrandedReadsAssigned:1474140 PositiveStrandReadsAssigned:1512830 NegativeStrandReadsAssigned:71431 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133472 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: ERR6133472-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,395,259 reads, 1,977,036 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,018 rounds 52973 ERR6133472.ke.tsv 35125 ERR6133472.se.tsv 88098 total ==> ERR6133472.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 36 17.6299 PNS24243 293 194 0 0 KQK14069 1603 1504 9 4.02065 KQK14071 474 375 0 0 ==> ERR6133472.se.tsv <== BRADI_1g14170v3 9 BRADI_1g53295v3 16 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 28 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 49 BRADI_1g48960v3 0 ERR6133472 completed mapping pipeline successfully