Starting /dee2/code/volunteer_pipeline.sh ERR6133340 current disk space = 1548172001280 free memory = 1600588672 ERR6133340 SRAfilesize ad265014c7c07b8e7d945b8d3ecda31d ERR6133340.sra ERR6133340.sra file validated ERR6133340 is single end ERR6133340 is conventional basespace ERR6133340 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133340_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 36.34025 37.0 37.0 37.0 33.0 37.0 2 36.56525 37.0 37.0 37.0 37.0 37.0 3 36.36625 37.0 37.0 37.0 37.0 37.0 4 36.254 37.0 37.0 37.0 33.0 37.0 5 36.43425 37.0 37.0 37.0 37.0 37.0 6 36.46525 37.0 37.0 37.0 37.0 37.0 7 38.518 40.0 37.0 40.0 37.0 40.0 8 38.64675 40.0 37.0 40.0 37.0 40.0 9 38.6615 40.0 37.0 40.0 37.0 40.0 10-11 38.694 40.0 37.0 40.0 37.0 40.0 12-13 38.684 40.0 37.0 40.0 37.0 40.0 14-15 38.600875 40.0 37.0 40.0 37.0 40.0 16-17 38.616125 40.0 37.0 40.0 37.0 40.0 18-19 38.678875 40.0 37.0 40.0 37.0 40.0 20-21 38.326125000000005 40.0 37.0 40.0 37.0 40.0 22-23 38.4685 40.0 37.0 40.0 37.0 40.0 24-25 38.434 40.0 37.0 40.0 37.0 40.0 26-27 38.352875 40.0 37.0 40.0 37.0 40.0 28-29 38.306625 40.0 37.0 40.0 37.0 40.0 30-31 38.26475 40.0 37.0 40.0 37.0 40.0 32-33 38.2845 40.0 37.0 40.0 37.0 40.0 34-35 38.2295 40.0 37.0 40.0 37.0 40.0 36-37 38.043499999999995 40.0 37.0 40.0 37.0 40.0 38-39 37.783 40.0 37.0 40.0 33.0 40.0 40-41 37.632125 37.0 37.0 40.0 33.0 40.0 42-43 37.622625 37.0 37.0 40.0 33.0 40.0 44-45 37.411625 37.0 37.0 40.0 33.0 40.0 46-47 37.23725 37.0 37.0 40.0 33.0 40.0 48-49 37.158500000000004 37.0 37.0 40.0 33.0 40.0 50-51 36.877625 37.0 37.0 40.0 33.0 40.0 52-53 36.726875 37.0 37.0 38.5 33.0 40.0 54-55 36.6045 37.0 37.0 37.0 33.0 40.0 56-57 36.445375 37.0 37.0 37.0 33.0 40.0 58-59 36.129125 37.0 37.0 37.0 33.0 40.0 60-61 35.961 37.0 37.0 37.0 33.0 38.5 62-63 35.495000000000005 37.0 33.0 37.0 33.0 37.0 64-65 35.194374999999994 37.0 33.0 37.0 33.0 37.0 66-67 35.027125 37.0 33.0 37.0 33.0 37.0 68-69 33.6235 35.0 33.0 37.0 30.0 37.0 70-71 33.47633985943775 33.0 33.0 37.0 30.0 37.0 72-73 33.89346171746436 33.0 33.0 37.0 33.0 37.0 74-75 33.854761579710186 33.0 33.0 37.0 33.0 37.0 76-77 33.56061775117642 33.0 33.0 37.0 27.0 37.0 78-79 33.21457640628637 33.0 33.0 37.0 27.0 37.0 80-81 32.942860563461736 33.0 33.0 37.0 27.0 37.0 82-83 32.73267572639702 33.0 33.0 37.0 27.0 37.0 84-85 32.20818588082291 33.0 33.0 35.0 27.0 37.0 86-87 32.05503448275862 33.0 33.0 33.0 27.0 37.0 88-89 31.999310344827585 33.0 33.0 33.0 27.0 37.0 90-91 31.228275862068966 33.0 30.0 33.0 24.5 37.0 92-93 30.31655172413793 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 3.0 22 7.0 23 6.0 24 7.0 25 8.0 26 14.0 27 18.0 28 14.0 29 22.0 30 54.0 31 45.0 32 69.0 33 114.0 34 187.0 35 645.0 36 1109.0 37 1367.0 38 292.0 39 17.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.05 9.025 9.125 15.8 2 48.449999999999996 25.4 15.825 10.325 3 29.75 37.025000000000006 18.875 14.35 4 30.349999999999998 28.025 20.825 20.8 5 23.825 27.975 28.475 19.725 6 20.025000000000002 34.5 27.800000000000004 17.675 7 34.225 25.874999999999996 23.225 16.675 8 26.575 27.925 26.775 18.725 9 24.125 27.325 29.299999999999997 19.25 10-11 24.224999999999998 28.6125 28.675 18.4875 12-13 24.15 27.6375 28.537499999999998 19.675 14-15 22.425 28.8625 29.775000000000002 18.9375 16-17 24.25 28.775000000000002 26.637499999999996 20.3375 18-19 24.349999999999998 25.424999999999997 29.599999999999998 20.625 20-21 25.0 25.35 29.15 20.5 22-23 26.2875 23.575 28.537499999999998 21.6 24-25 24.5625 25.4375 28.825 21.175 26-27 24.474999999999998 25.3 29.975 20.25 28-29 24.3 26.75 28.512500000000003 20.4375 30-31 25.95 25.474999999999998 28.15 20.424999999999997 32-33 24.3625 26.400000000000002 28.487499999999997 20.75 34-35 24.275 27.8875 27.900000000000002 19.9375 36-37 24.15 27.5875 26.775 21.4875 38-39 26.224999999999998 24.8625 29.212500000000002 19.7 40-41 25.337500000000002 26.2625 27.3625 21.0375 42-43 24.587500000000002 28.199999999999996 27.737499999999997 19.475 44-45 23.0625 27.287499999999998 28.999999999999996 20.65 46-47 25.5 26.8 27.325 20.375 48-49 24.349999999999998 25.5625 29.4 20.6875 50-51 22.8625 27.8875 28.775000000000002 20.474999999999998 52-53 24.2 28.075 27.0125 20.7125 54-55 23.9875 28.225 28.7 19.0875 56-57 24.3875 27.825 27.875 19.9125 58-59 24.125 28.4125 28.199999999999996 19.2625 60-61 25.4625 27.2625 27.075 20.200000000000003 62-63 22.75 28.675 30.312499999999996 18.2625 64-65 23.3 31.075000000000003 27.4125 18.212500000000002 66-67 23.4875 29.299999999999997 27.712500000000002 19.5 68-69 22.625 27.05 29.625 20.7 70-71 23.997995991983966 27.241983967935873 28.582164328657317 20.177855711422847 72-73 25.641674042230374 26.74168668605386 29.38424579592869 18.232393475787077 74-75 23.77479206653871 28.36852207293666 28.381317978246962 19.475367882277673 76-77 23.754045307443366 26.45954692556634 27.40453074433657 22.381877022653722 78-79 25.127734835582338 27.302502292676532 28.651906196777148 18.91785667496397 80-81 23.144336741468596 30.46076218297703 27.858186163856065 18.53671491169831 82-83 23.545294991224516 26.812474686107734 29.202106115836372 20.440124206831374 84-85 22.99560680944536 26.153212520593083 30.079626578802852 20.771554091158702 86-87 22.179310344827584 28.70344827586207 28.344827586206893 20.772413793103446 88-89 21.186206896551724 30.910344827586204 28.4 19.50344827586207 90-91 23.351724137931036 29.986206896551725 27.46206896551724 19.2 92-93 20.882758620689657 32.15172413793104 28.33103448275862 18.634482758620692 >>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 1.5 18 1.5 19 0.5 20 1.0 21 1.5 22 3.0 23 7.5 24 10.0 25 9.0 26 11.0 27 17.5 28 27.0 29 31.5 30 36.5 31 48.5 32 60.0 33 67.0 34 76.0 35 89.5 36 126.0 37 177.5 38 201.5 39 196.5 40 209.5 41 232.5 42 235.5 43 235.5 44 218.0 45 199.5 46 190.0 47 151.0 48 137.5 49 145.5 50 150.0 51 162.0 52 149.0 53 148.0 54 163.5 55 137.0 56 90.5 57 74.5 58 60.5 59 36.0 60 20.5 61 17.0 62 13.0 63 9.0 64 8.0 65 4.5 66 2.0 67 3.5 68 4.5 69 5.0 70 4.0 71 2.0 72 1.0 73 0.0 74 0.0 75 0.5 76 0.5 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 0.0127942681678608 76-77 0.02588326646822829 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 16.0 71 17.0 72 25.0 73 21.0 74 26.0 75 23.0 76 17.0 77 25.0 78 27.0 79 23.0 80 29.0 81 31.0 82 33.0 83 28.0 84 34.0 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 3625.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.15 #Duplication Level Percentage of deduplicated Percentage of total 1 92.01497192763568 73.75 2 4.023705552089832 6.45 3 1.7779164067373672 4.275 4 0.561447286338116 1.7999999999999998 5 0.43668122270742354 1.7500000000000002 6 0.3119151590767312 1.5 7 0.18714909544603867 1.05 8 0.0 0.0 9 0.1559575795383656 1.125 >10 0.4990642545227698 6.550000000000001 >50 0.031191515907673113 1.7500000000000002 >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 70 1.7500000000000002 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 34 0.8500000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 24 0.6 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 23 0.575 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 19 0.475 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 16 0.4 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 16 0.4 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 14 0.35000000000000003 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 13 0.325 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 12 0.3 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 12 0.3 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 7 0.17500000000000002 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 6 0.15 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 5 0.125 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit CGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGC 5 0.125 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89172 READS because READLEN < 1 Read 89172 spots for ERR6133340.sra Written 89172 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra Rejected 89166 READS because READLEN < 1 Read 89166 spots for ERR6133340.sra Written 89166 spots for ERR6133340.sra SRR ids: ['ERR6133340.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_pkfjz0lh ERR6133340.sra spots: 1783326 blocks: [[1, 89166], [89167, 178332], [178333, 267498], [267499, 356664], [356665, 445830], [445831, 534996], [534997, 624162], [624163, 713328], [713329, 802494], [802495, 891660], [891661, 980826], [980827, 1069992], [1069993, 1159158], [1159159, 1248324], [1248325, 1337490], [1337491, 1426656], [1426657, 1515822], [1515823, 1604988], [1604989, 1694154], [1694155, 1783326]] ERR6133340 file size 389837 ERR6133340 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 ERR6133340 ERR6133340_1.fastq Input file: ERR6133340_1.fastq trimmed: ERR6133340-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 01:01:05 2024 >> started Sat Dec 7 01:01:06 2024 >> done (0.958s) 1783326 reads processed; of these: 420 ( 0.02%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 1782899 (99.98%) reads available; of these: 27929 ( 1.57%) trimmed reads available after processing 1754970 (98.43%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 37 0.00% 19 52 0.00% 20 26 0.00% 21 30 0.00% 22 15 0.00% 23 30 0.00% 24 26 0.00% 25 27 0.00% 26 21 0.00% 27 47 0.00% 28 46 0.00% 29 15 0.00% 30 24 0.00% 31 20 0.00% 32 31 0.00% 33 19 0.00% 34 18 0.00% 35 52 0.00% 36 17 0.00% 37 22 0.00% 38 21 0.00% 39 44 0.00% 40 40 0.00% 41 22 0.00% 42 23 0.00% 43 164 0.01% 44 32 0.00% 45 111 0.01% 46 29 0.00% 47 7 0.00% 48 18 0.00% 49 6 0.00% 50 10 0.00% 51 41 0.00% 52 13 0.00% 53 3 0.00% 54 10 0.00% 55 8 0.00% 56 7 0.00% 57 16 0.00% 58 4 0.00% 59 9 0.00% 60 7 0.00% 61 14 0.00% 62 1 0.00% 63 2 0.00% 64 1 0.00% 65 2 0.00% 66 0 0.00% 67 8 0.00% 68 12 0.00% 69 46 0.00% 70 10635 0.60% 71 9814 0.55% 72 10688 0.60% 73 10036 0.56% 74 9502 0.53% 75 9662 0.54% 76 9290 0.52% 77 10389 0.58% 78 10376 0.58% 79 11034 0.62% 80 10946 0.61% 81 13691 0.77% 82 14110 0.79% 83 12051 0.68% 84 14272 0.80% 85 26 0.00% 86 43 0.00% 87 83 0.00% 88 180 0.01% 89 430 0.02% 90 961 0.05% 91 3333 0.19% 92 20331 1.14% 93 1589710 89.16% 1782899 reads passed initial QC criterion=sequence-density sequence-density=3.86 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=26 prefix-density=3.88 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=30.44 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=4.5 sequence=TTTTCTTCCTTCCAATTTTGTTTGCACAAAAGACAACTTTATTTTCTCTCCATTTTGTCGAGTCATTACACGGATTCCATAAATGATTATCAAGTGGTTCTTATTCGAAGAACCCTTGCCTTTTGTTTAGCTTGAGACTCAATCATCGTGGCTCTAGTATGAATCTAAGGTTTAAATTGAACTGATTCATAGGATCGCAACAAGATAATTTCTATCAGAAAACTACTAGAATTTTGGCTTTCTTTATTTACTAGTAAATAAAGAGTAAATCCGCATTACACACAAAAA 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 01:01:19 Started mapping on | Dec 07 01:01:20 Finished on | Dec 07 01:01:24 Mapping speed, Million of reads per hour | 1604.61 Number of input reads | 1782899 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1031574 Uniquely mapped reads % | 57.86% Average mapped length | 90.70 Number of splices: Total | 54157 Number of splices: Annotated (sjdb) | 45253 Number of splices: GT/AG | 52221 Number of splices: GC/AG | 863 Number of splices: AT/AC | 59 Number of splices: Non-canonical | 1014 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.68 Insertion rate per base | 0.02% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 657571 % of reads mapped to multiple loci | 36.88% Number of reads mapped to too many loci | 58384 % of reads mapped to too many loci | 3.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.83% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 93754 93754 93754 N_multimapping 657571 657571 657571 N_noFeature 80175 89608 988673 N_ambiguous 39297 5873 124 UnstrandedReadsAssigned:912102 PositiveStrandReadsAssigned:936093 NegativeStrandReadsAssigned:42777 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133340 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: ERR6133340-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,782,899 reads, 1,302,793 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 989 rounds 52973 ERR6133340.ke.tsv 35125 ERR6133340.se.tsv 88098 total ==> ERR6133340.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 12 8.9267 PNS24243 293 194 0 0 KQK14069 1603 1504 7 4.75022 KQK14071 474 375 0 0 ==> ERR6133340.se.tsv <== BRADI_1g14170v3 7 BRADI_1g53295v3 5 BRADI_1g59795v3 10 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 23 BRADI_1g48960v3 0 ERR6133340 completed mapping pipeline successfully