Starting /dee2/code/volunteer_pipeline.sh ERR6133493 current disk space = 1544552189952 free memory = 1607671068 ERR6133493 SRAfilesize 7cde0010cbeba7973699a90a3aec82d5 ERR6133493.sra ERR6133493.sra file validated ERR6133493 is single end ERR6133493 is conventional basespace ERR6133493 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133493_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 35.4225 37.0 33.0 37.0 33.0 37.0 2 36.46625 37.0 37.0 37.0 37.0 37.0 3 35.89425 37.0 37.0 37.0 33.0 37.0 4 35.482 37.0 37.0 37.0 33.0 37.0 5 35.51125 37.0 37.0 37.0 33.0 37.0 6 35.90325 37.0 37.0 37.0 33.0 37.0 7 37.7555 40.0 37.0 40.0 33.0 40.0 8 37.7835 40.0 37.0 40.0 33.0 40.0 9 37.8105 40.0 37.0 40.0 33.0 40.0 10-11 37.73975 40.0 37.0 40.0 33.0 40.0 12-13 37.633625 40.0 37.0 40.0 33.0 40.0 14-15 37.568250000000006 40.0 37.0 40.0 33.0 40.0 16-17 37.4435 37.0 37.0 40.0 33.0 40.0 18-19 37.3285 37.0 37.0 40.0 33.0 40.0 20-21 36.9705 37.0 37.0 40.0 33.0 40.0 22-23 36.923625 37.0 37.0 40.0 33.0 40.0 24-25 36.8525 37.0 37.0 40.0 33.0 40.0 26-27 37.156 37.0 37.0 40.0 33.0 40.0 28-29 37.12825 37.0 37.0 40.0 33.0 40.0 30-31 37.074375 37.0 37.0 40.0 33.0 40.0 32-33 36.895250000000004 37.0 37.0 40.0 33.0 40.0 34-35 36.922 37.0 37.0 40.0 33.0 40.0 36-37 36.72475 37.0 37.0 40.0 33.0 40.0 38-39 36.647375 37.0 37.0 40.0 33.0 40.0 40-41 36.4 37.0 37.0 40.0 33.0 40.0 42-43 36.349625 37.0 37.0 40.0 33.0 40.0 44-45 36.389250000000004 37.0 37.0 40.0 33.0 40.0 46-47 36.240125 37.0 37.0 40.0 33.0 40.0 48-49 36.172125 37.0 37.0 38.5 33.0 40.0 50-51 35.984625 37.0 37.0 37.0 33.0 40.0 52-53 35.7215 37.0 35.0 37.0 33.0 40.0 54-55 35.55375 37.0 33.0 37.0 33.0 40.0 56-57 35.358374999999995 37.0 33.0 37.0 33.0 40.0 58-59 34.39675 37.0 33.0 37.0 27.0 37.0 60-61 34.849374999999995 37.0 33.0 37.0 33.0 37.0 62-63 34.7605 37.0 33.0 37.0 33.0 37.0 64-65 34.67 37.0 33.0 37.0 33.0 37.0 66-67 34.732124999999996 37.0 33.0 37.0 33.0 37.0 68-69 33.973 35.0 33.0 37.0 30.0 37.0 70-71 34.021149007038716 35.0 33.0 37.0 27.0 37.0 72-73 34.3615448179783 37.0 33.0 37.0 30.0 37.0 74-75 34.29907385918693 37.0 33.0 37.0 30.0 37.0 76-77 34.06838980472472 37.0 33.0 37.0 27.0 37.0 78-79 34.04200810868292 37.0 33.0 37.0 27.0 37.0 80-81 33.95996837958409 37.0 33.0 37.0 27.0 37.0 82-83 33.848880820562954 37.0 33.0 37.0 27.0 37.0 84-85 33.713167376596765 37.0 33.0 37.0 27.0 37.0 86-87 33.635237068965516 37.0 33.0 37.0 27.0 37.0 88-89 33.77963362068965 37.0 33.0 37.0 27.0 37.0 90-91 33.38119612068965 35.0 33.0 37.0 27.0 37.0 92-93 33.404229525862064 35.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 8.0 21 10.0 22 8.0 23 11.0 24 29.0 25 21.0 26 20.0 27 40.0 28 45.0 29 74.0 30 84.0 31 91.0 32 145.0 33 177.0 34 266.0 35 440.0 36 768.0 37 1070.0 38 662.0 39 31.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.925 4.5249999999999995 5.8999999999999995 7.6499999999999995 2 60.150000000000006 23.0 10.875 5.975 3 30.725 36.325 17.974999999999998 14.975 4 30.725 26.224999999999998 21.2 21.85 5 22.95 28.475 28.15 20.424999999999997 6 19.325 35.275 26.450000000000003 18.95 7 32.425 29.849999999999998 20.95 16.775000000000002 8 29.9 30.025000000000002 23.400000000000002 16.675 9 24.3 26.1 28.825 20.775 10-11 25.474999999999998 26.887499999999996 27.474999999999998 20.1625 12-13 27.6375 26.825 27.1125 18.425 14-15 22.400000000000002 29.425 28.787499999999998 19.3875 16-17 24.15 31.05 26.087500000000002 18.712500000000002 18-19 23.7125 27.0125 27.3375 21.9375 20-21 24.32804100512564 25.87823477934742 28.703587948493563 21.09013626703338 22-23 26.937499999999996 24.175 27.775 21.1125 24-25 24.887500000000003 27.3875 27.6 20.125 26-27 25.137500000000003 26.337500000000002 30.25 18.275 28-29 25.887500000000003 25.9625 28.0875 20.0625 30-31 25.912499999999998 25.7125 27.712500000000002 20.6625 32-33 24.1625 27.8375 27.712500000000002 20.2875 34-35 24.587500000000002 27.05 27.875 20.4875 36-37 24.2875 26.0375 28.625 21.05 38-39 25.040650406504067 25.82864290181363 29.731081926203878 19.399624765478425 40-41 24.52169563586345 25.70964111541828 28.335625859697387 21.433037389020885 42-43 23.96549568696087 27.890986373296663 28.62857857232154 19.51493936742093 44-45 23.0625 26.8125 30.012499999999996 20.1125 46-47 25.637500000000003 25.45 28.1625 20.75 48-49 23.925 25.2 31.3125 19.5625 50-51 23.7 26.775 28.7 20.825 52-53 25.650976464697045 28.067100650976464 26.039058587881826 20.24286429644467 54-55 24.5 25.874999999999996 30.587500000000002 19.037499999999998 56-57 25.374999999999996 26.05 28.625 19.950000000000003 58-59 24.2375 25.687500000000004 29.725 20.349999999999998 60-61 23.4375 27.212500000000002 29.012500000000003 20.3375 62-63 22.325 29.037499999999998 30.887500000000003 17.75 64-65 22.45 28.487499999999997 29.6625 19.400000000000002 66-67 23.2875 27.8125 29.075 19.825 68-69 21.837500000000002 28.15 28.4125 21.6 70-71 23.31411381298571 26.046628227625973 30.070193030834798 20.56906492855352 72-73 24.84472049689441 25.681328431993915 29.97845100773229 19.49550006337939 74-75 24.015345268542198 26.994884910485933 29.335038363171357 19.654731457800512 76-77 23.01044756868309 25.551399458274215 29.472462272668643 21.96569070037405 78-79 24.225865209471767 26.20348685922456 30.418943533697636 19.151704397606036 80-81 24.047806671920146 28.53953244024166 29.393223010244284 18.019437877593905 82-83 22.586206896551726 27.02917771883289 29.92042440318302 20.464190981432363 84-85 22.35499462943072 24.01987110633727 33.04242749731471 20.582706766917294 86-87 21.511314655172413 27.38415948275862 31.47898706896552 19.62553879310345 88-89 20.60883620689655 29.445043103448278 30.482219827586203 19.463900862068968 90-91 23.248922413793103 27.45150862068966 30.105064655172413 19.19450431034483 92-93 21.43049568965517 31.53286637931034 27.85560344827586 19.181034482758623 >>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 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.5 17 9.0 18 12.0 19 4.5 20 2.5 21 2.5 22 2.0 23 5.5 24 7.0 25 8.0 26 16.5 27 20.0 28 25.5 29 34.0 30 32.5 31 37.5 32 55.5 33 74.5 34 96.0 35 116.0 36 127.5 37 155.0 38 188.0 39 183.5 40 194.0 41 220.0 42 229.5 43 239.0 44 205.5 45 184.5 46 191.5 47 158.0 48 152.0 49 165.5 50 166.5 51 152.5 52 137.0 53 141.5 54 114.5 55 75.5 56 52.0 57 44.0 58 47.0 59 41.5 60 32.5 61 33.0 62 37.0 63 29.5 64 25.5 65 22.0 66 16.0 67 14.0 68 11.0 69 8.5 70 6.0 71 8.0 72 6.0 73 2.5 74 0.5 75 0.0 76 0.0 77 0.5 78 0.5 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 0.0125 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 0.0625 40-41 0.0375 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.15 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 0.0 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 22.0 71 26.0 72 15.0 73 15.0 74 24.0 75 14.0 76 15.0 77 20.0 78 12.0 79 21.0 80 18.0 81 17.0 82 22.0 83 23.0 84 24.0 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 3712.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.60000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 92.64888337468983 74.675 2 4.249379652605459 6.8500000000000005 3 1.1476426799007444 2.775 4 0.5583126550868486 1.7999999999999998 5 0.15508684863523575 0.625 6 0.18610421836228289 0.8999999999999999 7 0.18610421836228289 1.05 8 0.15508684863523575 1.0 9 0.12406947890818859 0.8999999999999999 >10 0.5583126550868486 8.125 >50 0.031017369727047148 1.3 >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 TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 52 1.3 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 41 1.0250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 32 0.8 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 23 0.575 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 21 0.525 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 21 0.525 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 19 0.475 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 19 0.475 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 17 0.42500000000000004 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 17 0.42500000000000004 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 15 0.375 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 14 0.35000000000000003 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 9 0.22499999999999998 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 8 0.2 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 6 0.15 No Hit CATTACTGATGGAGTGATGGTCCATAGAGCATTAGTTTCACTACCTTCGC 6 0.15 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGTTCA 6 0.15 No Hit GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAAATTCGTTGACAA 6 0.15 No Hit GGGCCATTCACAGACACACACAACTACACAAGAGCTCTCAGCTGCTGCCC 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 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 0.0125 0.0 0.0 0.0 0.0 24-25 0.037500000000000006 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0125 0.0 34-35 0.1 0.0 0.0 0.025 0.0 36-37 0.1 0.0 0.0 0.025 0.0 38-39 0.1 0.0 0.0 0.025 0.0 40-41 0.1375 0.0 0.0 0.025 0.0 42-43 0.175 0.0 0.0 0.025 0.0 44-45 0.175 0.0 0.0 0.025 0.0 46-47 0.175 0.0 0.0 0.025 0.0 48-49 0.175 0.0 0.0 0.025 0.0 50-51 0.175 0.0 0.0 0.025 0.0 52-53 0.2 0.0 0.0 0.025 0.0 54-55 0.2 0.0 0.0 0.025 0.0 56-57 0.2 0.0 0.0 0.025 0.0 58-59 0.2 0.0 0.0 0.025 0.0 60-61 0.2 0.0 0.0 0.025 0.0 62-63 0.2 0.0 0.0 0.025 0.0 64-65 0.2 0.0 0.0 0.025 0.0 66-67 0.2 0.0 0.0 0.025 0.0 68-69 0.2 0.0 0.0 0.025 0.0 70-71 0.2 0.0 0.0 0.025 0.0 72-73 0.2 0.0 0.0 0.025 0.0 74-75 0.2 0.0 0.0 0.025 0.0 76-77 0.2 0.0 0.0 0.025 0.0 78-79 0.2 0.0 0.0 0.025 0.0 80-81 0.2 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGTTCAA 15 9.266554E-4 85.6625 3 GGCGTTC 15 9.266554E-4 85.6625 1 CAACCTA 15 9.266554E-4 85.6625 7 AACCTAA 15 9.266554E-4 85.6625 8 TCAACCT 15 9.266554E-4 85.6625 6 GTTCAAC 15 9.266554E-4 85.6625 4 GCGTTCA 15 9.266554E-4 85.6625 2 ACCTAAA 15 9.266554E-4 85.6625 9 GGGAAAT 20 0.0029028433 64.24687 1 >>END_MODULE Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145004 READS because READLEN < 1 Read 145004 spots for ERR6133493.sra Written 145004 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra Rejected 145003 READS because READLEN < 1 Read 145003 spots for ERR6133493.sra Written 145003 spots for ERR6133493.sra SRR ids: ['ERR6133493.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jg9aam2h ERR6133493.sra spots: 2900061 blocks: [[1, 145003], [145004, 290006], [290007, 435009], [435010, 580012], [580013, 725015], [725016, 870018], [870019, 1015021], [1015022, 1160024], [1160025, 1305027], [1305028, 1450030], [1450031, 1595033], [1595034, 1740036], [1740037, 1885039], [1885040, 2030042], [2030043, 2175045], [2175046, 2320048], [2320049, 2465051], [2465052, 2610054], [2610055, 2755057], [2755058, 2900061]] ERR6133493 file size 637008 ERR6133493 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 ERR6133493 ERR6133493_1.fastq Input file: ERR6133493_1.fastq trimmed: ERR6133493-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 07:14:00 2024 >> started Sat Dec 7 07:14:02 2024 >> done (1.634s) 2900061 reads processed; of these: 191 ( 0.01%) short reads filtered out after trimming by size control 31 ( 0.00%) empty reads filtered out after trimming by size control 2899839 (99.99%) reads available; of these: 48230 ( 1.66%) trimmed reads available after processing 2851609 (98.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 38 0.00% 19 52 0.00% 20 31 0.00% 21 47 0.00% 22 48 0.00% 23 8 0.00% 24 15 0.00% 25 7 0.00% 26 20 0.00% 27 16 0.00% 28 49 0.00% 29 98 0.00% 30 24 0.00% 31 24 0.00% 32 25 0.00% 33 23 0.00% 34 40 0.00% 35 330 0.01% 36 381 0.01% 37 52 0.00% 38 51 0.00% 39 165 0.01% 40 95 0.00% 41 52 0.00% 42 14 0.00% 43 20 0.00% 44 36 0.00% 45 18 0.00% 46 24 0.00% 47 19 0.00% 48 13 0.00% 49 15 0.00% 50 12 0.00% 51 48 0.00% 52 22 0.00% 53 13 0.00% 54 5 0.00% 55 9 0.00% 56 10 0.00% 57 14 0.00% 58 17 0.00% 59 17 0.00% 60 23 0.00% 61 22 0.00% 62 3 0.00% 63 2 0.00% 64 2 0.00% 65 8 0.00% 66 12 0.00% 67 26 0.00% 68 37 0.00% 69 102 0.00% 70 13928 0.48% 71 13435 0.46% 72 15065 0.52% 73 13142 0.45% 74 13224 0.46% 75 13198 0.46% 76 11711 0.40% 77 12384 0.43% 78 13879 0.48% 79 14871 0.51% 80 13865 0.48% 81 15243 0.53% 82 16922 0.58% 83 17529 0.60% 84 13977 0.48% 85 107 0.00% 86 183 0.01% 87 290 0.01% 88 507 0.02% 89 1021 0.04% 90 2060 0.07% 91 6408 0.22% 92 32021 1.10% 93 2642615 91.13% 2899839 reads passed initial QC criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=32 prefix-density=0.43 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=202.77 fanout-score-rank=1 prefix-density=0.56 prefix-fanout=5.3 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 07:15:08 Started mapping on | Dec 07 07:15:17 Finished on | Dec 07 07:15:22 Mapping speed, Million of reads per hour | 2087.88 Number of input reads | 2899839 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 2015553 Uniquely mapped reads % | 69.51% Average mapped length | 91.16 Number of splices: Total | 85308 Number of splices: Annotated (sjdb) | 69577 Number of splices: GT/AG | 81068 Number of splices: GC/AG | 2020 Number of splices: AT/AC | 27 Number of splices: Non-canonical | 2193 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.05% Deletion average length | 1.83 Insertion rate per base | 0.02% Insertion average length | 1.77 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 805725 % of reads mapped to multiple loci | 27.79% Number of reads mapped to too many loci | 20550 % of reads mapped to too many loci | 0.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.94% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 78561 78561 78561 N_multimapping 805725 805725 805725 N_noFeature 137774 158139 1923383 N_ambiguous 80405 8523 336 UnstrandedReadsAssigned:1797374 PositiveStrandReadsAssigned:1848891 NegativeStrandReadsAssigned:91834 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133493 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: ERR6133493-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,899,839 reads, 2,373,098 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 990 rounds 52973 ERR6133493.ke.tsv 35125 ERR6133493.se.tsv 88098 total ==> ERR6133493.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 46 19.1534 PNS24243 293 194 0 0 KQK14069 1603 1504 71 26.9682 KQK14071 474 375 0 0 ==> ERR6133493.se.tsv <== BRADI_1g14170v3 71 BRADI_1g53295v3 32 BRADI_1g59795v3 40 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 21 BRADI_1g74790v3 15 BRADI_1g09890v3 0 BRADI_1g77505v3 43 BRADI_1g48960v3 0 ERR6133493 completed mapping pipeline successfully