Starting /dee2/code/volunteer_pipeline.sh ERR6133564 current disk space = 1544529436672 free memory = 1421425452 ERR6133564 SRAfilesize b3ed6623c180ec4556614f64427d8d55 ERR6133564.sra ERR6133564.sra file validated ERR6133564 is single end ERR6133564 is conventional basespace ERR6133564 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133564_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 35.58475 37.0 33.0 37.0 33.0 37.0 2 36.44475 37.0 37.0 37.0 37.0 37.0 3 35.9915 37.0 37.0 37.0 33.0 37.0 4 35.385 37.0 37.0 37.0 33.0 37.0 5 35.19425 37.0 37.0 37.0 33.0 37.0 6 35.58675 37.0 37.0 37.0 33.0 37.0 7 37.50025 40.0 37.0 40.0 33.0 40.0 8 37.4845 40.0 37.0 40.0 33.0 40.0 9 37.6235 40.0 37.0 40.0 33.0 40.0 10-11 37.534625 37.0 37.0 40.0 33.0 40.0 12-13 37.479 37.0 37.0 40.0 33.0 40.0 14-15 37.452375 37.0 37.0 40.0 33.0 40.0 16-17 37.324875000000006 37.0 37.0 40.0 33.0 40.0 18-19 37.315125 37.0 37.0 40.0 33.0 40.0 20-21 37.097 37.0 37.0 40.0 33.0 40.0 22-23 37.189125000000004 37.0 37.0 40.0 33.0 40.0 24-25 37.233374999999995 37.0 37.0 40.0 33.0 40.0 26-27 37.286625 37.0 37.0 40.0 33.0 40.0 28-29 37.176625 37.0 37.0 40.0 33.0 40.0 30-31 37.064 37.0 37.0 40.0 33.0 40.0 32-33 36.9075 37.0 37.0 40.0 33.0 40.0 34-35 36.766 37.0 37.0 40.0 33.0 40.0 36-37 36.681625 37.0 37.0 40.0 33.0 40.0 38-39 36.28775 37.0 37.0 40.0 33.0 40.0 40-41 36.074375 37.0 37.0 40.0 33.0 40.0 42-43 36.08325 37.0 37.0 40.0 33.0 40.0 44-45 35.775499999999994 37.0 35.0 38.5 33.0 40.0 46-47 35.464 37.0 33.0 37.0 33.0 40.0 48-49 35.41025 37.0 33.0 37.0 33.0 40.0 50-51 35.311125000000004 37.0 33.0 37.0 33.0 40.0 52-53 34.955749999999995 37.0 33.0 37.0 27.0 40.0 54-55 35.04375 37.0 33.0 37.0 33.0 40.0 56-57 34.781375 37.0 33.0 37.0 27.0 38.5 58-59 33.538875000000004 35.0 33.0 37.0 27.0 37.0 60-61 34.246125000000006 37.0 33.0 37.0 27.0 37.0 62-63 34.418 37.0 33.0 37.0 27.0 37.0 64-65 34.312375 37.0 33.0 37.0 27.0 37.0 66-67 34.31075 37.0 33.0 37.0 27.0 37.0 68-69 33.533625 35.0 33.0 37.0 27.0 37.0 70-71 33.65368523153943 35.0 33.0 37.0 27.0 37.0 72-73 34.03140258984981 37.0 33.0 37.0 27.0 37.0 74-75 33.753814984365434 37.0 33.0 37.0 27.0 37.0 76-77 34.00986807178939 37.0 33.0 37.0 27.0 37.0 78-79 33.9457084448361 37.0 33.0 37.0 27.0 37.0 80-81 33.84093343173741 37.0 33.0 37.0 27.0 37.0 82-83 33.77060836123728 37.0 33.0 37.0 27.0 37.0 84-85 33.73478619600656 37.0 33.0 37.0 27.0 37.0 86-87 33.538191738113795 37.0 33.0 37.0 27.0 37.0 88-89 33.715250714471296 37.0 33.0 37.0 27.0 37.0 90-91 33.4933749025721 37.0 33.0 37.0 27.0 37.0 92-93 33.412444790854764 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 8.0 21 15.0 22 24.0 23 26.0 24 27.0 25 40.0 26 34.0 27 35.0 28 62.0 29 76.0 30 79.0 31 107.0 32 121.0 33 159.0 34 250.0 35 410.0 36 927.0 37 966.0 38 619.0 39 15.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.375 3.325 3.95 7.35 2 68.10000000000001 19.325 7.6499999999999995 4.925 3 36.9 36.175000000000004 15.0 11.924999999999999 4 31.474999999999998 29.825000000000003 18.4 20.3 5 28.349999999999998 28.95 24.95 17.75 6 18.725 40.5 24.925 15.85 7 37.625 27.625 19.900000000000002 14.85 8 28.975 29.325000000000003 22.275 19.425 9 23.849999999999998 30.599999999999998 27.025 18.525 10-11 23.95 28.9375 28.15 18.9625 12-13 25.900000000000002 27.6125 26.950000000000003 19.537499999999998 14-15 21.3625 32.6375 27.825 18.175 16-17 24.375 31.087500000000002 23.7625 20.775 18-19 24.075 26.2625 28.4125 21.25 20-21 26.25 25.275 28.549999999999997 19.925 22-23 29.575000000000003 21.8625 28.487499999999997 20.075000000000003 24-25 24.224999999999998 24.575 29.2 22.0 26-27 26.775 24.975 28.9375 19.3125 28-29 25.2 27.962500000000002 28.012500000000003 18.825 30-31 28.449999999999996 25.662499999999998 26.8375 19.05 32-33 24.7 25.7 26.9625 22.6375 34-35 23.2875 29.875 26.150000000000002 20.6875 36-37 25.85 24.5 26.424999999999997 23.225 38-39 28.38159709163846 24.608248715055787 28.94571894195813 18.064435251347625 40-41 25.975655665704604 23.880035136152593 28.886936880411596 21.257372317731207 42-43 25.922682347053673 29.20055048167146 26.2729888652571 18.603778306017766 44-45 23.5875 26.674999999999997 29.6625 20.075000000000003 46-47 26.087500000000002 23.5125 27.450000000000003 22.95 48-49 24.925 23.724999999999998 30.2125 21.1375 50-51 23.375 27.700000000000003 28.1125 20.8125 52-53 25.0313047833709 26.82193839218633 26.233408464813422 21.91334835962935 54-55 24.125 28.262500000000003 27.712500000000002 19.900000000000002 56-57 26.337500000000002 27.187499999999996 27.737499999999997 18.7375 58-59 23.775 26.7625 29.0875 20.375 60-61 27.325 25.5625 28.65 18.462500000000002 62-63 21.55 27.800000000000004 31.137500000000003 19.5125 64-65 23.25 30.95 27.787499999999998 18.0125 66-67 25.162499999999998 29.299999999999997 27.6875 17.849999999999998 68-69 21.5 26.724999999999998 27.775 24.0 70-71 23.939962476547844 26.929330831769853 26.641651031894938 22.489055659787365 72-73 27.245358755644755 24.96236828901154 29.15203211239338 18.640240842950327 74-75 24.30354216563721 27.820496659523506 28.791125677549477 19.084835497289802 76-77 22.77855241475472 24.920775763721636 27.95031055900621 24.350361262517428 78-79 25.925925925925924 25.658648339060708 28.891434389716174 19.523991345297187 80-81 22.094214029697902 32.94930875576037 26.497695852534562 18.45878136200717 82-83 24.076219904725118 27.140466074417407 27.53959057551178 21.243723445345694 84-85 22.252497729336966 25.652004671078238 31.919034643830287 20.17646295575451 86-87 22.174590802805923 26.929072486360095 29.670044167316185 21.226292543517797 88-89 20.252013510002598 28.22811119771369 30.475448168355417 21.044427123928294 90-91 25.863860743050143 27.65653416471811 27.461678358015067 19.01792673421668 92-93 22.135619641465315 28.81267861782281 28.72174590802806 20.32995583268381 >>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 1.5 17 8.5 18 8.5 19 3.0 20 2.0 21 2.5 22 5.5 23 10.0 24 11.0 25 8.0 26 8.0 27 14.5 28 25.5 29 31.0 30 30.5 31 33.0 32 51.0 33 65.5 34 72.0 35 82.0 36 102.5 37 143.5 38 170.0 39 165.0 40 172.0 41 175.5 42 190.0 43 214.0 44 212.5 45 197.0 46 193.0 47 195.5 48 172.0 49 153.5 50 161.0 51 169.0 52 150.0 53 138.0 54 185.5 55 151.5 56 63.5 57 55.0 58 56.0 59 44.0 60 36.0 61 30.5 62 21.0 63 20.5 64 21.5 65 20.0 66 17.5 67 16.0 68 11.5 69 12.0 70 11.0 71 7.0 72 6.0 73 4.0 74 1.5 75 1.0 76 1.0 77 0.0 78 1.0 79 2.0 80 1.0 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 0.0 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 0.2875 40-41 0.3875 42-43 0.08750000000000001 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.17500000000000002 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 5.0 71 5.0 72 8.0 73 10.0 74 11.0 75 13.0 76 7.0 77 9.0 78 7.0 79 15.0 80 8.0 81 10.0 82 17.0 83 17.0 84 9.0 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 3849.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.425 #Duplication Level Percentage of deduplicated Percentage of total 1 93.16323192672554 71.2 2 3.4674517500817794 5.3 3 0.8505070330389269 1.95 4 0.7523716061498201 2.3 5 0.39254170755642787 1.5 6 0.2944062806673209 1.35 7 0.19627085377821393 1.05 8 0.09813542688910697 0.6 9 0.09813542688910697 0.675 >10 0.6542361792607131 10.025 >50 0.0 0.0 >100 0.03271180896303566 4.05 >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 162 4.05 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 50 1.25 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 42 1.05 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 28 0.7000000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 25 0.625 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 25 0.625 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 24 0.6 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 23 0.575 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 21 0.525 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 20 0.5 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 19 0.475 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 15 0.375 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 14 0.35000000000000003 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 11 0.27499999999999997 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 9 0.22499999999999998 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 7 0.17500000000000002 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 6 0.15 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 5 0.125 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGGTGTGAGCTGGAGAGACGATCGGGTCTCTCAGCCGGCGTCTTCATCAG 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 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 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 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 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 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 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.025 42-43 0.025 0.0 0.0 0.0 0.025 44-45 0.025 0.0 0.0 0.0 0.025 46-47 0.025 0.0 0.0 0.0 0.025 48-49 0.025 0.0 0.0 0.0 0.025 50-51 0.025 0.0 0.0 0.0 0.025 52-53 0.025 0.0 0.0 0.0 0.025 54-55 0.025 0.0 0.0 0.0 0.025 56-57 0.025 0.0 0.0 0.0 0.025 58-59 0.025 0.0 0.0 0.0 0.025 60-61 0.025 0.0 0.0 0.0 0.025 62-63 0.025 0.0 0.0 0.0 0.025 64-65 0.025 0.0 0.0 0.0 0.025 66-67 0.025 0.0 0.0 0.0 0.025 68-69 0.025 0.0 0.0 0.0 0.025 70-71 0.025 0.0 0.0 0.0 0.025 72-73 0.025 0.0 0.0 0.0 0.025 74-75 0.025 0.0 0.0 0.0 0.025 76-77 0.025 0.0 0.0 0.0 0.025 78-79 0.025 0.0 0.0 0.0 0.025 80-81 0.025 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATGAT 15 8.758201E-4 86.8875 2 ATGATTC 15 8.758201E-4 86.8875 4 TGATTCT 15 8.758201E-4 86.8875 5 GATGATT 15 8.758201E-4 86.8875 3 GATTCTG 15 8.758201E-4 86.8875 6 GGGATGA 15 8.758201E-4 86.8875 1 AATACAA 35 4.7111826E-10 86.8875 9 ATTCTGT 15 8.758201E-4 86.8875 7 GCAATAC 40 1.3587851E-9 76.026566 7 GGGAGAG 40 1.3587851E-9 76.026566 1 CAATACA 40 1.3587851E-9 76.026566 8 GAGCAAT 40 1.3587851E-9 76.026566 5 AGAGCAA 40 1.3587851E-9 76.026566 4 AGCAATA 40 1.3587851E-9 76.026566 6 GGAGAGC 45 3.4524419E-9 67.57917 2 GAGAGCA 45 3.4524419E-9 67.57917 3 TTCTGTA 20 0.0027439385 65.16563 8 TCTGTAT 20 0.0027439385 65.16563 9 TTCAATT 25 0.0066407924 52.1325 4 CAATTTC 25 0.0066407924 52.1325 6 >>END_MODULE Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441517 READS because READLEN < 1 Read 441517 spots for ERR6133564.sra Written 441517 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra Rejected 441510 READS because READLEN < 1 Read 441510 spots for ERR6133564.sra Written 441510 spots for ERR6133564.sra SRR ids: ['ERR6133564.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_nurtvdx2 ERR6133564.sra spots: 8830207 blocks: [[1, 441510], [441511, 883020], [883021, 1324530], [1324531, 1766040], [1766041, 2207550], [2207551, 2649060], [2649061, 3090570], [3090571, 3532080], [3532081, 3973590], [3973591, 4415100], [4415101, 4856610], [4856611, 5298120], [5298121, 5739630], [5739631, 6181140], [6181141, 6622650], [6622651, 7064160], [7064161, 7505670], [7505671, 7947180], [7947181, 8388690], [8388691, 8830207]] ERR6133564 file size 1952704 ERR6133564 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 ERR6133564 ERR6133564_1.fastq Input file: ERR6133564_1.fastq trimmed: ERR6133564-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 08:45:05 2024 >> started Sat Dec 7 08:45:30 2024 >> done (24.748s) 8830207 reads processed; of these: 230 ( 0.00%) short reads filtered out after trimming by size control 50 ( 0.00%) empty reads filtered out after trimming by size control 8829927 (100.00%) reads available; of these: 168067 ( 1.90%) trimmed reads available after processing 8661860 (98.10%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 47 0.00% 19 62 0.00% 20 32 0.00% 21 42 0.00% 22 48 0.00% 23 9 0.00% 24 13 0.00% 25 12 0.00% 26 16 0.00% 27 16 0.00% 28 36 0.00% 29 26 0.00% 30 20 0.00% 31 35 0.00% 32 36 0.00% 33 29 0.00% 34 32 0.00% 35 176 0.00% 36 1038 0.01% 37 52 0.00% 38 47 0.00% 39 139 0.00% 40 83 0.00% 41 46 0.00% 42 21 0.00% 43 13 0.00% 44 22 0.00% 45 26 0.00% 46 23 0.00% 47 26 0.00% 48 16 0.00% 49 24 0.00% 50 24 0.00% 51 38 0.00% 52 25 0.00% 53 13 0.00% 54 18 0.00% 55 16 0.00% 56 11 0.00% 57 22 0.00% 58 24 0.00% 59 11 0.00% 60 26 0.00% 61 26 0.00% 62 6 0.00% 63 4 0.00% 64 9 0.00% 65 10 0.00% 66 22 0.00% 67 29 0.00% 68 77 0.00% 69 208 0.00% 70 23125 0.26% 71 21822 0.25% 72 24503 0.28% 73 22158 0.25% 74 22798 0.26% 75 22624 0.26% 76 20293 0.23% 77 20784 0.24% 78 23233 0.26% 79 26586 0.30% 80 24572 0.28% 81 26877 0.30% 82 30895 0.35% 83 31162 0.35% 84 27661 0.31% 85 308 0.00% 86 597 0.01% 87 1009 0.01% 88 2009 0.02% 89 3639 0.04% 90 7543 0.09% 91 22503 0.25% 92 123611 1.40% 93 8296733 93.96% 8829927 reads passed initial QC criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=3.98 fanout-score-rank=25 prefix-density=0.99 prefix-fanout=3.2 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=205.54 fanout-score-rank=1 prefix-density=0.59 prefix-fanout=6.6 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 08:46:55 Started mapping on | Dec 07 08:46:56 Finished on | Dec 07 08:48:18 Mapping speed, Million of reads per hour | 387.66 Number of input reads | 8829927 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 5570957 Uniquely mapped reads % | 63.09% Average mapped length | 91.81 Number of splices: Total | 235232 Number of splices: Annotated (sjdb) | 196170 Number of splices: GT/AG | 226933 Number of splices: GC/AG | 4880 Number of splices: AT/AC | 129 Number of splices: Non-canonical | 3290 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 1.72 Insertion rate per base | 0.02% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3008911 % of reads mapped to multiple loci | 34.08% Number of reads mapped to too many loci | 116419 % of reads mapped to too many loci | 1.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.43% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 250059 250059 250059 N_multimapping 3008911 3008911 3008911 N_noFeature 388542 451805 5316072 N_ambiguous 221131 29436 819 UnstrandedReadsAssigned:4961284 PositiveStrandReadsAssigned:5089716 NegativeStrandReadsAssigned:254066 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133564 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: ERR6133564-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,829,927 reads, 6,858,401 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,162 rounds 52973 ERR6133564.ke.tsv 35125 ERR6133564.se.tsv 88098 total ==> ERR6133564.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 133 18.8967 PNS24243 293 194 0 0 KQK14069 1603 1504 66 8.5543 KQK14071 474 375 0 0 ==> ERR6133564.se.tsv <== BRADI_1g14170v3 66 BRADI_1g53295v3 83 BRADI_1g59795v3 51 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 108 BRADI_1g74790v3 54 BRADI_1g09890v3 0 BRADI_1g77505v3 118 BRADI_1g48960v3 0 ERR6133564 completed mapping pipeline successfully