Starting /dee2/code/volunteer_pipeline.sh ERR6133460 current disk space = 1545382039552 free memory = 1440804620 ERR6133460 SRAfilesize 55358a23ddf1ef39749e67a667683bd2 ERR6133460.sra ERR6133460.sra file validated ERR6133460 is single end ERR6133460 is conventional basespace ERR6133460 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133460_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 34.649 37.0 33.0 37.0 33.0 37.0 2 36.14575 37.0 37.0 37.0 33.0 37.0 3 35.1615 37.0 33.0 37.0 33.0 37.0 4 34.7655 37.0 33.0 37.0 27.0 37.0 5 34.69075 37.0 33.0 37.0 27.0 37.0 6 35.0825 37.0 37.0 37.0 33.0 37.0 7 36.4995 37.0 37.0 40.0 33.0 40.0 8 36.8655 37.0 37.0 40.0 33.0 40.0 9 36.955 37.0 37.0 40.0 33.0 40.0 10-11 36.874375 37.0 37.0 40.0 33.0 40.0 12-13 36.750875 37.0 37.0 40.0 33.0 40.0 14-15 36.645625 37.0 37.0 40.0 33.0 40.0 16-17 36.561375 37.0 37.0 40.0 33.0 40.0 18-19 36.220875 37.0 37.0 40.0 33.0 40.0 20-21 36.169 37.0 35.0 40.0 33.0 40.0 22-23 35.82825 37.0 33.0 40.0 33.0 40.0 24-25 35.91525 37.0 35.0 40.0 33.0 40.0 26-27 36.10225 37.0 35.0 40.0 33.0 40.0 28-29 36.075375 37.0 33.0 40.0 33.0 40.0 30-31 36.109 37.0 33.0 40.0 33.0 40.0 32-33 36.124375 37.0 33.0 40.0 33.0 40.0 34-35 35.951499999999996 37.0 33.0 40.0 33.0 40.0 36-37 35.906625 37.0 33.0 40.0 33.0 40.0 38-39 35.908500000000004 37.0 33.0 40.0 33.0 40.0 40-41 35.734375 37.0 33.0 40.0 33.0 40.0 42-43 35.772625000000005 37.0 33.0 40.0 33.0 40.0 44-45 35.536500000000004 37.0 33.0 38.5 33.0 40.0 46-47 35.408625 37.0 33.0 37.0 33.0 40.0 48-49 35.4135 37.0 33.0 37.0 33.0 40.0 50-51 35.267125 37.0 33.0 37.0 33.0 40.0 52-53 34.982625 37.0 33.0 37.0 30.0 40.0 54-55 34.818 37.0 33.0 37.0 27.0 40.0 56-57 34.721375 37.0 33.0 37.0 27.0 37.0 58-59 34.139125 37.0 33.0 37.0 27.0 37.0 60-61 34.283249999999995 37.0 33.0 37.0 27.0 37.0 62-63 34.164875 37.0 33.0 37.0 27.0 37.0 64-65 34.078125 37.0 33.0 37.0 27.0 37.0 66-67 33.762125 37.0 33.0 37.0 27.0 37.0 68-69 33.044125 35.0 33.0 37.0 27.0 37.0 70-71 33.15399648594378 33.0 33.0 37.0 27.0 37.0 72-73 33.54673709422859 37.0 33.0 37.0 27.0 37.0 74-75 33.572992765826946 37.0 33.0 37.0 27.0 37.0 76-77 33.59327209484316 37.0 33.0 37.0 27.0 37.0 78-79 33.57454341329994 37.0 33.0 37.0 27.0 37.0 80-81 33.429400374956515 37.0 33.0 37.0 27.0 37.0 82-83 33.25568395037902 33.0 33.0 37.0 27.0 37.0 84-85 33.112092030824485 33.0 33.0 37.0 27.0 37.0 86-87 33.02231793265466 33.0 33.0 37.0 27.0 37.0 88-89 33.13886713651788 33.0 33.0 37.0 27.0 37.0 90-91 32.78021404333072 33.0 33.0 37.0 27.0 37.0 92-93 32.8566953797964 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 13.0 21 12.0 22 20.0 23 25.0 24 35.0 25 47.0 26 47.0 27 57.0 28 78.0 29 86.0 30 112.0 31 151.0 32 176.0 33 210.0 34 292.0 35 506.0 36 798.0 37 901.0 38 430.0 39 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.1 3.45 2.9250000000000003 6.525 2 70.05 17.25 7.85 4.8500000000000005 3 36.65 38.475 14.274999999999999 10.6 4 33.15 28.025 18.65 20.175 5 24.9 31.674999999999997 25.224999999999998 18.2 6 20.45 36.525 25.35 17.675 7 35.55 28.65 20.0 15.8 8 30.3 31.35 21.925 16.425 9 27.500000000000004 28.799999999999997 25.2 18.5 10-11 27.3875 26.775 27.3375 18.5 12-13 28.9 26.137500000000003 26.474999999999998 18.4875 14-15 22.7 28.875 28.762500000000003 19.662499999999998 16-17 24.8 31.2875 25.1875 18.725 18-19 24.775 28.025 26.075 21.125 20-21 25.26263131565783 26.725862931465734 27.063531765882942 20.947973986993496 22-23 26.6125 24.25 26.4625 22.675 24-25 25.887500000000003 24.575 27.6375 21.9 26-27 25.5 24.8625 29.7125 19.925 28-29 25.724999999999998 26.450000000000003 27.675 20.150000000000002 30-31 27.700000000000003 25.162499999999998 26.0125 21.125 32-33 24.725 27.487499999999997 27.0625 20.724999999999998 34-35 26.05 25.424999999999997 27.425 21.099999999999998 36-37 25.2375 24.825 28.15 21.7875 38-39 26.465808226028255 24.753094136767096 29.416177022127766 19.364920615076883 40-41 26.190773846730842 25.428178522315285 26.790848856107015 21.590198774846854 42-43 25.319148936170212 28.035043804755944 26.670838548185234 19.97496871088861 44-45 24.128016002000248 24.953119139892486 30.078759844980624 20.840105013126642 46-47 25.074999999999996 24.075 27.9375 22.912499999999998 48-49 25.1 24.5625 30.049999999999997 20.2875 50-51 24.875 26.437500000000004 28.275 20.4125 52-53 24.893510398396394 26.685041343021798 27.31145076421949 21.109997494362315 54-55 23.455863965991497 28.28207051762941 28.394598649662417 19.86746686671668 56-57 26.0375 26.05 28.425 19.4875 58-59 23.8375 25.55 29.1125 21.5 60-61 24.099999999999998 25.2875 29.2875 21.325 62-63 22.625 28.1875 30.362499999999997 18.825 64-65 22.8375 26.674999999999997 29.45 21.0375 66-67 25.3125 27.3 28.299999999999997 19.0875 68-69 23.102887860982623 26.878359794974372 28.2410301287661 21.77772221527691 70-71 24.28607214428858 25.613727454909817 27.90581162324649 22.194388777555112 72-73 26.41057934508816 24.811083123425693 28.45088161209068 20.327455919395465 74-75 24.10872313527181 27.964601769911507 28.1795195954488 19.74715549936789 76-77 22.19679633867277 25.184337655733536 30.05339435545385 22.56547165013984 78-79 23.328228688106176 25.331801939765185 30.704441041347625 20.63552833078101 80-81 23.89767322277928 28.705489137421264 29.21969404807816 18.1771435917213 82-83 23.828630597980844 25.95133316075589 29.12244369660885 21.097592544654415 84-85 23.614552092841308 24.657712869996086 30.890598513495892 20.83713652366671 86-87 23.153223701383453 28.256329939963454 29.6528321587053 18.937614199947795 88-89 21.978595666927696 29.313495170973635 29.35264943878883 19.35525972330984 90-91 25.463325502479773 27.303576089793786 29.248238057948317 17.984860349778124 92-93 22.239624119028974 29.169929522317933 29.665883581310364 18.92456277734273 >>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 0.5 17 9.0 18 10.0 19 1.5 20 1.5 21 4.5 22 3.5 23 4.5 24 6.0 25 6.0 26 8.0 27 10.5 28 20.0 29 28.0 30 29.0 31 31.0 32 40.0 33 59.0 34 71.0 35 82.0 36 98.0 37 133.0 38 174.5 39 164.5 40 170.0 41 204.5 42 215.0 43 218.5 44 208.5 45 199.0 46 220.5 47 218.0 48 184.5 49 169.5 50 155.0 51 131.5 52 122.0 53 132.0 54 129.0 55 98.0 56 69.5 57 62.0 58 57.0 59 49.0 60 42.5 61 42.0 62 39.0 63 32.0 64 35.0 65 34.0 66 23.5 67 21.0 68 19.5 69 14.5 70 12.0 71 11.0 72 7.5 73 4.0 74 5.0 75 4.5 76 2.0 77 1.0 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 0.05 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 0.0125 42-43 0.125 44-45 0.0125 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.22499999999999998 54-55 0.025 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 16.0 71 9.0 72 10.0 73 6.0 74 8.0 75 16.0 76 4.0 77 8.0 78 10.0 79 16.0 80 15.0 81 12.0 82 14.0 83 18.0 84 7.0 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 3831.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.675 #Duplication Level Percentage of deduplicated Percentage of total 1 93.52887813728455 77.325 2 3.3262775929845785 5.5 3 1.3305110371938311 3.3000000000000003 4 0.6350166313879648 2.1 5 0.21167221046265497 0.8750000000000001 6 0.18143332325370426 0.8999999999999999 7 0.15119443604475355 0.8750000000000001 8 0.12095554883580284 0.8 9 0.03023888720895071 0.22499999999999998 >10 0.48382219534321136 8.1 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 39 0.975 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 39 0.975 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 30 0.75 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 23 0.575 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 23 0.575 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 21 0.525 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 19 0.475 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 17 0.42500000000000004 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 16 0.4 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 14 0.35000000000000003 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 13 0.325 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 12 0.3 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 12 0.3 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 9 0.22499999999999998 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 8 0.2 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTT 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 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 0.0125 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 0.025 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 0.05 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 0.075 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 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 25 6.81408E-7 86.2375 2 GCAATAC 20 2.4888033E-5 86.2375 7 GAGCAAT 20 2.4888033E-5 86.2375 5 AGCAATA 20 2.4888033E-5 86.2375 6 GAGAGCA 30 2.016057E-6 71.86458 3 AGAGCAA 25 7.52677E-5 68.99 4 AATACAA 25 7.52677E-5 68.99 9 CAATACA 30 1.8560234E-4 57.491665 8 GGGAGAG 40 1.1121243E-5 53.898438 1 AGTAGCC 20 6.752912E-4 44.798702 70-71 CAGTAGC 20 6.752912E-4 44.798702 70-71 TAGCCGA 20 6.752912E-4 44.798702 72-73 CATCACT 20 6.752912E-4 44.798702 82-83 ATCACTA 20 6.752912E-4 44.798702 84-85 CGAAAGC 20 6.752912E-4 44.798702 76-77 AGCATCA 20 6.752912E-4 44.798702 80-81 CACTAGC 20 6.752912E-4 44.798702 86-87 TCACTAG 20 6.752912E-4 44.798702 84-85 ACTAGCT 20 6.752912E-4 44.798702 86-87 AGCCGAA 20 6.752912E-4 44.798702 74-75 >>END_MODULE Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83863 READS because READLEN < 1 Read 83863 spots for ERR6133460.sra Written 83863 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra Rejected 83850 READS because READLEN < 1 Read 83850 spots for ERR6133460.sra Written 83850 spots for ERR6133460.sra SRR ids: ['ERR6133460.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_6iepts5x ERR6133460.sra spots: 1677013 blocks: [[1, 83850], [83851, 167700], [167701, 251550], [251551, 335400], [335401, 419250], [419251, 503100], [503101, 586950], [586951, 670800], [670801, 754650], [754651, 838500], [838501, 922350], [922351, 1006200], [1006201, 1090050], [1090051, 1173900], [1173901, 1257750], [1257751, 1341600], [1341601, 1425450], [1425451, 1509300], [1509301, 1593150], [1593151, 1677013]] ERR6133460 file size 368914 ERR6133460 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 ERR6133460 ERR6133460_1.fastq Input file: ERR6133460_1.fastq trimmed: ERR6133460-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 06:30:41 2024 >> started Sat Dec 7 06:30:43 2024 >> done (1.298s) 1677013 reads processed; of these: 237 ( 0.01%) short reads filtered out after trimming by size control 31 ( 0.00%) empty reads filtered out after trimming by size control 1676745 (99.98%) reads available; of these: 28629 ( 1.71%) trimmed reads available after processing 1648116 (98.29%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 50 0.00% 20 30 0.00% 21 17 0.00% 22 27 0.00% 23 20 0.00% 24 13 0.00% 25 11 0.00% 26 23 0.00% 27 29 0.00% 28 159 0.01% 29 41 0.00% 30 22 0.00% 31 29 0.00% 32 41 0.00% 33 36 0.00% 34 22 0.00% 35 99 0.01% 36 583 0.03% 37 17 0.00% 38 36 0.00% 39 81 0.00% 40 52 0.00% 41 54 0.00% 42 17 0.00% 43 18 0.00% 44 20 0.00% 45 8 0.00% 46 19 0.00% 47 16 0.00% 48 13 0.00% 49 6 0.00% 50 14 0.00% 51 40 0.00% 52 17 0.00% 53 4 0.00% 54 10 0.00% 55 5 0.00% 56 12 0.00% 57 10 0.00% 58 17 0.00% 59 12 0.00% 60 8 0.00% 61 6 0.00% 62 2 0.00% 63 3 0.00% 64 3 0.00% 65 2 0.00% 66 7 0.00% 67 12 0.00% 68 21 0.00% 69 55 0.00% 70 5399 0.32% 71 5263 0.31% 72 5131 0.31% 73 4700 0.28% 74 4908 0.29% 75 4899 0.29% 76 4360 0.26% 77 4457 0.27% 78 4757 0.28% 79 5053 0.30% 80 4566 0.27% 81 4600 0.27% 82 5557 0.33% 83 5682 0.34% 84 4410 0.26% 85 84 0.01% 86 132 0.01% 87 219 0.01% 88 386 0.02% 89 838 0.05% 90 1645 0.10% 91 4846 0.29% 92 17646 1.05% 93 1575317 93.95% 1676745 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=5.71 fanout-score-rank=19 prefix-density=0.71 prefix-fanout=2.4 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATCATCTTACTGTTTTAAATAAATCTGTTTCA criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=56.51 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=6.7 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 06:31:00 Started mapping on | Dec 07 06:31:01 Finished on | Dec 07 06:31:05 Mapping speed, Million of reads per hour | 1509.07 Number of input reads | 1676745 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1209863 Uniquely mapped reads % | 72.16% Average mapped length | 91.90 Number of splices: Total | 64896 Number of splices: Annotated (sjdb) | 54130 Number of splices: GT/AG | 62592 Number of splices: GC/AG | 1474 Number of splices: AT/AC | 35 Number of splices: Non-canonical | 795 Mismatch rate per base, % | 0.47% Deletion rate per base | 0.04% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 402327 % of reads mapped to multiple loci | 23.99% Number of reads mapped to too many loci | 8295 % of reads mapped to too many loci | 0.49% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.30% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 64555 64555 64555 N_multimapping 402327 402327 402327 N_noFeature 76395 88068 1159107 N_ambiguous 43669 4678 147 UnstrandedReadsAssigned:1089799 PositiveStrandReadsAssigned:1117117 NegativeStrandReadsAssigned:50609 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133460 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: ERR6133460-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,676,745 reads, 1,389,238 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 914 rounds 52973 ERR6133460.ke.tsv 35125 ERR6133460.se.tsv 88098 total ==> ERR6133460.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 32.6196 PNS24243 293 194 0 0 KQK14069 1603 1504 76 49.1633 KQK14071 474 375 0 0 ==> ERR6133460.se.tsv <== BRADI_1g14170v3 76 BRADI_1g53295v3 38 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 9 BRADI_1g74790v3 15 BRADI_1g09890v3 0 BRADI_1g77505v3 49 BRADI_1g48960v3 0 ERR6133460 completed mapping pipeline successfully