Starting /dee2/code/volunteer_pipeline.sh ERR6133549 current disk space = 1544533352448 free memory = 1447479460 ERR6133549 SRAfilesize 12a2d8cead7025aa7e7acf0a1ad1cd29 ERR6133549.sra ERR6133549.sra file validated ERR6133549 is single end ERR6133549 is conventional basespace ERR6133549 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133549_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 33.95625 37.0 33.0 37.0 33.0 37.0 2 36.018 37.0 37.0 37.0 33.0 37.0 3 35.14175 37.0 33.0 37.0 33.0 37.0 4 35.21475 37.0 37.0 37.0 33.0 37.0 5 35.115 37.0 37.0 37.0 33.0 37.0 6 35.46425 37.0 37.0 37.0 33.0 37.0 7 37.338 37.0 37.0 40.0 33.0 40.0 8 37.36625 37.0 37.0 40.0 33.0 40.0 9 37.3585 37.0 37.0 40.0 33.0 40.0 10-11 37.490750000000006 37.0 37.0 40.0 33.0 40.0 12-13 37.375375000000005 37.0 37.0 40.0 33.0 40.0 14-15 37.38775 37.0 37.0 40.0 33.0 40.0 16-17 37.3335 37.0 37.0 40.0 33.0 40.0 18-19 37.208875 37.0 37.0 40.0 33.0 40.0 20-21 37.155 37.0 37.0 40.0 33.0 40.0 22-23 37.15625 37.0 37.0 40.0 33.0 40.0 24-25 37.207750000000004 37.0 37.0 40.0 33.0 40.0 26-27 37.192499999999995 37.0 37.0 40.0 33.0 40.0 28-29 37.068875 37.0 37.0 40.0 33.0 40.0 30-31 36.967 37.0 37.0 40.0 33.0 40.0 32-33 36.816500000000005 37.0 37.0 40.0 33.0 40.0 34-35 36.724000000000004 37.0 37.0 40.0 33.0 40.0 36-37 36.601124999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.4375 37.0 37.0 40.0 33.0 40.0 40-41 36.208124999999995 37.0 37.0 40.0 33.0 40.0 42-43 36.1135 37.0 37.0 40.0 33.0 40.0 44-45 35.8455 37.0 35.0 40.0 33.0 40.0 46-47 35.491 37.0 33.0 37.0 33.0 40.0 48-49 35.576499999999996 37.0 33.0 37.0 33.0 40.0 50-51 35.5085 37.0 33.0 37.0 33.0 40.0 52-53 35.274625 37.0 33.0 37.0 33.0 40.0 54-55 35.123374999999996 37.0 33.0 37.0 33.0 40.0 56-57 35.013374999999996 37.0 33.0 37.0 33.0 37.0 58-59 34.3925 37.0 33.0 37.0 27.0 37.0 60-61 34.655874999999995 37.0 33.0 37.0 27.0 37.0 62-63 34.51975 37.0 33.0 37.0 27.0 37.0 64-65 34.591499999999996 37.0 33.0 37.0 33.0 37.0 66-67 34.618625 37.0 33.0 37.0 33.0 37.0 68-69 33.756125 35.0 33.0 37.0 27.0 37.0 70-71 33.8097858485836 35.0 33.0 37.0 27.0 37.0 72-73 34.099881290341315 37.0 33.0 37.0 27.0 37.0 74-75 34.20338150899126 37.0 33.0 37.0 27.0 37.0 76-77 34.178198292739125 37.0 33.0 37.0 27.0 37.0 78-79 34.17920073401629 37.0 33.0 37.0 27.0 37.0 80-81 34.180978177935295 37.0 33.0 37.0 27.0 37.0 82-83 34.121145970739015 37.0 33.0 37.0 27.0 37.0 84-85 34.02708138750363 37.0 33.0 37.0 27.0 37.0 86-87 33.92267365661861 37.0 33.0 37.0 27.0 37.0 88-89 33.94089121887287 37.0 33.0 37.0 27.0 37.0 90-91 33.796985583224114 37.0 33.0 37.0 27.0 37.0 92-93 33.62935779816514 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 17.0 21 15.0 22 10.0 23 18.0 24 17.0 25 25.0 26 51.0 27 45.0 28 64.0 29 57.0 30 85.0 31 99.0 32 126.0 33 162.0 34 253.0 35 398.0 36 950.0 37 899.0 38 699.0 39 10.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.25 2.3 1.95 6.5 2 74.575 15.25 6.25 3.925 3 37.6 39.025 12.325 11.05 4 32.875 28.725 18.224999999999998 20.175 5 25.525 32.225 23.974999999999998 18.275 6 19.900000000000002 37.4 26.1 16.6 7 38.05 27.975 19.0 14.975 8 30.275000000000002 30.425 23.7 15.6 9 26.924999999999997 29.099999999999998 27.125 16.85 10-11 26.150000000000002 27.6125 27.775 18.462500000000002 12-13 28.262500000000003 26.5375 28.287499999999998 16.9125 14-15 22.287499999999998 30.575000000000003 28.849999999999998 18.2875 16-17 23.3 31.887500000000003 26.275 18.5375 18-19 24.224999999999998 26.75 28.799999999999997 20.225 20-21 23.91548943617952 27.065883235404424 29.1911488936117 19.82747843480435 22-23 26.9625 23.200000000000003 28.512500000000003 21.325 24-25 25.374999999999996 24.525 29.1375 20.962500000000002 26-27 23.95 26.337500000000002 30.7625 18.95 28-29 25.162499999999998 27.4125 27.987499999999997 19.4375 30-31 26.575 26.337500000000002 27.5875 19.5 32-33 23.200000000000003 26.8 29.3875 20.6125 34-35 24.154770848985724 27.335336839469072 27.39794640621087 21.111945905334334 36-37 24.1125 24.425 28.6125 22.85 38-39 26.387500000000003 24.75 31.1875 17.675 40-41 27.36828932549118 24.752846952821926 27.593542735577525 20.285320986109372 42-43 25.02818489289741 28.09720656394839 27.495928848803707 19.378679694350495 44-45 22.944048066090875 25.234697709350357 30.779822255601452 21.041431968957315 46-47 24.25 25.162499999999998 28.549999999999997 22.037499999999998 48-49 23.265408176022003 25.91573946743343 29.828728591073883 20.990123765470685 50-51 23.4125 27.325 30.112499999999997 19.15 52-53 24.261761761761765 26.814314314314313 27.665165165165167 21.25875875875876 54-55 22.775000000000002 30.049999999999997 28.599999999999998 18.575 56-57 24.637500000000003 26.187500000000004 29.762499999999996 19.412499999999998 58-59 24.25 24.875 29.25 21.625 60-61 24.8125 26.900000000000002 28.962500000000002 19.325 62-63 20.6875 28.812500000000004 32.1125 18.387500000000003 64-65 23.175 28.012500000000003 29.5375 19.275000000000002 66-67 24.3 27.9125 28.449999999999996 19.3375 68-69 22.8875 26.987499999999997 27.875 22.25 70-71 24.60883715108274 25.697834522468394 28.752034046814366 20.941294279634498 72-73 25.425867507886434 25.4006309148265 29.955835962145112 19.217665615141954 74-75 23.215646431292864 27.432054864109727 29.603759207518415 19.748539497078994 76-77 22.885254280603117 27.370304114490164 28.648096089956553 21.096345514950166 78-79 23.08185783936361 26.122658455221963 31.601231716705158 19.19425198870926 80-81 22.321198037696877 28.98270074877356 29.58946553059644 19.106635682933128 82-83 22.878709005726183 26.288391462779803 30.67412805830297 20.158771473191045 84-85 22.655840754321634 24.423782084861184 32.3205866946045 20.599790466212678 86-87 22.608125819134994 27.22149410222805 30.99606815203145 19.174311926605505 88-89 20.19659239842726 28.990825688073397 30.94364351245085 19.868938401048492 90-91 25.29488859764089 27.024901703800786 28.990825688073397 18.68938401048493 92-93 21.756225425950195 29.475753604193972 29.515072083879424 19.25294888597641 >>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 6.5 18 7.0 19 0.5 20 2.0 21 3.5 22 4.5 23 5.0 24 4.0 25 7.5 26 14.0 27 15.0 28 17.5 29 23.5 30 34.0 31 38.0 32 52.5 33 81.5 34 87.0 35 106.5 36 131.5 37 144.0 38 180.5 39 193.5 40 199.5 41 215.5 42 217.0 43 218.0 44 201.0 45 182.5 46 206.0 47 203.5 48 169.0 49 165.0 50 152.5 51 142.5 52 132.5 53 123.0 54 120.0 55 91.5 56 63.5 57 58.0 58 53.0 59 45.0 60 35.0 61 31.5 62 31.0 63 23.0 64 19.0 65 19.0 66 16.5 67 12.5 68 9.0 69 7.5 70 6.5 71 5.0 72 5.5 73 3.5 74 1.0 75 1.0 76 1.0 77 0.5 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 0.0125 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 0.17500000000000002 36-37 0.0 38-39 0.0 40-41 0.11249999999999999 42-43 0.21250000000000002 44-45 0.13749999999999998 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.1 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 11.0 71 18.0 72 17.0 73 12.0 74 10.0 75 14.0 76 10.0 77 6.0 78 10.0 79 13.0 80 12.0 81 16.0 82 18.0 83 12.0 84 6.0 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 3815.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.425 #Duplication Level Percentage of deduplicated Percentage of total 1 92.75722723033883 74.6 2 4.351880634131178 7.000000000000001 3 0.83929126515387 2.025 4 0.6216972334473112 2.0 5 0.2175940317065589 0.8750000000000001 6 0.24867889337892446 1.2 7 0.1554243083618278 0.8750000000000001 8 0.18650917003419334 1.2 9 0.031084861672365557 0.22499999999999998 >10 0.5906123717749456 10.0 >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 fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 46 1.15 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 34 0.8500000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 34 0.8500000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 33 0.8250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 32 0.8 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 30 0.75 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 25 0.625 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 24 0.6 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 18 0.44999999999999996 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 17 0.42500000000000004 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTT 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGATAATGACAGATCGAGAGGCTCGACTAAACAGAATTGGGGGAGAAGTC 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 6 0.15 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit GGGTGTAACATGTAAATTTGTACGCGTGCTGCGTGCACGCTTGTAATATT 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 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 0.025 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 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 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 15 8.904918E-4 86.525 1 GGAGAGC 20 0.0027898033 64.893745 2 GGAGTAT 25 0.006751546 51.914997 1 >>END_MODULE Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306706 READS because READLEN < 1 Read 306706 spots for ERR6133549.sra Written 306706 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra Rejected 306692 READS because READLEN < 1 Read 306692 spots for ERR6133549.sra Written 306692 spots for ERR6133549.sra SRR ids: ['ERR6133549.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_08uog2ds ERR6133549.sra spots: 6133854 blocks: [[1, 306692], [306693, 613384], [613385, 920076], [920077, 1226768], [1226769, 1533460], [1533461, 1840152], [1840153, 2146844], [2146845, 2453536], [2453537, 2760228], [2760229, 3066920], [3066921, 3373612], [3373613, 3680304], [3680305, 3986996], [3986997, 4293688], [4293689, 4600380], [4600381, 4907072], [4907073, 5213764], [5213765, 5520456], [5520457, 5827148], [5827149, 6133854]] ERR6133549 file size 1353589 ERR6133549 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 ERR6133549 ERR6133549_1.fastq Input file: ERR6133549_1.fastq trimmed: ERR6133549-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 08:25:41 2024 >> started Sat Dec 7 08:25:44 2024 >> done (3.337s) 6133854 reads processed; of these: 245 ( 0.00%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 6133589 (100.00%) reads available; of these: 89030 ( 1.45%) trimmed reads available after processing 6044559 (98.55%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 33 0.00% 19 127 0.00% 20 31 0.00% 21 20 0.00% 22 19 0.00% 23 12 0.00% 24 16 0.00% 25 10 0.00% 26 9 0.00% 27 9 0.00% 28 24 0.00% 29 355 0.01% 30 11 0.00% 31 26 0.00% 32 41 0.00% 33 18 0.00% 34 9 0.00% 35 85 0.00% 36 450 0.01% 37 32 0.00% 38 47 0.00% 39 112 0.00% 40 155 0.00% 41 40 0.00% 42 16 0.00% 43 25 0.00% 44 20 0.00% 45 12 0.00% 46 11 0.00% 47 7 0.00% 48 4 0.00% 49 6 0.00% 50 17 0.00% 51 62 0.00% 52 10 0.00% 53 12 0.00% 54 11 0.00% 55 6 0.00% 56 13 0.00% 57 14 0.00% 58 19 0.00% 59 9 0.00% 60 17 0.00% 61 16 0.00% 62 7 0.00% 63 8 0.00% 64 9 0.00% 65 9 0.00% 66 8 0.00% 67 31 0.00% 68 56 0.00% 69 201 0.00% 70 22314 0.36% 71 19663 0.32% 72 20740 0.34% 73 19071 0.31% 74 20876 0.34% 75 20196 0.33% 76 17912 0.29% 77 18540 0.30% 78 21282 0.35% 79 24288 0.40% 80 21536 0.35% 81 24314 0.40% 82 26094 0.43% 83 26320 0.43% 84 22684 0.37% 85 188 0.00% 86 412 0.01% 87 576 0.01% 88 1109 0.02% 89 2228 0.04% 90 4727 0.08% 91 14121 0.23% 92 60385 0.98% 93 5721686 93.28% 6133589 reads passed initial QC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=31 prefix-density=0.66 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=121.26 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=6.6 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 08:26:02 Started mapping on | Dec 07 08:26:02 Finished on | Dec 07 08:26:10 Mapping speed, Million of reads per hour | 2760.12 Number of input reads | 6133589 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 4318798 Uniquely mapped reads % | 70.41% Average mapped length | 91.66 Number of splices: Total | 168421 Number of splices: Annotated (sjdb) | 138431 Number of splices: GT/AG | 160179 Number of splices: GC/AG | 4698 Number of splices: AT/AC | 101 Number of splices: Non-canonical | 3443 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.84 Insertion rate per base | 0.03% Insertion average length | 1.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1664774 % of reads mapped to multiple loci | 27.14% Number of reads mapped to too many loci | 62413 % of reads mapped to too many loci | 1.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.36% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 150017 150017 150017 N_multimapping 1664774 1664774 1664774 N_noFeature 336047 375207 4125648 N_ambiguous 176303 22227 716 UnstrandedReadsAssigned:3806448 PositiveStrandReadsAssigned:3921364 NegativeStrandReadsAssigned:192434 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133549 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: ERR6133549-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,133,589 reads, 5,047,806 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,028 rounds 52973 ERR6133549.ke.tsv 35125 ERR6133549.se.tsv 88098 total ==> ERR6133549.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 96 18.5021 PNS24243 293 194 0 0 KQK14069 1603 1504 157 27.6029 KQK14071 474 375 0 0 ==> ERR6133549.se.tsv <== BRADI_1g14170v3 157 BRADI_1g53295v3 16 BRADI_1g59795v3 35 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 55 BRADI_1g74790v3 24 BRADI_1g09890v3 0 BRADI_1g77505v3 108 BRADI_1g48960v3 1 ERR6133549 completed mapping pipeline successfully