Starting /dee2/code/volunteer_pipeline.sh ERR6133389 current disk space = 1547242577920 free memory = 1385227036 ERR6133389 SRAfilesize baedd4e481375e1ec32846e345204373 ERR6133389.sra ERR6133389.sra file validated ERR6133389 is single end ERR6133389 is conventional basespace ERR6133389 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133389_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.8845 37.0 37.0 37.0 37.0 37.0 2 36.776 37.0 37.0 37.0 37.0 37.0 3 36.614 37.0 37.0 37.0 37.0 37.0 4 36.08 37.0 37.0 37.0 33.0 37.0 5 36.14825 37.0 37.0 37.0 33.0 37.0 6 36.34375 37.0 37.0 37.0 37.0 37.0 7 38.23925 40.0 37.0 40.0 37.0 40.0 8 38.185 40.0 37.0 40.0 37.0 40.0 9 38.198 40.0 37.0 40.0 37.0 40.0 10-11 38.18925 40.0 37.0 40.0 37.0 40.0 12-13 38.183625 40.0 37.0 40.0 37.0 40.0 14-15 38.12575 40.0 37.0 40.0 37.0 40.0 16-17 38.010374999999996 40.0 37.0 40.0 35.0 40.0 18-19 37.90075 40.0 37.0 40.0 33.0 40.0 20-21 37.794875000000005 40.0 37.0 40.0 33.0 40.0 22-23 37.787375 40.0 37.0 40.0 33.0 40.0 24-25 37.65112499999999 40.0 37.0 40.0 33.0 40.0 26-27 37.48525 37.0 37.0 40.0 33.0 40.0 28-29 37.412499999999994 37.0 37.0 40.0 33.0 40.0 30-31 37.334125 37.0 37.0 40.0 33.0 40.0 32-33 37.1205 37.0 37.0 40.0 33.0 40.0 34-35 36.898250000000004 37.0 37.0 40.0 33.0 40.0 36-37 36.831500000000005 37.0 37.0 40.0 33.0 40.0 38-39 36.923 37.0 37.0 40.0 33.0 40.0 40-41 37.169 37.0 37.0 40.0 33.0 40.0 42-43 37.170375 37.0 37.0 40.0 33.0 40.0 44-45 37.078125 37.0 37.0 40.0 33.0 40.0 46-47 36.812625 37.0 37.0 40.0 33.0 40.0 48-49 36.766875 37.0 37.0 40.0 33.0 40.0 50-51 36.595625 37.0 37.0 38.5 33.0 40.0 52-53 36.40375 37.0 37.0 37.0 33.0 40.0 54-55 36.28975 37.0 37.0 37.0 33.0 40.0 56-57 36.083875 37.0 37.0 37.0 33.0 40.0 58-59 35.853375 37.0 37.0 37.0 33.0 40.0 60-61 35.747749999999996 37.0 37.0 37.0 33.0 37.0 62-63 35.52675000000001 37.0 33.0 37.0 33.0 37.0 64-65 35.340625 37.0 33.0 37.0 33.0 37.0 66-67 35.355625 37.0 33.0 37.0 33.0 37.0 68-69 34.36987499999999 35.0 33.0 37.0 30.0 37.0 70-71 34.46615727832203 37.0 33.0 37.0 33.0 37.0 72-73 35.00694413903716 37.0 33.0 37.0 33.0 37.0 74-75 34.988493073466245 37.0 33.0 37.0 33.0 37.0 76-77 34.86282303222961 37.0 33.0 37.0 33.0 37.0 78-79 35.017700407806345 37.0 33.0 37.0 33.0 37.0 80-81 34.87168590027183 37.0 33.0 37.0 33.0 37.0 82-83 34.66490616130007 37.0 33.0 37.0 33.0 37.0 84-85 34.63017105418823 37.0 33.0 37.0 33.0 37.0 86-87 34.51119503641759 37.0 33.0 37.0 33.0 37.0 88-89 34.577825735095765 37.0 33.0 37.0 33.0 37.0 90-91 34.34259509036957 37.0 33.0 37.0 33.0 37.0 92-93 34.096304289182626 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 6.0 22 6.0 23 13.0 24 11.0 25 11.0 26 17.0 27 31.0 28 38.0 29 38.0 30 47.0 31 58.0 32 87.0 33 126.0 34 197.0 35 349.0 36 864.0 37 1094.0 38 965.0 39 38.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 80.80000000000001 4.6 4.65 9.950000000000001 2 59.52499999999999 23.05 11.375 6.05 3 34.699999999999996 35.575 17.0 12.725 4 34.35 25.45 19.7 20.5 5 20.7 33.5 26.125 19.675 6 19.85 38.75 26.974999999999998 14.424999999999999 7 35.075 28.475 21.0 15.45 8 28.799999999999997 30.4 23.95 16.85 9 26.55 26.775 27.800000000000004 18.875 10-11 24.325 28.037499999999998 27.8625 19.775000000000002 12-13 29.037499999999998 24.2 27.925 18.8375 14-15 22.05 25.8 31.7 20.45 16-17 25.5375 30.587500000000002 26.6125 17.2625 18-19 23.6875 26.687499999999996 27.5125 22.112499999999997 20-21 24.4375 26.3625 27.537499999999998 21.6625 22-23 26.275 23.7625 28.487499999999997 21.475 24-25 26.3 24.0 28.812500000000004 20.8875 26-27 25.224999999999998 25.2125 29.975 19.5875 28-29 24.5 25.9875 28.212500000000002 21.3 30-31 27.212500000000002 25.324999999999996 27.250000000000004 20.2125 32-33 23.8375 27.6625 28.299999999999997 20.200000000000003 34-35 25.5125 24.2625 28.6375 21.587500000000002 36-37 24.75 24.4375 29.45 21.3625 38-39 24.025 26.1 30.587500000000002 19.287499999999998 40-41 24.8 26.200000000000003 27.325 21.675 42-43 23.7125 28.787499999999998 27.425 20.075000000000003 44-45 23.1875 26.187500000000004 29.7125 20.9125 46-47 23.5 24.85 28.425 23.225 48-49 24.1375 26.224999999999998 29.275000000000002 20.3625 50-51 24.55 27.0125 29.075 19.3625 52-53 24.7 27.8375 27.325 20.1375 54-55 22.7625 29.212500000000002 28.1125 19.9125 56-57 25.0125 26.437500000000004 28.1375 20.4125 58-59 22.825 26.75 29.725 20.7 60-61 24.7375 25.1875 29.2 20.875 62-63 22.325 28.599999999999998 30.475 18.6 64-65 24.1125 27.537499999999998 28.9875 19.3625 66-67 24.55 28.012500000000003 28.037499999999998 19.400000000000002 68-69 24.525 26.1 29.2375 20.1375 70-71 24.99686756045608 25.297581756672095 28.179426137075552 21.526124545796264 72-73 25.104443600455756 25.534877832637044 28.775794404354983 20.58488416255222 74-75 23.73098069300601 27.31108553893364 28.973277074542896 19.98465669351745 76-77 21.38340431023358 27.706800877532583 30.933023615950443 19.97677119628339 78-79 23.7126841350541 24.977186807456654 30.30895580758702 21.00117324990223 80-81 24.472016895459344 26.74234424498416 29.17106652587117 19.614572333685324 82-83 25.03664223850766 24.51698867421719 30.179880079946702 20.26648900732845 84-85 24.198761109614868 24.2795583086453 29.97576084029087 21.545919741448962 86-87 21.985432964661452 25.93741570002698 32.047477744807125 20.02967359050445 88-89 21.324521176153226 29.606150526031833 30.887510115996765 18.181818181818183 90-91 24.52117615322363 27.205287294308068 29.687078500134877 18.586458052333423 92-93 21.432425141623952 29.56568653898031 29.552198543296466 19.449689776099273 >>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 4.0 18 5.5 19 2.0 20 1.0 21 3.0 22 4.0 23 3.0 24 2.5 25 5.0 26 11.0 27 15.5 28 26.0 29 32.0 30 28.0 31 38.5 32 56.0 33 74.5 34 97.0 35 112.5 36 127.0 37 141.5 38 154.5 39 179.5 40 199.5 41 207.5 42 199.5 43 190.5 44 195.0 45 201.5 46 224.0 47 209.5 48 169.0 49 162.5 50 166.0 51 147.5 52 129.5 53 138.0 54 118.0 55 90.5 56 80.0 57 69.5 58 63.5 59 43.0 60 28.0 61 36.0 62 46.0 63 33.0 64 19.0 65 15.5 66 12.0 67 12.0 68 10.0 69 9.0 70 6.5 71 3.0 72 1.5 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 0.0 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 19.0 71 23.0 72 17.0 73 21.0 74 19.0 75 17.0 76 19.0 77 17.0 78 25.0 79 25.0 80 20.0 81 17.0 82 17.0 83 25.0 84 12.0 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 3707.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.075 #Duplication Level Percentage of deduplicated Percentage of total 1 93.25910321998194 77.47500000000001 2 4.03250075233223 6.7 3 1.0532651218778213 2.625 4 0.331026181161601 1.0999999999999999 5 0.2708396027685826 1.125 6 0.21065302437556424 1.05 7 0.15046644598254588 0.8750000000000001 8 0.12037315678603672 0.8 9 0.15046644598254588 1.125 >10 0.39121275955461937 5.800000000000001 >50 0.03009328919650918 1.325 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 53 1.325 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 33 0.8250000000000001 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 28 0.7000000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 27 0.675 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 27 0.675 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 19 0.475 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 18 0.44999999999999996 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 15 0.375 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 10 0.25 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 9 0.22499999999999998 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 8 0.2 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 8 0.2 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 7 0.17500000000000002 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit AATCGCTTTTGCTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCC 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit TAGTTTCCACCGCCTGTCCAGGGTTGAGCCCTGGGATTTGACGGCGGACT 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 6 0.15 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGGCAAGGTTGTCCGTGGACCTGCTCCCCTGTCGCTGGCCCTGGTTCATG 5 0.125 No Hit CAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit GACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCAT 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.037500000000000006 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 0.075 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 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1375 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 GGGCAAG 20 0.0028203723 64.71563 1 GCTCGTG 25 0.001891305 36.33158 80-81 TTGCTCG 25 0.001891305 36.33158 78-79 >>END_MODULE Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95779 READS because READLEN < 1 Read 95779 spots for ERR6133389.sra Written 95779 spots for ERR6133389.sra Rejected 95782 READS because READLEN < 1 Read 95782 spots for ERR6133389.sra Written 95782 spots for ERR6133389.sra SRR ids: ['ERR6133389.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0_xy8yug ERR6133389.sra spots: 1915583 blocks: [[1, 95779], [95780, 191558], [191559, 287337], [287338, 383116], [383117, 478895], [478896, 574674], [574675, 670453], [670454, 766232], [766233, 862011], [862012, 957790], [957791, 1053569], [1053570, 1149348], [1149349, 1245127], [1245128, 1340906], [1340907, 1436685], [1436686, 1532464], [1532465, 1628243], [1628244, 1724022], [1724023, 1819801], [1819802, 1915583]] ERR6133389 file size 420099 ERR6133389 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 ERR6133389 ERR6133389_1.fastq Input file: ERR6133389_1.fastq trimmed: ERR6133389-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 02:50:10 2024 >> started Sat Dec 7 02:50:11 2024 >> done (1.544s) 1915583 reads processed; of these: 361 ( 0.02%) short reads filtered out after trimming by size control 13 ( 0.00%) empty reads filtered out after trimming by size control 1915209 (99.98%) reads available; of these: 75570 ( 3.95%) trimmed reads available after processing 1839639 (96.05%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 57 0.00% 19 61 0.00% 20 21 0.00% 21 18 0.00% 22 22 0.00% 23 12 0.00% 24 11 0.00% 25 10 0.00% 26 12 0.00% 27 13 0.00% 28 15 0.00% 29 16 0.00% 30 21 0.00% 31 13 0.00% 32 45 0.00% 33 11 0.00% 34 4 0.00% 35 6 0.00% 36 9 0.00% 37 9 0.00% 38 47 0.00% 39 104 0.01% 40 166 0.01% 41 20 0.00% 42 19 0.00% 43 16 0.00% 44 23 0.00% 45 24 0.00% 46 47 0.00% 47 56 0.00% 48 106 0.01% 49 630 0.03% 50 213 0.01% 51 267 0.01% 52 190 0.01% 53 188 0.01% 54 249 0.01% 55 296 0.02% 56 280 0.01% 57 364 0.02% 58 387 0.02% 59 420 0.02% 60 576 0.03% 61 474 0.02% 62 420 0.02% 63 704 0.04% 64 594 0.03% 65 612 0.03% 66 716 0.04% 67 784 0.04% 68 1113 0.06% 69 517 0.03% 70 9549 0.50% 71 9099 0.48% 72 11458 0.60% 73 9543 0.50% 74 9878 0.52% 75 10093 0.53% 76 8766 0.46% 77 8900 0.46% 78 10310 0.54% 79 11235 0.59% 80 9971 0.52% 81 9747 0.51% 82 11630 0.61% 83 13974 0.73% 84 10263 0.54% 85 3121 0.16% 86 3355 0.18% 87 3918 0.20% 88 5080 0.27% 89 4842 0.25% 90 6659 0.35% 91 7928 0.41% 92 8065 0.42% 93 1706817 89.12% 1915209 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=6.61 fanout-score-rank=18 prefix-density=0.64 prefix-fanout=2.7 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATCATCTTACTGTTTTAAATAAATCTGTTTCAGATC criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=272.17 fanout-score-rank=1 prefix-density=0.48 prefix-fanout=5.9 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 02:50:29 Started mapping on | Dec 07 02:50:29 Finished on | Dec 07 02:50:34 Mapping speed, Million of reads per hour | 1378.95 Number of input reads | 1915209 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1398945 Uniquely mapped reads % | 73.04% Average mapped length | 90.95 Number of splices: Total | 63043 Number of splices: Annotated (sjdb) | 51110 Number of splices: GT/AG | 59749 Number of splices: GC/AG | 1546 Number of splices: AT/AC | 22 Number of splices: Non-canonical | 1726 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.04% Deletion average length | 1.86 Insertion rate per base | 0.03% Insertion average length | 2.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 431921 % of reads mapped to multiple loci | 22.55% Number of reads mapped to too many loci | 17735 % of reads mapped to too many loci | 0.93% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.36% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 84343 84343 84343 N_multimapping 431921 431921 431921 N_noFeature 73659 87290 1334457 N_ambiguous 55507 4639 236 UnstrandedReadsAssigned:1269779 PositiveStrandReadsAssigned:1307016 NegativeStrandReadsAssigned:64252 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133389 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: ERR6133389-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,915,209 reads, 1,587,797 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 928 rounds 52973 ERR6133389.ke.tsv 35125 ERR6133389.se.tsv 88098 total ==> ERR6133389.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 41 26.0216 PNS24243 293 194 0 0 KQK14069 1603 1504 50 28.9485 KQK14071 474 375 0 0 ==> ERR6133389.se.tsv <== BRADI_1g14170v3 50 BRADI_1g53295v3 8 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 10 BRADI_1g74790v3 15 BRADI_1g09890v3 0 BRADI_1g77505v3 56 BRADI_1g48960v3 0 ERR6133389 completed mapping pipeline successfully