Starting /dee2/code/volunteer_pipeline.sh ERR6133326 current disk space = 1548193456128 free memory = 1598790976 ERR6133326 SRAfilesize 9e8899671b5d642c77364a6cb43008bf ERR6133326.sra ERR6133326.sra file validated ERR6133326 is single end ERR6133326 is conventional basespace ERR6133326 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133326_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4045 37.0 37.0 37.0 33.0 37.0 2 36.5355 37.0 37.0 37.0 37.0 37.0 3 36.37875 37.0 37.0 37.0 37.0 37.0 4 36.43175 37.0 37.0 37.0 37.0 37.0 5 36.4385 37.0 37.0 37.0 37.0 37.0 6 36.527 37.0 37.0 37.0 37.0 37.0 7 38.6325 40.0 37.0 40.0 37.0 40.0 8 38.69575 40.0 37.0 40.0 37.0 40.0 9 38.71275 40.0 37.0 40.0 37.0 40.0 10-11 38.736125 40.0 37.0 40.0 37.0 40.0 12-13 38.767875000000004 40.0 37.0 40.0 37.0 40.0 14-15 38.710750000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.685125 40.0 37.0 40.0 37.0 40.0 18-19 38.732749999999996 40.0 37.0 40.0 37.0 40.0 20-21 38.556875000000005 40.0 37.0 40.0 37.0 40.0 22-23 38.671375 40.0 37.0 40.0 37.0 40.0 24-25 38.532 40.0 37.0 40.0 37.0 40.0 26-27 38.469750000000005 40.0 37.0 40.0 37.0 40.0 28-29 38.49375 40.0 37.0 40.0 37.0 40.0 30-31 38.425625 40.0 37.0 40.0 37.0 40.0 32-33 38.38849999999999 40.0 37.0 40.0 37.0 40.0 34-35 38.279875000000004 40.0 37.0 40.0 37.0 40.0 36-37 38.159125 40.0 37.0 40.0 37.0 40.0 38-39 37.967124999999996 40.0 37.0 40.0 37.0 40.0 40-41 37.8495 40.0 37.0 40.0 35.0 40.0 42-43 37.808875 37.0 37.0 40.0 37.0 40.0 44-45 37.574124999999995 37.0 37.0 40.0 33.0 40.0 46-47 37.41575 37.0 37.0 40.0 33.0 40.0 48-49 37.292875 37.0 37.0 40.0 33.0 40.0 50-51 37.061625 37.0 37.0 40.0 33.0 40.0 52-53 36.909375 37.0 37.0 40.0 33.0 40.0 54-55 36.6955 37.0 37.0 37.0 33.0 40.0 56-57 36.525 37.0 37.0 37.0 33.0 40.0 58-59 36.23075 37.0 37.0 37.0 33.0 40.0 60-61 35.997749999999996 37.0 37.0 37.0 33.0 38.5 62-63 35.545500000000004 37.0 33.0 37.0 33.0 37.0 64-65 35.208875 37.0 33.0 37.0 33.0 37.0 66-67 35.061 37.0 33.0 37.0 33.0 37.0 68-69 33.758125 35.0 33.0 37.0 30.0 37.0 70-71 33.57805433140267 33.0 33.0 37.0 30.0 37.0 72-73 33.98571246314393 33.0 33.0 37.0 33.0 37.0 74-75 33.88324930070317 33.0 33.0 37.0 33.0 37.0 76-77 33.57057001465267 33.0 33.0 37.0 27.0 37.0 78-79 33.34801589968183 33.0 33.0 37.0 27.0 37.0 80-81 32.956835999609886 33.0 33.0 37.0 27.0 37.0 82-83 32.92042731450337 33.0 33.0 37.0 27.0 37.0 84-85 32.30236093903255 33.0 33.0 35.0 27.0 37.0 86-87 32.0511679644049 33.0 33.0 33.0 27.0 37.0 88-89 31.996384872080093 33.0 33.0 33.0 27.0 37.0 90-91 31.11179087875417 33.0 30.0 33.0 24.5 37.0 92-93 30.294215795328142 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 3.0 22 4.0 23 3.0 24 3.0 25 5.0 26 9.0 27 18.0 28 16.0 29 26.0 30 37.0 31 46.0 32 70.0 33 96.0 34 209.0 35 609.0 36 1089.0 37 1449.0 38 292.0 39 15.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 63.87500000000001 10.174999999999999 8.6 17.349999999999998 2 45.95 26.75 16.625 10.674999999999999 3 30.225 37.05 17.849999999999998 14.875 4 30.5 26.924999999999997 21.224999999999998 21.349999999999998 5 22.75 27.750000000000004 29.875 19.625 6 19.075 33.800000000000004 29.049999999999997 18.075 7 30.099999999999998 28.225 24.425 17.25 8 27.3 27.675 27.0 18.025 9 25.8 26.0 29.45 18.75 10-11 23.5625 27.474999999999998 29.4 19.5625 12-13 24.3 27.525 29.2875 18.8875 14-15 22.0 27.200000000000003 31.2125 19.5875 16-17 23.625 29.7375 26.7125 19.925 18-19 22.8125 25.8 30.337500000000002 21.05 20-21 24.2375 26.5625 29.075 20.125 22-23 25.412499999999998 24.337500000000002 29.075 21.175 24-25 24.7375 25.874999999999996 29.012500000000003 20.375 26-27 23.375 25.95 30.562499999999996 20.1125 28-29 23.150000000000002 26.887499999999996 28.9125 21.05 30-31 24.1375 26.137500000000003 28.9375 20.7875 32-33 23.0625 26.674999999999997 30.0375 20.225 34-35 23.9375 27.462500000000002 27.8125 20.7875 36-37 23.9875 27.9125 27.425 20.674999999999997 38-39 24.087500000000002 25.7625 29.462500000000002 20.6875 40-41 24.975 26.375 28.349999999999998 20.3 42-43 24.462500000000002 27.500000000000004 29.1875 18.85 44-45 22.1875 28.7375 29.049999999999997 20.025000000000002 46-47 24.0 26.875 28.4125 20.7125 48-49 23.75 26.7625 29.9625 19.525000000000002 50-51 22.6375 27.8625 29.862499999999997 19.6375 52-53 25.0625 27.8875 28.487499999999997 18.5625 54-55 22.900000000000002 29.462500000000002 28.975 18.6625 56-57 24.337500000000002 26.575 29.262500000000003 19.825 58-59 23.5 27.375 28.799999999999997 20.325 60-61 24.5125 27.5875 28.050000000000004 19.85 62-63 22.237499999999997 29.212500000000002 29.812499999999996 18.7375 64-65 22.125 29.912499999999998 29.275000000000002 18.6875 66-67 23.775 28.4375 28.925 18.862499999999997 68-69 21.9375 28.725 29.212500000000002 20.125 70-71 23.409860745201357 28.164596662903023 28.64132480240873 19.784217789486892 72-73 24.546722454672246 27.41219728667427 28.971725624445288 19.069354634208192 74-75 23.278520041109967 27.440904419321686 29.753340184994858 19.527235354573484 76-77 21.577574967405475 27.314211212516298 30.273794002607563 20.834419817470664 78-79 22.418567849136224 27.50890149017539 30.185942239219305 19.886588421469074 80-81 22.725450901803608 29.24515698062792 28.63059452237809 19.39879759519038 82-83 21.80114099429503 27.574028796522683 29.54360228198859 21.081227927193698 84-85 22.16231162726393 27.180976081847092 31.14890087100788 19.5078114198811 86-87 21.621245828698555 29.254727474972192 28.35094549499444 20.77308120133482 88-89 20.64794215795328 29.57452725250278 30.255839822024473 19.521690767519466 90-91 22.58064516129032 30.39488320355951 28.045050055617356 18.979421579532815 92-93 21.0650723025584 32.80033370411569 26.946607341490548 19.187986651835374 >>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 3.5 22 5.5 23 8.0 24 11.0 25 11.5 26 15.5 27 20.5 28 28.0 29 34.5 30 40.0 31 37.5 32 52.5 33 81.5 34 93.0 35 101.0 36 138.5 37 207.0 38 224.0 39 205.5 40 225.5 41 235.0 42 254.0 43 279.5 44 224.5 45 182.0 46 186.0 47 167.5 48 144.5 49 147.5 50 158.0 51 155.5 52 144.0 53 144.0 54 120.5 55 78.5 56 71.5 57 72.0 58 48.0 59 21.0 60 18.0 61 13.0 62 7.5 63 8.0 64 5.5 65 5.0 66 6.0 67 4.0 68 5.5 69 5.5 70 1.5 71 0.0 72 0.0 73 0.5 74 1.5 75 1.0 76 0.5 77 0.5 78 0.0 79 0.5 80 0.5 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 0.025687130747495505 76-77 0.026068821689259645 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 29.0 71 15.0 72 25.0 73 23.0 74 30.0 75 29.0 76 26.0 77 22.0 78 19.0 79 28.0 80 23.0 81 34.0 82 32.0 83 28.0 84 41.0 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 3596.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.875 #Duplication Level Percentage of deduplicated Percentage of total 1 91.17370892018779 72.82499999999999 2 4.663536776212832 7.449999999999999 3 1.6275430359937404 3.9 4 0.8450704225352111 2.7 5 0.4068857589984351 1.625 6 0.28169014084507044 1.35 7 0.18779342723004694 1.05 8 0.06259780907668232 0.4 9 0.1564945226917058 1.125 >10 0.5946791862284819 7.575 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 27 0.675 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 20 0.5 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 20 0.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 19 0.475 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 18 0.44999999999999996 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 17 0.42500000000000004 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 17 0.42500000000000004 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 14 0.35000000000000003 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 13 0.325 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 12 0.3 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 12 0.3 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 9 0.22499999999999998 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 7 0.17500000000000002 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 7 0.17500000000000002 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 7 0.17500000000000002 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 6 0.15 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 6 0.15 No Hit GCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAG 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit CGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATG 5 0.125 No Hit CGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGG 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 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 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 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 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 20 0.0029988212 63.721878 1 >>END_MODULE Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra Rejected 59532 READS because READLEN < 1 Read 59532 spots for ERR6133326.sra Written 59532 spots for ERR6133326.sra Rejected 59518 READS because READLEN < 1 Read 59518 spots for ERR6133326.sra Written 59518 spots for ERR6133326.sra SRR ids: ['ERR6133326.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fqq4o326 ERR6133326.sra spots: 1190374 blocks: [[1, 59518], [59519, 119036], [119037, 178554], [178555, 238072], [238073, 297590], [297591, 357108], [357109, 416626], [416627, 476144], [476145, 535662], [535663, 595180], [595181, 654698], [654699, 714216], [714217, 773734], [773735, 833252], [833253, 892770], [892771, 952288], [952289, 1011806], [1011807, 1071324], [1071325, 1130842], [1130843, 1190374]] ERR6133326 file size 259388 ERR6133326 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 ERR6133326 ERR6133326_1.fastq Input file: ERR6133326_1.fastq trimmed: ERR6133326-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 00:43:24 2024 >> started Sat Dec 7 00:43:25 2024 >> done (0.713s) 1190374 reads processed; of these: 310 ( 0.03%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 1190057 (99.97%) reads available; of these: 17998 ( 1.51%) trimmed reads available after processing 1172059 (98.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 22 0.00% 19 38 0.00% 20 21 0.00% 21 18 0.00% 22 14 0.00% 23 19 0.00% 24 21 0.00% 25 11 0.00% 26 9 0.00% 27 15 0.00% 28 21 0.00% 29 16 0.00% 30 12 0.00% 31 12 0.00% 32 24 0.00% 33 19 0.00% 34 12 0.00% 35 32 0.00% 36 8 0.00% 37 2 0.00% 38 23 0.00% 39 38 0.00% 40 45 0.00% 41 22 0.00% 42 15 0.00% 43 17 0.00% 44 18 0.00% 45 12 0.00% 46 17 0.00% 47 6 0.00% 48 8 0.00% 49 7 0.00% 50 13 0.00% 51 65 0.01% 52 13 0.00% 53 4 0.00% 54 10 0.00% 55 5 0.00% 56 5 0.00% 57 19 0.00% 58 11 0.00% 59 7 0.00% 60 12 0.00% 61 5 0.00% 62 0 0.00% 63 1 0.00% 64 0 0.00% 65 1 0.00% 66 1 0.00% 67 2 0.00% 68 7 0.00% 69 38 0.00% 70 7151 0.60% 71 6703 0.56% 72 7114 0.60% 73 7037 0.59% 74 6722 0.56% 75 6519 0.55% 76 6380 0.54% 77 6921 0.58% 78 7157 0.60% 79 7739 0.65% 80 7497 0.63% 81 9420 0.79% 82 9884 0.83% 83 8868 0.75% 84 10036 0.84% 85 7 0.00% 86 24 0.00% 87 45 0.00% 88 107 0.01% 89 262 0.02% 90 649 0.05% 91 2203 0.19% 92 13105 1.10% 93 1057714 88.88% 1190057 reads passed initial QC criterion=sequence-density sequence-density=3.45 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=29 prefix-density=3.47 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=31.78 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=1.5 sequence=CAAGGAAGGCGTCGCCAACGGAACCCTCAAGCTCGTGGGCGGCCACTACGACTTCGTCTCCGGCAAGTTCGACACATGGGAGCTCTAAGTCCTCTCATCCGGTTAACTCCTATACATACAACGTATACTTATACATACAGATATGGAGATGACCCTACAGATCGATCCATTGATGTGGATGCGATGCCATGGAGTATATGTACTCGCTATTTTCCAGTACTGCATGCCGGATGGCTCGATGTGAATTTGTAATAAGCAATAGAAGTTTCTACCATTTTCTGACGTGGGGTTGTACTTGTGATGCGTAATTTGGTCATCTTGTGACCAAAAGACATCAACTATATAATTATAATACCATTTTCATCAAGACTCTGTATTTG 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 00:43:37 Started mapping on | Dec 07 00:43:37 Finished on | Dec 07 00:43:40 Mapping speed, Million of reads per hour | 1428.07 Number of input reads | 1190057 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 661142 Uniquely mapped reads % | 55.56% Average mapped length | 90.58 Number of splices: Total | 28201 Number of splices: Annotated (sjdb) | 23399 Number of splices: GT/AG | 27195 Number of splices: GC/AG | 505 Number of splices: AT/AC | 48 Number of splices: Non-canonical | 453 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.05% Deletion average length | 1.71 Insertion rate per base | 0.01% Insertion average length | 1.63 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 456960 % of reads mapped to multiple loci | 38.40% Number of reads mapped to too many loci | 37862 % of reads mapped to too many loci | 3.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.70% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 71955 71955 71955 N_multimapping 456960 456960 456960 N_noFeature 54624 60553 634878 N_ambiguous 24018 3663 106 UnstrandedReadsAssigned:582500 PositiveStrandReadsAssigned:596926 NegativeStrandReadsAssigned:26158 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133326 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: ERR6133326-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,190,057 reads, 884,772 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 861 rounds 52973 ERR6133326.ke.tsv 35125 ERR6133326.se.tsv 88098 total ==> ERR6133326.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 14 15.3028 PNS24243 293 194 0 0 KQK14069 1603 1504 4 3.98849 KQK14071 474 375 0 0 ==> ERR6133326.se.tsv <== BRADI_1g14170v3 4 BRADI_1g53295v3 5 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 8 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 10 BRADI_1g48960v3 0 ERR6133326 completed mapping pipeline successfully