Starting /dee2/code/volunteer_pipeline.sh ERR6133346 current disk space = 1548448141312 free memory = 1603137264 ERR6133346 SRAfilesize c311ffc4923e6bcf872969a6ecaf6e60 ERR6133346.sra ERR6133346.sra file validated ERR6133346 is single end ERR6133346 is conventional basespace ERR6133346 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133346_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4525 37.0 37.0 37.0 37.0 37.0 2 36.5275 37.0 37.0 37.0 37.0 37.0 3 36.36675 37.0 37.0 37.0 33.0 37.0 4 36.3415 37.0 37.0 37.0 37.0 37.0 5 36.43 37.0 37.0 37.0 37.0 37.0 6 36.463 37.0 37.0 37.0 37.0 37.0 7 38.53 40.0 37.0 40.0 37.0 40.0 8 38.666 40.0 37.0 40.0 37.0 40.0 9 38.653 40.0 37.0 40.0 37.0 40.0 10-11 38.654624999999996 40.0 37.0 40.0 37.0 40.0 12-13 38.626125 40.0 37.0 40.0 37.0 40.0 14-15 38.603375 40.0 37.0 40.0 37.0 40.0 16-17 38.624875 40.0 37.0 40.0 37.0 40.0 18-19 38.679625 40.0 37.0 40.0 37.0 40.0 20-21 38.298500000000004 40.0 37.0 40.0 37.0 40.0 22-23 38.43775 40.0 37.0 40.0 37.0 40.0 24-25 38.49275 40.0 37.0 40.0 37.0 40.0 26-27 38.338 40.0 37.0 40.0 37.0 40.0 28-29 38.347375 40.0 37.0 40.0 37.0 40.0 30-31 38.36175 40.0 37.0 40.0 37.0 40.0 32-33 38.310874999999996 40.0 37.0 40.0 37.0 40.0 34-35 38.277375 40.0 37.0 40.0 37.0 40.0 36-37 38.1105 40.0 37.0 40.0 37.0 40.0 38-39 37.912125 40.0 37.0 40.0 37.0 40.0 40-41 37.761125 37.0 37.0 40.0 35.0 40.0 42-43 37.755 37.0 37.0 40.0 33.0 40.0 44-45 37.5015 37.0 37.0 40.0 33.0 40.0 46-47 37.351875 37.0 37.0 40.0 33.0 40.0 48-49 37.312875 37.0 37.0 40.0 33.0 40.0 50-51 36.9915 37.0 37.0 40.0 33.0 40.0 52-53 36.863375 37.0 37.0 40.0 33.0 40.0 54-55 36.6945 37.0 37.0 37.0 33.0 40.0 56-57 36.467625 37.0 37.0 37.0 33.0 40.0 58-59 36.180875 37.0 37.0 37.0 33.0 40.0 60-61 35.947 37.0 37.0 37.0 33.0 38.5 62-63 35.41875 37.0 33.0 37.0 33.0 37.0 64-65 35.170874999999995 37.0 33.0 37.0 33.0 37.0 66-67 35.00925 37.0 33.0 37.0 33.0 37.0 68-69 33.565875000000005 35.0 33.0 37.0 30.0 37.0 70-71 33.4664606918239 33.0 33.0 37.0 30.0 37.0 72-73 33.88919910975585 33.0 33.0 37.0 33.0 37.0 74-75 33.865924793391805 33.0 33.0 37.0 30.0 37.0 76-77 33.65050584779506 33.0 33.0 37.0 30.0 37.0 78-79 33.23426350435341 33.0 33.0 37.0 27.0 37.0 80-81 32.97188863047392 33.0 33.0 37.0 27.0 37.0 82-83 32.930347666004735 33.0 33.0 37.0 27.0 37.0 84-85 32.250496972012364 33.0 33.0 35.0 27.0 37.0 86-87 32.10504434589801 33.0 33.0 33.0 27.0 37.0 88-89 32.176690687361415 33.0 33.0 33.0 27.0 37.0 90-91 31.549334811529935 33.0 30.0 33.0 27.0 37.0 92-93 30.478935698447895 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 7.0 24 7.0 25 11.0 26 8.0 27 10.0 28 21.0 29 36.0 30 36.0 31 55.0 32 73.0 33 97.0 34 209.0 35 630.0 36 1052.0 37 1448.0 38 273.0 39 23.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 65.025 9.65 8.875 16.45 2 46.575 26.474999999999998 16.575 10.375 3 30.675 37.8 17.299999999999997 14.224999999999998 4 29.825000000000003 27.650000000000002 22.3 20.225 5 24.975 26.875 28.425 19.725 6 18.875 35.05 28.249999999999996 17.825 7 31.624999999999996 27.6 23.95 16.825000000000003 8 27.125 27.474999999999998 27.175 18.224999999999998 9 24.9 26.85 28.799999999999997 19.45 10-11 23.2625 28.375 29.812499999999996 18.55 12-13 22.6375 28.599999999999998 29.175 19.5875 14-15 21.2 29.362500000000004 29.849999999999998 19.5875 16-17 24.9125 29.075 25.9875 20.025000000000002 18-19 23.3375 25.637500000000003 30.887500000000003 20.1375 20-21 24.8125 25.3125 29.5375 20.3375 22-23 26.0125 24.725 28.249999999999996 21.0125 24-25 23.9875 26.8125 29.275000000000002 19.925 26-27 24.1125 26.2125 29.6625 20.0125 28-29 24.3125 27.1125 28.475 20.1 30-31 25.9875 25.974999999999998 28.537499999999998 19.5 32-33 23.8625 26.187500000000004 29.175 20.775 34-35 22.8625 30.55 27.462500000000002 19.125 36-37 24.212500000000002 27.825 26.025 21.9375 38-39 26.200000000000003 25.15 28.349999999999998 20.3 40-41 24.4875 26.0 29.512500000000003 20.0 42-43 24.8 28.325 28.0625 18.8125 44-45 23.3375 27.275 29.1875 20.200000000000003 46-47 24.9375 26.55 28.050000000000004 20.4625 48-49 23.8625 24.6 30.337500000000002 21.2 50-51 22.112499999999997 28.0625 28.825 21.0 52-53 22.7125 27.487499999999997 29.275000000000002 20.525 54-55 23.8875 26.687499999999996 29.025000000000002 20.4 56-57 24.0375 28.237499999999997 28.6375 19.0875 58-59 23.9 28.875 28.275 18.95 60-61 26.5875 27.525 27.3875 18.5 62-63 20.9 28.575 31.624999999999996 18.9 64-65 21.8875 31.874999999999996 27.237499999999997 19.0 66-67 24.4375 29.0875 27.762500000000003 18.712500000000002 68-69 21.375 28.449999999999996 29.5 20.674999999999997 70-71 23.724137931034484 28.225705329153605 28.376175548589345 19.67398119122257 72-73 24.403855910705225 27.96803652968037 29.41400304414003 18.21410451547438 74-75 24.61183113050173 27.807006287694087 28.538431926087515 19.04273065571667 76-77 22.347600518806747 26.60181582360571 28.69001297016861 22.36057068741894 78-79 24.85868279216511 27.75075588273958 29.131063494150123 18.259497830945183 80-81 23.20021370375317 31.61479898490717 27.30065446774409 17.884332843595566 82-83 21.4081826831589 28.15006116623624 28.89764849802909 21.54410765257578 84-85 21.346764178280665 26.604112046364015 32.05464330067615 19.99448047467918 86-87 21.52161862527716 29.545454545454547 27.36973392461197 21.56319290465632 88-89 19.830931263858094 31.222283813747225 28.256651884700666 20.690133037694014 90-91 22.15909090909091 31.3470066518847 26.898558758314856 19.595343680709533 92-93 20.745565410199557 32.427937915742795 27.217294900221727 19.60920177383592 >>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 2.0 18 2.0 19 1.5 20 0.5 21 2.0 22 4.5 23 8.0 24 8.0 25 6.0 26 11.0 27 14.0 28 25.0 29 35.5 30 37.0 31 43.0 32 52.0 33 68.5 34 88.0 35 112.5 36 152.0 37 195.0 38 217.5 39 211.0 40 233.5 41 242.0 42 230.5 43 240.5 44 222.0 45 195.5 46 173.0 47 161.5 48 155.5 49 143.0 50 138.0 51 141.5 52 129.0 53 136.0 54 172.0 55 135.5 56 72.5 57 60.0 58 48.0 59 26.5 60 14.5 61 14.0 62 12.0 63 6.0 64 4.5 65 2.5 66 0.0 67 1.0 68 2.0 69 3.0 70 2.0 71 0.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 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 0.0 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 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 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 0.012968486577616392 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 25.0 71 17.0 72 32.0 73 19.0 74 21.0 75 19.0 76 23.0 77 25.0 78 31.0 79 32.0 80 25.0 81 36.0 82 33.0 83 23.0 84 31.0 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 3608.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.7 #Duplication Level Percentage of deduplicated Percentage of total 1 91.21532364597094 69.05 2 4.095112285336857 6.2 3 1.486129458388375 3.375 4 1.1228533685601056 3.4000000000000004 5 0.6274768824306473 2.375 6 0.33025099075297226 1.5 7 0.09907529722589167 0.525 8 0.13210039630118892 0.8 9 0.16512549537648613 1.125 >10 0.6935270805812417 9.375 >50 0.03302509907529723 2.275 >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 91 2.275 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 35 0.8750000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 30 0.75 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 28 0.7000000000000001 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 24 0.6 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 24 0.6 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 19 0.475 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 14 0.35000000000000003 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 13 0.325 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 13 0.325 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 10 0.25 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 9 0.22499999999999998 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 9 0.22499999999999998 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 9 0.22499999999999998 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 9 0.22499999999999998 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 7 0.17500000000000002 No Hit CTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGAT 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 6 0.15 No Hit CAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAACCTG 6 0.15 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGC 5 0.125 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAGA 5 0.125 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 5 0.125 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAG 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 5 0.125 No Hit CGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTC 5 0.125 No Hit CGGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGA 5 0.125 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 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 0.025 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 0.05 0.0 0.0 0.0 0.0 16-17 0.0625 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 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 0.0875 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 35 2.0096071E-4 33.48826 86-87 >>END_MODULE Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra Rejected 110892 READS because READLEN < 1 Read 110892 spots for ERR6133346.sra Written 110892 spots for ERR6133346.sra Rejected 110889 READS because READLEN < 1 Read 110889 spots for ERR6133346.sra Written 110889 spots for ERR6133346.sra SRR ids: ['ERR6133346.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_aumqfq5o ERR6133346.sra spots: 2217783 blocks: [[1, 110889], [110890, 221778], [221779, 332667], [332668, 443556], [443557, 554445], [554446, 665334], [665335, 776223], [776224, 887112], [887113, 998001], [998002, 1108890], [1108891, 1219779], [1219780, 1330668], [1330669, 1441557], [1441558, 1552446], [1552447, 1663335], [1663336, 1774224], [1774225, 1885113], [1885114, 1996002], [1996003, 2106891], [2106892, 2217783]] ERR6133346 file size 485225 ERR6133346 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 ERR6133346 ERR6133346_1.fastq Input file: ERR6133346_1.fastq trimmed: ERR6133346-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 01:08:50 2024 >> started Sat Dec 7 01:08:51 2024 >> done (1.262s) 2217783 reads processed; of these: 438 ( 0.02%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 2217330 (99.98%) reads available; of these: 32430 ( 1.46%) trimmed reads available after processing 2184900 (98.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 57 0.00% 20 34 0.00% 21 29 0.00% 22 30 0.00% 23 29 0.00% 24 34 0.00% 25 23 0.00% 26 25 0.00% 27 23 0.00% 28 46 0.00% 29 19 0.00% 30 26 0.00% 31 20 0.00% 32 42 0.00% 33 17 0.00% 34 23 0.00% 35 77 0.00% 36 16 0.00% 37 17 0.00% 38 28 0.00% 39 69 0.00% 40 90 0.00% 41 24 0.00% 42 14 0.00% 43 21 0.00% 44 31 0.00% 45 23 0.00% 46 13 0.00% 47 20 0.00% 48 18 0.00% 49 14 0.00% 50 15 0.00% 51 77 0.00% 52 23 0.00% 53 6 0.00% 54 6 0.00% 55 13 0.00% 56 13 0.00% 57 25 0.00% 58 16 0.00% 59 15 0.00% 60 13 0.00% 61 12 0.00% 62 0 0.00% 63 2 0.00% 64 4 0.00% 65 4 0.00% 66 4 0.00% 67 7 0.00% 68 15 0.00% 69 66 0.00% 70 13172 0.59% 71 12734 0.57% 72 13582 0.61% 73 12761 0.58% 74 11972 0.54% 75 11844 0.53% 76 11628 0.52% 77 13391 0.60% 78 13195 0.60% 79 13713 0.62% 80 13540 0.61% 81 17443 0.79% 82 18316 0.83% 83 15682 0.71% 84 18244 0.82% 85 31 0.00% 86 48 0.00% 87 90 0.00% 88 207 0.01% 89 461 0.02% 90 1122 0.05% 91 3816 0.17% 92 23792 1.07% 93 1975223 89.08% 2217330 reads passed initial QC criterion=sequence-density sequence-density=3.90 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=30 prefix-density=3.94 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=20.70 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=3.6 sequence=TGCATGGTTCCTTGGTAACCTCTAGTTTGATCAGGGAAACTACTGAAAATGAATCTGCTAATGAGGGTTACAAATTTGGTCAAGAGGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAATCTTCCAATATGCTAGTTTCAACAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGCTATTAATGGATAAGGTTTTTCCGCTAACATA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:09:06 Started mapping on | Dec 07 01:09:06 Finished on | Dec 07 01:09:10 Mapping speed, Million of reads per hour | 1995.60 Number of input reads | 2217330 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1157129 Uniquely mapped reads % | 52.19% Average mapped length | 90.49 Number of splices: Total | 54004 Number of splices: Annotated (sjdb) | 45400 Number of splices: GT/AG | 51781 Number of splices: GC/AG | 1032 Number of splices: AT/AC | 39 Number of splices: Non-canonical | 1152 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.67 Insertion rate per base | 0.02% Insertion average length | 1.79 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 922114 % of reads mapped to multiple loci | 41.59% Number of reads mapped to too many loci | 72274 % of reads mapped to too many loci | 3.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.81% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 138087 138087 138087 N_multimapping 922114 922114 922114 N_noFeature 100558 111651 1109017 N_ambiguous 43397 6321 229 UnstrandedReadsAssigned:1013174 PositiveStrandReadsAssigned:1039157 NegativeStrandReadsAssigned:47883 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133346 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: ERR6133346-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,217,330 reads, 1,564,000 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 956 rounds 52973 ERR6133346.ke.tsv 35125 ERR6133346.se.tsv 88098 total ==> ERR6133346.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 22 13.6844 PNS24243 293 194 0 0 KQK14069 1603 1504 7 3.97198 KQK14071 474 375 0 0 ==> ERR6133346.se.tsv <== BRADI_1g14170v3 7 BRADI_1g53295v3 17 BRADI_1g59795v3 11 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 29 BRADI_1g48960v3 0 ERR6133346 completed mapping pipeline successfully