Starting /dee2/code/volunteer_pipeline.sh ERR6133454 current disk space = 1545719943168 free memory = 1597589760 ERR6133454 SRAfilesize 29edc4c20c25c667ed5444ea82965f1a ERR6133454.sra ERR6133454.sra file validated ERR6133454 is single end ERR6133454 is conventional basespace ERR6133454 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133454_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.89 37.0 33.0 37.0 33.0 37.0 2 36.28375 37.0 37.0 37.0 33.0 37.0 3 35.1915 37.0 33.0 37.0 33.0 37.0 4 34.6495 37.0 33.0 37.0 27.0 37.0 5 34.53075 37.0 33.0 37.0 27.0 37.0 6 34.9615 37.0 33.0 37.0 33.0 37.0 7 36.40225 37.0 37.0 40.0 33.0 40.0 8 36.684 37.0 37.0 40.0 33.0 40.0 9 36.855 37.0 37.0 40.0 33.0 40.0 10-11 36.853625 37.0 37.0 40.0 33.0 40.0 12-13 36.773375 37.0 37.0 40.0 33.0 40.0 14-15 36.680625 37.0 37.0 40.0 33.0 40.0 16-17 36.481375 37.0 37.0 40.0 33.0 40.0 18-19 36.1995 37.0 37.0 40.0 33.0 40.0 20-21 35.956374999999994 37.0 33.0 40.0 33.0 40.0 22-23 35.7395 37.0 33.0 40.0 33.0 40.0 24-25 35.801249999999996 37.0 33.0 40.0 33.0 40.0 26-27 36.05325 37.0 35.0 40.0 33.0 40.0 28-29 36.000625 37.0 33.0 40.0 33.0 40.0 30-31 36.1295 37.0 35.0 40.0 33.0 40.0 32-33 35.964749999999995 37.0 33.0 40.0 33.0 40.0 34-35 35.7605 37.0 33.0 40.0 33.0 40.0 36-37 35.82025 37.0 33.0 40.0 33.0 40.0 38-39 35.752 37.0 33.0 40.0 33.0 40.0 40-41 35.513125 37.0 33.0 40.0 33.0 40.0 42-43 35.535624999999996 37.0 33.0 37.0 33.0 40.0 44-45 35.123625 37.0 33.0 37.0 30.0 40.0 46-47 35.227000000000004 37.0 33.0 37.0 33.0 40.0 48-49 35.28875 37.0 33.0 37.0 30.0 40.0 50-51 35.181124999999994 37.0 33.0 37.0 33.0 40.0 52-53 34.817625 37.0 33.0 37.0 27.0 40.0 54-55 34.89025 37.0 33.0 37.0 33.0 37.0 56-57 34.741375000000005 37.0 33.0 37.0 33.0 37.0 58-59 34.128625 37.0 33.0 37.0 27.0 37.0 60-61 34.2495 37.0 33.0 37.0 27.0 37.0 62-63 34.306125 37.0 33.0 37.0 27.0 37.0 64-65 34.133125 37.0 33.0 37.0 27.0 37.0 66-67 33.89975 37.0 33.0 37.0 27.0 37.0 68-69 33.12775 35.0 33.0 37.0 27.0 37.0 70-71 33.27404896745932 33.0 33.0 37.0 27.0 37.0 72-73 33.73294447989421 37.0 33.0 37.0 27.0 37.0 74-75 33.646793636380806 37.0 33.0 37.0 27.0 37.0 76-77 33.79819423425503 37.0 33.0 37.0 27.0 37.0 78-79 33.66960290321174 37.0 33.0 37.0 27.0 37.0 80-81 33.662017980708626 37.0 33.0 37.0 27.0 37.0 82-83 33.521099677213954 37.0 33.0 37.0 27.0 37.0 84-85 33.33041545661343 35.0 33.0 37.0 27.0 37.0 86-87 33.28032036613273 33.0 33.0 37.0 27.0 37.0 88-89 33.46122552758709 35.0 33.0 37.0 27.0 37.0 90-91 33.0021612001017 33.0 33.0 37.0 27.0 37.0 92-93 33.0860666158149 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 20.0 22 19.0 23 20.0 24 25.0 25 33.0 26 47.0 27 52.0 28 79.0 29 84.0 30 113.0 31 146.0 32 177.0 33 239.0 34 285.0 35 549.0 36 948.0 37 797.0 38 352.0 39 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.1 2.375 2.45 6.075 2 76.175 14.774999999999999 5.375 3.675 3 41.675000000000004 36.125 12.45 9.75 4 30.65 34.275 16.75 18.325 5 30.125 27.500000000000004 25.55 16.825000000000003 6 18.9 42.55 22.275 16.275000000000002 7 40.849999999999994 27.975 17.75 13.425 8 27.725 28.7 20.5 23.075000000000003 9 24.525 34.825 24.525 16.125 10-11 23.4625 28.812500000000004 30.612499999999997 17.1125 12-13 24.65 29.425 23.95 21.975 14-15 20.2125 37.262499999999996 24.95 17.575 16-17 26.8 28.375 22.3 22.525000000000002 18-19 25.837500000000002 25.362499999999997 29.8875 18.912499999999998 20-21 26.42240840315118 23.846442415905962 30.949105914718018 18.782043266224836 22-23 29.25 21.5375 28.775000000000002 20.4375 24-25 23.7875 23.8125 28.65 23.75 26-27 25.974999999999998 22.6375 30.45 20.9375 28-29 23.95 28.975 29.575000000000003 17.5 30-31 32.85 23.674999999999997 25.087500000000002 18.387500000000003 32-33 27.750000000000004 23.275000000000002 25.362499999999997 23.6125 34-35 23.1625 33.85 23.775 19.2125 36-37 27.625 23.3625 23.6625 25.35 38-39 32.829103637954745 23.31541442680335 26.828353544193025 17.027128391048883 40-41 25.937500000000004 22.825 31.5375 19.7 42-43 27.331914360836358 30.361837986728435 23.588331037936648 18.717916614498563 44-45 27.05 23.1375 30.412499999999998 19.400000000000002 46-47 27.187499999999996 22.925 25.4625 24.425 48-49 27.762500000000003 22.375 27.650000000000002 22.2125 50-51 23.175 29.425 25.112499999999997 22.287499999999998 52-53 22.67886229795765 25.924069665455455 23.731361984713693 27.6657060518732 54-55 22.040255031878985 24.840605075634453 31.091386423302914 22.027753469183647 56-57 29.462500000000002 26.75 24.9875 18.8 58-59 22.8125 26.775 29.475 20.9375 60-61 31.45 23.5125 26.2625 18.775 62-63 20.6625 26.2625 32.65 20.424999999999997 64-65 21.725 34.175 27.125 16.975 66-67 26.987499999999997 29.849999999999998 24.9375 18.224999999999998 68-69 20.852606575821977 24.70308788598575 29.303662957869737 25.14064258032254 70-71 22.926829268292686 28.505315822388994 25.278298936835526 23.289555972482802 72-73 27.346785311442535 22.997869407193882 29.37711492668254 20.278230354681035 74-75 27.09223422970596 29.153053531037948 25.43352601156069 18.321186227695403 76-77 22.661462923328717 23.253178899660078 25.166813546518945 28.91854463049226 78-79 25.927327781983344 26.8483472117083 28.387585162755492 18.836739843552863 80-81 20.956719817767656 35.14300177170336 27.10706150341686 16.793216907112125 82-83 24.81307819034343 24.648333544544418 25.294639462679 25.243948802433152 84-85 22.205284552845526 24.059959349593495 32.698170731707314 21.036585365853657 86-87 21.078057462496822 29.60844139333842 28.33714721586575 20.97635392829901 88-89 19.209255021612 26.722603610475463 32.023900330536485 22.04424103737605 90-91 29.557589626239512 25.92168827866768 26.074243579964403 18.4464785151284 92-93 20.01017035341978 27.68878718535469 30.56191202644292 21.73913043478261 >>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 7.0 18 7.5 19 0.5 20 0.5 21 2.0 22 2.0 23 3.0 24 5.0 25 6.5 26 7.5 27 10.0 28 17.0 29 21.0 30 23.0 31 33.5 32 41.0 33 48.0 34 58.5 35 68.0 36 83.0 37 117.0 38 173.0 39 173.0 40 169.5 41 186.0 42 183.0 43 188.5 44 177.5 45 160.0 46 163.5 47 159.5 48 146.5 49 159.0 50 161.0 51 149.0 52 143.0 53 161.5 54 296.0 55 264.5 56 90.5 57 61.0 58 60.0 59 45.5 60 27.0 61 25.5 62 30.0 63 30.0 64 27.5 65 21.5 66 16.0 67 15.0 68 12.5 69 11.5 70 10.5 71 9.0 72 7.0 73 3.5 74 4.5 75 4.5 76 1.5 77 0.5 78 0.0 79 1.0 80 1.0 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 0.0375 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 0.0 42-43 0.1625 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2375 54-55 0.0125 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 5.0 71 4.0 72 3.0 73 7.0 74 4.0 75 4.0 76 3.0 77 5.0 78 4.0 79 8.0 80 4.0 81 2.0 82 3.0 83 5.0 84 6.0 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 3933.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 68.45 #Duplication Level Percentage of deduplicated Percentage of total 1 91.85536888239591 62.875 2 4.200146092037984 5.75 3 1.3513513513513513 2.775 4 0.4747991234477721 1.3 5 0.2921840759678598 1.0 6 0.2556610664718773 1.05 7 0.3287070854638422 1.575 8 0.18261504747991236 1.0 9 0.18261504747991236 1.125 >10 0.8035062089116143 11.125 >50 0.03652300949598247 2.0500000000000003 >100 0.03652300949598247 8.375 >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 335 8.375 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 82 2.0500000000000003 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 48 1.2 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 45 1.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 35 0.8750000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 33 0.8250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 33 0.8250000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 25 0.625 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 23 0.575 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 18 0.44999999999999996 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 18 0.44999999999999996 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 18 0.44999999999999996 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 17 0.42500000000000004 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 16 0.4 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 15 0.375 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 13 0.325 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 12 0.3 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 11 0.27499999999999997 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 11 0.27499999999999997 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 11 0.27499999999999997 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 10 0.25 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 10 0.25 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 10 0.25 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 9 0.22499999999999998 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 8 0.2 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 7 0.17500000000000002 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.0625 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 fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAATACA 50 9.276846E-11 69.43 8 GGAGAGC 45 3.4851837E-9 67.50139 2 GGGAGAG 45 3.4851837E-9 67.50139 1 GAGCAAT 45 3.4851837E-9 67.50139 5 AGAGCAA 45 3.4851837E-9 67.50139 4 GCAATAC 55 2.1645974E-10 63.118187 7 GAGAGCA 50 8.019924E-9 60.75125 3 AGCAATA 50 8.019924E-9 60.75125 6 AATACAA 75 3.3942342E-9 46.286667 9 CACTAGC 45 1.907938E-8 39.060482 86-87 ACTAGCT 45 1.907938E-8 39.060482 86-87 GCGAAGC 45 2.1380401E-8 38.572224 30-31 CGAAGCG 45 2.1380401E-8 38.572224 32-33 GGCGAAG 45 2.1380401E-8 38.572224 30-31 AGGCGAA 45 2.1380401E-8 38.572224 28-29 GCTGCTA 45 2.1380401E-8 38.572224 22-23 TGCTAGG 45 2.1380401E-8 38.572224 24-25 CTGCTAG 45 2.1380401E-8 38.572224 24-25 TAGGCGA 45 2.1380401E-8 38.572224 28-29 AAGCGTT 40 3.885125E-7 37.969532 14-15 >>END_MODULE Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105859 READS because READLEN < 1 Read 105859 spots for ERR6133454.sra Written 105859 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra Rejected 105848 READS because READLEN < 1 Read 105848 spots for ERR6133454.sra Written 105848 spots for ERR6133454.sra SRR ids: ['ERR6133454.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_g121nh0v ERR6133454.sra spots: 2116971 blocks: [[1, 105848], [105849, 211696], [211697, 317544], [317545, 423392], [423393, 529240], [529241, 635088], [635089, 740936], [740937, 846784], [846785, 952632], [952633, 1058480], [1058481, 1164328], [1164329, 1270176], [1270177, 1376024], [1376025, 1481872], [1481873, 1587720], [1587721, 1693568], [1693569, 1799416], [1799417, 1905264], [1905265, 2011112], [2011113, 2116971]] ERR6133454 file size 468199 ERR6133454 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 ERR6133454 ERR6133454_1.fastq Input file: ERR6133454_1.fastq trimmed: ERR6133454-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 06:21:04 2024 >> started Sat Dec 7 06:21:05 2024 >> done (1.215s) 2116971 reads processed; of these: 387 ( 0.02%) short reads filtered out after trimming by size control 32 ( 0.00%) empty reads filtered out after trimming by size control 2116552 (99.98%) reads available; of these: 33369 ( 1.58%) trimmed reads available after processing 2083183 (98.42%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 25 0.00% 19 44 0.00% 20 40 0.00% 21 40 0.00% 22 21 0.00% 23 22 0.00% 24 19 0.00% 25 24 0.00% 26 24 0.00% 27 62 0.00% 28 386 0.02% 29 78 0.00% 30 28 0.00% 31 18 0.00% 32 65 0.00% 33 85 0.00% 34 23 0.00% 35 38 0.00% 36 496 0.02% 37 11 0.00% 38 13 0.00% 39 24 0.00% 40 23 0.00% 41 18 0.00% 42 17 0.00% 43 117 0.01% 44 17 0.00% 45 41 0.00% 46 8 0.00% 47 5 0.00% 48 5 0.00% 49 4 0.00% 50 4 0.00% 51 12 0.00% 52 5 0.00% 53 5 0.00% 54 3 0.00% 55 3 0.00% 56 7 0.00% 57 5 0.00% 58 5 0.00% 59 5 0.00% 60 8 0.00% 61 9 0.00% 62 2 0.00% 63 0 0.00% 64 8 0.00% 65 2 0.00% 66 5 0.00% 67 8 0.00% 68 14 0.00% 69 29 0.00% 70 2185 0.10% 71 1880 0.09% 72 2029 0.10% 73 1794 0.08% 74 1979 0.09% 75 1894 0.09% 76 1802 0.09% 77 1838 0.09% 78 2068 0.10% 79 2404 0.11% 80 2160 0.10% 81 2482 0.12% 82 2791 0.13% 83 2684 0.13% 84 2466 0.12% 85 95 0.00% 86 156 0.01% 87 271 0.01% 88 480 0.02% 89 894 0.04% 90 1891 0.09% 91 5632 0.27% 92 21345 1.01% 93 2051352 96.92% 2116552 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=31 prefix-density=0.38 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=116.84 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=8.1 sequence=AGGAAGAGGAGGATGCAGTCAGGGCTCACAAACAACCTGCCACTGCCGCCATTGGCCTTCTAAAACAGGAGAGGAGGGGTTAGATAGTTTCGATCTGCAAGGGGGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACAGTAGCGTACTTGAGGTGTTGTATTTTTATTTATTT Started job on | Dec 07 06:21:18 Started mapping on | Dec 07 06:21:18 Finished on | Dec 07 06:21:22 Mapping speed, Million of reads per hour | 1904.90 Number of input reads | 2116552 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1200915 Uniquely mapped reads % | 56.74% Average mapped length | 92.30 Number of splices: Total | 67969 Number of splices: Annotated (sjdb) | 57365 Number of splices: GT/AG | 64849 Number of splices: GC/AG | 1869 Number of splices: AT/AC | 22 Number of splices: Non-canonical | 1229 Mismatch rate per base, % | 0.53% Deletion rate per base | 0.05% Deletion average length | 1.93 Insertion rate per base | 0.02% Insertion average length | 1.71 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 856919 % of reads mapped to multiple loci | 40.49% Number of reads mapped to too many loci | 15233 % of reads mapped to too many loci | 0.72% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.98% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 58718 58718 58718 N_multimapping 856919 856919 856919 N_noFeature 99924 110829 1148779 N_ambiguous 47308 6091 174 UnstrandedReadsAssigned:1053683 PositiveStrandReadsAssigned:1083995 NegativeStrandReadsAssigned:51962 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133454 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: ERR6133454-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,116,552 reads, 1,553,299 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 945 rounds 52973 ERR6133454.ke.tsv 35125 ERR6133454.se.tsv 88098 total ==> ERR6133454.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 31 18.7254 PNS24243 293 194 0 0 KQK14069 1603 1504 14 7.71444 KQK14071 474 375 0 0 ==> ERR6133454.se.tsv <== BRADI_1g14170v3 14 BRADI_1g53295v3 22 BRADI_1g59795v3 10 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 21 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 36 BRADI_1g48960v3 0 ERR6133454 completed mapping pipeline successfully