Starting /dee2/code/volunteer_pipeline.sh ERR6133468 current disk space = 1545125470208 free memory = 1418424192 ERR6133468 SRAfilesize 842000de53b56b1735772181adca89b7 ERR6133468.sra ERR6133468.sra file validated ERR6133468 is single end ERR6133468 is conventional basespace ERR6133468 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133468_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 34.81975 37.0 33.0 37.0 33.0 37.0 2 36.2265 37.0 37.0 37.0 33.0 37.0 3 35.345 37.0 33.0 37.0 33.0 37.0 4 34.99025 37.0 33.0 37.0 33.0 37.0 5 34.82975 37.0 33.0 37.0 27.0 37.0 6 35.1995 37.0 37.0 37.0 33.0 37.0 7 36.6685 37.0 37.0 40.0 33.0 40.0 8 36.879 37.0 37.0 40.0 33.0 40.0 9 36.92525 37.0 37.0 40.0 33.0 40.0 10-11 36.876999999999995 37.0 37.0 40.0 33.0 40.0 12-13 36.784000000000006 37.0 37.0 40.0 33.0 40.0 14-15 36.799625000000006 37.0 37.0 40.0 33.0 40.0 16-17 36.53625 37.0 37.0 40.0 33.0 40.0 18-19 36.25675 37.0 37.0 40.0 33.0 40.0 20-21 36.102875 37.0 37.0 40.0 33.0 40.0 22-23 35.7825 37.0 33.0 40.0 33.0 40.0 24-25 35.961125 37.0 35.0 40.0 33.0 40.0 26-27 36.177875 37.0 37.0 40.0 33.0 40.0 28-29 36.1865 37.0 37.0 40.0 33.0 40.0 30-31 36.2345 37.0 37.0 40.0 33.0 40.0 32-33 36.1115 37.0 35.0 40.0 33.0 40.0 34-35 35.95425 37.0 33.0 40.0 33.0 40.0 36-37 35.981625 37.0 37.0 40.0 33.0 40.0 38-39 35.913375 37.0 35.0 40.0 33.0 40.0 40-41 35.803250000000006 37.0 33.0 40.0 33.0 40.0 42-43 35.743625 37.0 33.0 40.0 33.0 40.0 44-45 35.405375 37.0 33.0 38.5 30.0 40.0 46-47 35.535375 37.0 33.0 37.0 33.0 40.0 48-49 35.41525 37.0 33.0 37.0 30.0 40.0 50-51 35.203625 37.0 33.0 37.0 30.0 40.0 52-53 34.930125000000004 37.0 33.0 37.0 27.0 40.0 54-55 34.93875 37.0 33.0 37.0 27.0 40.0 56-57 34.732 37.0 33.0 37.0 27.0 38.5 58-59 34.1545 37.0 33.0 37.0 27.0 37.0 60-61 34.487125 37.0 33.0 37.0 27.0 37.0 62-63 34.34375 37.0 33.0 37.0 27.0 37.0 64-65 34.146125 37.0 33.0 37.0 27.0 37.0 66-67 34.059125 37.0 33.0 37.0 27.0 37.0 68-69 33.140875 35.0 33.0 37.0 27.0 37.0 70-71 33.257245060030016 35.0 33.0 37.0 27.0 37.0 72-73 33.71557292078468 37.0 33.0 37.0 27.0 37.0 74-75 33.785419606296514 37.0 33.0 37.0 27.0 37.0 76-77 33.827228524197686 37.0 33.0 37.0 27.0 37.0 78-79 33.82937258892018 37.0 33.0 37.0 27.0 37.0 80-81 33.82072316488098 37.0 33.0 37.0 27.0 37.0 82-83 33.7046258087419 37.0 33.0 37.0 27.0 37.0 84-85 33.54577059350831 37.0 33.0 37.0 27.0 37.0 86-87 33.391006097560975 35.0 33.0 37.0 27.0 37.0 88-89 33.436356707317074 37.0 33.0 37.0 27.0 37.0 90-91 33.07113821138211 33.0 33.0 37.0 27.0 37.0 92-93 33.09933943089431 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 13.0 21 14.0 22 18.0 23 27.0 24 27.0 25 51.0 26 48.0 27 54.0 28 70.0 29 84.0 30 106.0 31 123.0 32 158.0 33 191.0 34 291.0 35 525.0 36 897.0 37 842.0 38 455.0 39 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.625 3.0 3.8 7.575 2 69.975 18.25 6.950000000000001 4.825 3 38.5 37.675 13.275 10.549999999999999 4 33.800000000000004 30.625000000000004 16.625 18.95 5 27.35 29.799999999999997 24.525 18.325 6 18.775 42.325 23.625 15.275 7 37.974999999999994 28.599999999999998 18.224999999999998 15.2 8 28.125 30.125 22.625 19.125 9 25.124999999999996 32.45 25.2 17.224999999999998 10-11 23.400000000000002 30.025000000000002 27.487499999999997 19.0875 12-13 25.924999999999997 27.750000000000004 25.324999999999996 21.0 14-15 21.762500000000003 33.5 27.3875 17.349999999999998 16-17 25.687500000000004 29.325000000000003 24.349999999999998 20.6375 18-19 24.925 26.0375 28.537499999999998 20.5 20-21 26.25 25.912499999999998 29.275000000000002 18.5625 22-23 27.725 24.462500000000002 26.8 21.0125 24-25 24.5 24.349999999999998 29.2375 21.912499999999998 26-27 25.4375 25.3125 29.512500000000003 19.7375 28-29 24.2625 28.525 27.787499999999998 19.425 30-31 31.137500000000003 25.5 24.4375 18.925 32-33 25.45 26.5625 26.6 21.3875 34-35 24.3625 31.2375 25.5125 18.8875 36-37 25.9625 24.4125 25.575 24.05 38-39 29.353669208651077 23.31541442680335 29.353669208651077 17.97724715589449 40-41 26.215776972121514 24.840605075634453 29.49118639829979 19.452431553944244 42-43 26.903807615230463 30.398296593186373 24.837174348697395 17.860721442885772 44-45 25.340667583447928 24.815601950243778 29.678709838729837 20.165020627578446 46-47 25.937500000000004 22.925 26.087500000000002 25.05 48-49 25.624999999999996 23.7375 29.7375 20.9 50-51 23.4875 28.1875 27.375 20.95 52-53 24.01807002133266 25.82507215459907 25.674488643493536 24.48236918057473 54-55 22.545954733024885 26.53495060647743 30.261348005502064 20.657746654995623 56-57 27.287499999999998 26.700000000000003 26.8 19.2125 58-59 23.2125 26.1125 30.2375 20.4375 60-61 28.4 24.4375 28.262500000000003 18.9 62-63 19.662499999999998 27.737499999999997 32.275 20.325 64-65 21.6125 31.900000000000002 26.937499999999996 19.55 66-67 25.887500000000003 29.8375 26.525 17.75 68-69 21.915239404925615 26.753344168021005 28.641080135016878 22.690336292036505 70-71 24.5311327831958 26.93173293323331 26.281570392598148 22.255563890972745 72-73 27.041583166332668 23.08366733466934 30.01002004008016 19.864729458917836 74-75 25.404998116287832 28.73288961446691 27.71568504332538 18.14642722591988 76-77 21.66855417138543 25.51906379765949 27.997986661633323 24.81439536932176 78-79 25.365423387096776 25.78125 29.044858870967744 19.808467741935484 80-81 21.74627242860753 32.66363406621178 28.746525145312106 16.843568359868588 82-83 23.62623448974424 24.879716383894657 28.007090402633576 23.486958723727525 84-85 22.528239624317806 24.54626221601726 32.174133773321486 20.751364386343443 86-87 21.023882113821138 28.772865853658537 30.03048780487805 20.172764227642276 88-89 20.426829268292682 28.315548780487802 31.008638211382113 20.2489837398374 90-91 27.76930894308943 27.515243902439025 27.35010162601626 17.365345528455283 92-93 21.430386178861788 28.036077235772357 29.865345528455283 20.66819105691057 >>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 2.0 17 13.0 18 12.5 19 2.0 20 1.0 21 4.5 22 7.0 23 6.5 24 10.5 25 9.5 26 8.0 27 14.0 28 24.0 29 30.5 30 28.0 31 34.5 32 51.0 33 63.5 34 62.0 35 68.5 36 102.0 37 139.0 38 155.0 39 158.0 40 189.5 41 201.5 42 186.0 43 186.5 44 179.5 45 174.5 46 177.0 47 162.5 48 151.0 49 160.5 50 151.0 51 145.5 52 156.5 53 172.0 54 237.5 55 185.5 56 78.0 57 73.5 58 62.0 59 41.0 60 28.5 61 28.0 62 25.5 63 23.5 64 25.0 65 21.0 66 16.5 67 15.5 68 12.5 69 8.5 70 7.0 71 6.0 72 4.5 73 2.0 74 0.5 75 0.5 76 0.5 77 0.0 78 0.0 79 0.0 80 0.5 81 0.5 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 0.0 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 0.0125 40-41 0.0125 42-43 0.2 44-45 0.0125 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.3875 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 0.0125 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 2.0 71 4.0 72 4.0 73 6.0 74 5.0 75 4.0 76 3.0 77 2.0 78 4.0 79 6.0 80 6.0 81 2.0 82 6.0 83 3.0 84 7.0 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 3936.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.375 #Duplication Level Percentage of deduplicated Percentage of total 1 91.92504258943782 67.45 2 4.463373083475298 6.550000000000001 3 1.1584327086882453 2.55 4 0.6473594548551959 1.9 5 0.4770017035775128 1.7500000000000002 6 0.17035775127768313 0.75 7 0.1362862010221465 0.7000000000000001 8 0.10221465076660989 0.6 9 0.10221465076660989 0.675 >10 0.7495741056218058 9.950000000000001 >50 0.034071550255536626 1.9 >100 0.034071550255536626 5.225 >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 209 5.225 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 76 1.9 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 39 0.975 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 36 0.8999999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 32 0.8 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 25 0.625 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 21 0.525 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 20 0.5 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 19 0.475 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 18 0.44999999999999996 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 18 0.44999999999999996 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 13 0.325 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 13 0.325 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 12 0.3 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 12 0.3 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 10 0.25 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 10 0.25 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 9 0.22499999999999998 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 8 0.2 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 7 0.17500000000000002 No Hit GAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTA 7 0.17500000000000002 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 6 0.15 No Hit GGGAAAGAATCAATATACTTTTAATGTCGAATCAGGATTCACTAAGACAG 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit TTAGACTTAGAACACTAACAGGTAAAATGTGAGATTTTTATTAAGTAAAA 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 6 0.15 No Hit GGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTAT 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACC 5 0.125 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GGGCCATTCACAGACACACACAACTACACAAGAGCTCTCAGCTGCTGCCC 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GGGATTGAGGGGGTCCGTCGAATGCAGCGGCTGCAAAAGCTGTATCCTGA 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 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 0.0 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 0.0125 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 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0125 0.0 0.0 0.0 66-67 0.025 0.025 0.0 0.0 0.0 68-69 0.025 0.025 0.0 0.0 0.0 70-71 0.025 0.025 0.0 0.0 0.0 72-73 0.05 0.025 0.0 0.0 0.0 74-75 0.05 0.025 0.0 0.0 0.0 76-77 0.05 0.025 0.0 0.0 0.0 78-79 0.05 0.025 0.0 0.0 0.0 80-81 0.05 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 30 1.8205126E-4 57.716667 2 GCAATAC 30 1.8205126E-4 57.716667 7 CAATACA 30 1.8205126E-4 57.716667 8 GAGCAAT 30 1.8205126E-4 57.716667 5 AGAGCAA 30 1.8205126E-4 57.716667 4 GAGAGCA 30 1.8205126E-4 57.716667 3 AATACAA 30 1.8205126E-4 57.716667 9 AGCAATA 30 1.8205126E-4 57.716667 6 CATCACT 20 7.0648314E-4 44.397438 82-83 AGCATCA 20 7.0648314E-4 44.397438 80-81 CACTAGC 20 7.0648314E-4 44.397438 86-87 GCATCAC 20 7.0648314E-4 44.397438 82-83 GGGAGAG 45 0.0013455654 38.47778 1 TAGCCGA 25 0.002117268 35.51795 72-73 ATCACTA 25 0.002117268 35.51795 84-85 TCACTAG 25 0.002117268 35.51795 84-85 ACTAGCT 25 0.002117268 35.51795 86-87 AGCCGAA 25 0.002117268 35.51795 74-75 AAAGCAT 25 0.002117268 35.51795 78-79 GCCGAAA 25 0.002117268 35.51795 74-75 >>END_MODULE Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172174 READS because READLEN < 1 Read 172174 spots for ERR6133468.sra Written 172174 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra Rejected 172169 READS because READLEN < 1 Read 172169 spots for ERR6133468.sra Written 172169 spots for ERR6133468.sra SRR ids: ['ERR6133468.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f9plh4ah ERR6133468.sra spots: 3443385 blocks: [[1, 172169], [172170, 344338], [344339, 516507], [516508, 688676], [688677, 860845], [860846, 1033014], [1033015, 1205183], [1205184, 1377352], [1377353, 1549521], [1549522, 1721690], [1721691, 1893859], [1893860, 2066028], [2066029, 2238197], [2238198, 2410366], [2410367, 2582535], [2582536, 2754704], [2754705, 2926873], [2926874, 3099042], [3099043, 3271211], [3271212, 3443385]] ERR6133468 file size 762400 ERR6133468 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 ERR6133468 ERR6133468_1.fastq Input file: ERR6133468_1.fastq trimmed: ERR6133468-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 06:42:10 2024 >> started Sat Dec 7 06:42:20 2024 >> done (10.192s) 3443385 reads processed; of these: 98 ( 0.00%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 3443272 (100.00%) reads available; of these: 49131 ( 1.43%) trimmed reads available after processing 3394141 (98.57%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 18 0.00% 20 16 0.00% 21 10 0.00% 22 20 0.00% 23 4 0.00% 24 7 0.00% 25 1 0.00% 26 7 0.00% 27 5 0.00% 28 9 0.00% 29 85 0.00% 30 7 0.00% 31 7 0.00% 32 14 0.00% 33 12 0.00% 34 14 0.00% 35 87 0.00% 36 360 0.01% 37 9 0.00% 38 13 0.00% 39 41 0.00% 40 47 0.00% 41 21 0.00% 42 7 0.00% 43 5 0.00% 44 8 0.00% 45 15 0.00% 46 8 0.00% 47 4 0.00% 48 4 0.00% 49 7 0.00% 50 8 0.00% 51 16 0.00% 52 8 0.00% 53 4 0.00% 54 2 0.00% 55 4 0.00% 56 3 0.00% 57 8 0.00% 58 2 0.00% 59 3 0.00% 60 5 0.00% 61 2 0.00% 62 2 0.00% 63 1 0.00% 64 1 0.00% 65 1 0.00% 66 6 0.00% 67 3 0.00% 68 18 0.00% 69 55 0.00% 70 4687 0.14% 71 3989 0.12% 72 4211 0.12% 73 3967 0.12% 74 4160 0.12% 75 4313 0.13% 76 3756 0.11% 77 3819 0.11% 78 4523 0.13% 79 5345 0.16% 80 4843 0.14% 81 5203 0.15% 82 5911 0.17% 83 6198 0.18% 84 5333 0.15% 85 122 0.00% 86 230 0.01% 87 396 0.01% 88 693 0.02% 89 1382 0.04% 90 2807 0.08% 91 8725 0.25% 92 32726 0.95% 93 3324894 96.56% 3443272 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=33 prefix-density=0.30 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=45.99 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=2.3 sequence=CAAGGAAGGCGTCGCCAACGGAACCCTCAAGCTCGTGGGCGGCCACTACGACTTCGTCTCCGGCAAGTTCGACACATGGGAGCTCTAAGTCCTCTCATCCGGTTAACTCCTATACATACAACGTATACTTATACATACAGATATGGAGATGACCCTACAGATCGATCCATTGATGTGGATGCGATGCCATGGAGTATATGTACTCGCTATTTTCCAGTACTGCATGCCGGATGGCTCGATGTGAATTTGTAATAAGCAATAGAAGTTTCTACCATTTTCTGACGTGGGGTTGTACTTGTGATGCGTAATTTGGTCATCTTGTGACCAAAAGACATCAACTATATAATTATAATACCATTTTCATCAAGACTCT Started job on | Dec 07 06:44:05 Started mapping on | Dec 07 06:44:06 Finished on | Dec 07 06:44:41 Mapping speed, Million of reads per hour | 354.17 Number of input reads | 3443272 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2099547 Uniquely mapped reads % | 60.98% Average mapped length | 92.36 Number of splices: Total | 96365 Number of splices: Annotated (sjdb) | 79368 Number of splices: GT/AG | 93602 Number of splices: GC/AG | 2207 Number of splices: AT/AC | 98 Number of splices: Non-canonical | 458 Mismatch rate per base, % | 0.29% Deletion rate per base | 0.02% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1291957 % of reads mapped to multiple loci | 37.52% Number of reads mapped to too many loci | 20867 % of reads mapped to too many loci | 0.61% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.85% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 51768 51768 51768 N_multimapping 1291957 1291957 1291957 N_noFeature 156677 179355 2010245 N_ambiguous 78480 11855 377 UnstrandedReadsAssigned:1864390 PositiveStrandReadsAssigned:1908337 NegativeStrandReadsAssigned:88925 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133468 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: ERR6133468-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,443,272 reads, 2,733,442 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 963 rounds 52973 ERR6133468.ke.tsv 35125 ERR6133468.se.tsv 88098 total ==> ERR6133468.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 72 24.482 PNS24243 293 194 0 0 KQK14069 1603 1504 83 25.7453 KQK14071 474 375 0 0 ==> ERR6133468.se.tsv <== BRADI_1g14170v3 83 BRADI_1g53295v3 11 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 17 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 44 BRADI_1g48960v3 0 ERR6133468 completed mapping pipeline successfully