Starting /dee2/code/volunteer_pipeline.sh ERR6133492 current disk space = 1544558731264 free memory = 1600183068 ERR6133492 SRAfilesize 2bd614ff3392a3d6dca1e8ebe4839cb4 ERR6133492.sra ERR6133492.sra file validated ERR6133492 is single end ERR6133492 is conventional basespace ERR6133492 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133492_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 35.435 37.0 33.0 37.0 33.0 37.0 2 36.5015 37.0 37.0 37.0 37.0 37.0 3 35.873 37.0 37.0 37.0 33.0 37.0 4 35.39425 37.0 37.0 37.0 33.0 37.0 5 35.44475 37.0 37.0 37.0 33.0 37.0 6 35.644 37.0 37.0 37.0 33.0 37.0 7 37.49375 40.0 37.0 40.0 33.0 40.0 8 37.5525 40.0 37.0 40.0 33.0 40.0 9 37.5855 40.0 37.0 40.0 33.0 40.0 10-11 37.574375 38.5 37.0 40.0 33.0 40.0 12-13 37.469875 37.0 37.0 40.0 33.0 40.0 14-15 37.47725 37.0 37.0 40.0 33.0 40.0 16-17 37.242875 37.0 37.0 40.0 33.0 40.0 18-19 37.032875000000004 37.0 37.0 40.0 33.0 40.0 20-21 36.779624999999996 37.0 37.0 40.0 33.0 40.0 22-23 36.864125 37.0 37.0 40.0 33.0 40.0 24-25 36.624875 37.0 37.0 40.0 33.0 40.0 26-27 37.0535 37.0 37.0 40.0 33.0 40.0 28-29 36.958124999999995 37.0 37.0 40.0 33.0 40.0 30-31 36.946375 37.0 37.0 40.0 33.0 40.0 32-33 36.862375 37.0 37.0 40.0 33.0 40.0 34-35 36.831375 37.0 37.0 40.0 33.0 40.0 36-37 36.649625 37.0 37.0 40.0 33.0 40.0 38-39 36.5495 37.0 37.0 40.0 33.0 40.0 40-41 36.199 37.0 37.0 40.0 33.0 40.0 42-43 36.25125 37.0 37.0 40.0 33.0 40.0 44-45 36.182249999999996 37.0 37.0 40.0 33.0 40.0 46-47 36.060874999999996 37.0 37.0 40.0 33.0 40.0 48-49 36.055875 37.0 37.0 38.5 33.0 40.0 50-51 35.9285 37.0 37.0 37.0 33.0 40.0 52-53 35.656125 37.0 33.0 37.0 33.0 40.0 54-55 35.555625000000006 37.0 33.0 37.0 33.0 40.0 56-57 35.204625 37.0 33.0 37.0 33.0 40.0 58-59 34.129375 37.0 33.0 37.0 27.0 37.0 60-61 34.815375 37.0 33.0 37.0 33.0 37.0 62-63 34.668375 37.0 33.0 37.0 30.0 37.0 64-65 34.599125 37.0 33.0 37.0 33.0 37.0 66-67 34.577875 37.0 33.0 37.0 33.0 37.0 68-69 33.781625000000005 35.0 33.0 37.0 30.0 37.0 70-71 33.92797134958532 35.0 33.0 37.0 27.0 37.0 72-73 34.25671272358288 37.0 33.0 37.0 27.0 37.0 74-75 34.20029708281406 37.0 33.0 37.0 27.0 37.0 76-77 34.12168852880659 37.0 33.0 37.0 27.0 37.0 78-79 33.97588583102591 37.0 33.0 37.0 27.0 37.0 80-81 33.915517525175474 37.0 33.0 37.0 27.0 37.0 82-83 33.76943392045007 37.0 33.0 37.0 27.0 37.0 84-85 33.49719154041053 37.0 33.0 37.0 27.0 37.0 86-87 33.59036305392418 37.0 33.0 37.0 27.0 37.0 88-89 33.6476241324079 37.0 33.0 37.0 27.0 37.0 90-91 33.40309663641217 35.0 33.0 37.0 27.0 37.0 92-93 33.37146289375334 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 6.0 22 10.0 23 12.0 24 17.0 25 21.0 26 36.0 27 50.0 28 58.0 29 66.0 30 93.0 31 108.0 32 121.0 33 208.0 34 281.0 35 418.0 36 857.0 37 975.0 38 634.0 39 19.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.05 4.375 7.5249999999999995 7.049999999999999 2 61.724999999999994 22.3 10.274999999999999 5.7 3 32.475 34.975 16.975 15.575 4 31.075000000000003 27.55 18.275 23.1 5 25.35 26.275 29.625 18.75 6 17.5 37.125 27.3 18.075 7 35.775 27.250000000000004 20.375 16.6 8 27.800000000000004 29.95 22.825 19.425 9 22.400000000000002 29.525000000000002 28.050000000000004 20.025000000000002 10-11 22.400000000000002 27.925 29.9 19.775000000000002 12-13 24.5 28.037499999999998 26.137500000000003 21.325 14-15 21.25 32.9625 27.6 18.1875 16-17 24.425 30.9625 24.525 20.0875 18-19 23.7 28.212500000000002 28.499999999999996 19.5875 20-21 24.928116014501814 26.828353544193025 29.378672334041756 18.86485810726341 22-23 28.9 21.875 29.1375 20.0875 24-25 23.525 26.1625 28.3875 21.925 26-27 26.4125 25.224999999999998 29.45 18.912499999999998 28-29 24.725 28.725 26.85 19.7 30-31 27.950000000000003 25.5625 27.400000000000002 19.0875 32-33 24.8625 27.212500000000002 26.9625 20.962500000000002 34-35 21.975 30.587500000000002 27.4125 20.025000000000002 36-37 25.650000000000002 25.2125 25.95 23.1875 38-39 28.008506379784837 24.130597948461347 29.522141606204656 18.33875406554916 40-41 24.45917218957109 26.334875578341876 28.223083656371138 20.982868575715894 42-43 25.156289072268066 30.670167541885473 25.568892223055762 18.6046511627907 44-45 22.662499999999998 27.150000000000002 30.55 19.6375 46-47 25.775 24.7875 27.55 21.8875 48-49 24.375 26.0625 28.925 20.6375 50-51 21.3125 29.2 27.3 22.1875 52-53 24.88421579672049 26.81186631618475 25.1971460758543 23.106771811240456 54-55 24.803100387548444 26.35329416177022 30.45380672584073 18.389798724840606 56-57 26.669167291822955 26.969242310577645 27.081770442610654 19.279819954988746 58-59 22.2625 26.900000000000002 30.325000000000003 20.5125 60-61 26.025 27.775 28.4 17.8 62-63 20.525 30.725 30.85 17.9 64-65 21.975 30.825000000000003 28.725 18.475 66-67 23.549999999999997 30.8 27.3375 18.3125 68-69 22.037499999999998 26.6 28.012500000000003 23.35 70-71 22.37122446421857 28.211555332748468 27.28412081714501 22.133099385887956 72-73 26.29517311094263 24.728329542582763 29.59312610563558 19.38337124083902 74-75 23.181760285313974 29.282893898866387 27.945484651636733 19.589861164182906 76-77 21.701745379876797 26.463039014373717 26.373203285420942 25.46201232032854 78-79 26.261972560186386 25.79601346104064 29.23893347139529 18.70308050737769 80-81 22.479101358411704 33.46394984326019 26.88087774294671 17.1760710553814 82-83 23.365840801265154 27.161307327358987 27.5830258302583 21.889826041117555 84-85 21.655117270788914 23.73400852878465 33.48880597014926 21.122068230277186 86-87 20.221569674319273 27.89642285104111 29.93860117458623 21.94340630005339 88-89 18.86011745862253 31.52696209289909 29.004271222637477 20.608649225840896 90-91 25.17351841964762 28.190069407367858 27.97650827549386 18.659903897490658 92-93 21.556326748531767 31.260010678056595 27.816337426588362 19.367325146823276 >>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 28.5 18 29.5 19 2.5 20 4.0 21 6.0 22 6.5 23 10.0 24 9.5 25 6.5 26 13.5 27 16.0 28 26.0 29 38.0 30 31.0 31 42.5 32 53.0 33 58.0 34 71.5 35 83.0 36 114.0 37 158.5 38 189.5 39 182.5 40 197.0 41 200.5 42 200.5 43 229.0 44 205.0 45 183.5 46 190.5 47 166.5 48 139.0 49 155.0 50 193.5 51 194.5 52 134.0 53 113.0 54 166.5 55 130.0 56 49.0 57 40.0 58 39.0 59 32.0 60 30.5 61 36.0 62 30.0 63 23.5 64 22.5 65 18.5 66 16.0 67 16.0 68 13.0 69 8.5 70 6.0 71 5.0 72 3.0 73 3.0 74 2.5 75 0.0 76 0.5 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 0.0 36-37 0.0 38-39 0.075 40-41 0.0375 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.13749999999999998 54-55 0.0125 56-57 0.025 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 21.0 71 11.0 72 22.0 73 14.0 74 13.0 75 15.0 76 16.0 77 9.0 78 32.0 79 13.0 80 12.0 81 19.0 82 18.0 83 27.0 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 3746.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.075 #Duplication Level Percentage of deduplicated Percentage of total 1 90.75990010702817 63.6 2 5.351409204423831 7.5 3 1.1773100249732429 2.475 4 0.784873349982162 2.1999999999999997 5 0.2497324295397788 0.8750000000000001 6 0.2497324295397788 1.05 7 0.28540849090260434 1.4000000000000001 8 0.07135212272565108 0.4 9 0.10702818408847663 0.675 >10 0.8205494113449875 10.95 >50 0.07135212272565108 2.7 >100 0.07135212272565108 6.175 >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 142 3.55 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 105 2.625 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 55 1.375 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 53 1.325 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 40 1.0 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 40 1.0 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 33 0.8250000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 28 0.7000000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 24 0.6 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 23 0.575 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 22 0.5499999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 18 0.44999999999999996 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 18 0.44999999999999996 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 18 0.44999999999999996 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 17 0.42500000000000004 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 16 0.4 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 15 0.375 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 15 0.375 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 14 0.35000000000000003 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 14 0.35000000000000003 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 13 0.325 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 11 0.27499999999999997 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 11 0.27499999999999997 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 10 0.25 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 9 0.22499999999999998 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAGA 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 7 0.17500000000000002 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 7 0.17500000000000002 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 7 0.17500000000000002 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 6 0.15 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 5 0.125 No Hit GGAGGAGGTCAAGAAGGAGTACCCGGACGCCTACGTCCGCATCATCGGCT 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGA 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 5 0.125 No Hit CAACATAGGTCATCGAAAAGATCTCGGACGACTCACCAAAGCACGAAAGC 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 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 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 0.025 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 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 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 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 30 2.0653915E-6 71.572914 2 GCAATAC 25 7.6799704E-5 68.71 7 GGGAGAG 25 7.6799704E-5 68.71 1 CAATACA 25 7.6799704E-5 68.71 8 GAGCAAT 25 7.6799704E-5 68.71 5 AGAGCAA 25 7.6799704E-5 68.71 4 GAGAGCA 25 7.6799704E-5 68.71 3 AATACAA 25 7.6799704E-5 68.71 9 AGCAATA 25 7.6799704E-5 68.71 6 CATCACT 20 6.041177E-4 45.806667 82-83 AGCATCA 20 6.041177E-4 45.806667 80-81 CACTAGC 20 6.041177E-4 45.806667 86-87 TCACTAG 20 6.041177E-4 45.806667 84-85 AAAGCAT 20 6.041177E-4 45.806667 78-79 GCATCAC 20 6.041177E-4 45.806667 82-83 AAGCATC 20 6.041177E-4 45.806667 80-81 CCGAAAG 20 6.041177E-4 45.806667 76-77 AGCCGAA 20 6.245041E-4 45.50331 74-75 GCCGAAA 20 6.245041E-4 45.50331 74-75 AGTAGCC 20 6.889613E-4 44.616886 70-71 >>END_MODULE Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140389 READS because READLEN < 1 Read 140389 spots for ERR6133492.sra Written 140389 spots for ERR6133492.sra Rejected 140394 READS because READLEN < 1 Read 140394 spots for ERR6133492.sra Written 140394 spots for ERR6133492.sra SRR ids: ['ERR6133492.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_u0gnxn83 ERR6133492.sra spots: 2807785 blocks: [[1, 140389], [140390, 280778], [280779, 421167], [421168, 561556], [561557, 701945], [701946, 842334], [842335, 982723], [982724, 1123112], [1123113, 1263501], [1263502, 1403890], [1403891, 1544279], [1544280, 1684668], [1684669, 1825057], [1825058, 1965446], [1965447, 2105835], [2105836, 2246224], [2246225, 2386613], [2386614, 2527002], [2527003, 2667391], [2667392, 2807785]] ERR6133492 file size 617066 ERR6133492 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 ERR6133492 ERR6133492_1.fastq Input file: ERR6133492_1.fastq trimmed: ERR6133492-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 07:12:53 2024 >> started Sat Dec 7 07:12:55 2024 >> done (2.322s) 2807785 reads processed; of these: 226 ( 0.01%) short reads filtered out after trimming by size control 32 ( 0.00%) empty reads filtered out after trimming by size control 2807527 (99.99%) reads available; of these: 45030 ( 1.60%) trimmed reads available after processing 2762497 (98.40%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 53 0.00% 19 63 0.00% 20 26 0.00% 21 32 0.00% 22 41 0.00% 23 25 0.00% 24 15 0.00% 25 9 0.00% 26 18 0.00% 27 29 0.00% 28 51 0.00% 29 31 0.00% 30 16 0.00% 31 22 0.00% 32 23 0.00% 33 20 0.00% 34 37 0.00% 35 401 0.01% 36 421 0.01% 37 30 0.00% 38 48 0.00% 39 136 0.00% 40 87 0.00% 41 44 0.00% 42 16 0.00% 43 26 0.00% 44 19 0.00% 45 19 0.00% 46 15 0.00% 47 18 0.00% 48 18 0.00% 49 16 0.00% 50 18 0.00% 51 54 0.00% 52 17 0.00% 53 14 0.00% 54 11 0.00% 55 8 0.00% 56 18 0.00% 57 10 0.00% 58 18 0.00% 59 4 0.00% 60 17 0.00% 61 8 0.00% 62 2 0.00% 63 3 0.00% 64 4 0.00% 65 10 0.00% 66 13 0.00% 67 14 0.00% 68 36 0.00% 69 115 0.00% 70 13719 0.49% 71 11462 0.41% 72 13278 0.47% 73 11317 0.40% 74 11572 0.41% 75 12057 0.43% 76 9922 0.35% 77 10704 0.38% 78 13086 0.47% 79 15110 0.54% 80 13431 0.48% 81 14132 0.50% 82 14678 0.52% 83 16640 0.59% 84 11969 0.43% 85 91 0.00% 86 135 0.00% 87 257 0.01% 88 491 0.02% 89 924 0.03% 90 2033 0.07% 91 6031 0.21% 92 30068 1.07% 93 2572201 91.62% 2807527 reads passed initial QC criterion=sequence-density sequence-density=3.93 sequence-density-rank=1 fanout-score=1.71 fanout-score-rank=32 prefix-density=0.25 prefix-fanout=1.7 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGCGAAGTAGTACCGTGAGGGAAA criterion=fanout-score sequence-density=0.04 sequence-density-rank=18 fanout-score=45.20 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=12.9 sequence=TTTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA 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: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGCGAAGTAGTACCGTGAGGGAAA -o ERR6133492 - Input file: STDIN trimmed: ERR6133492-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sat Dec 7 07:13:04 2024 >> started Sat Dec 7 07:13:05 2024 >> done (1.337s) 1403764 reads processed; of these: 2775 ( 0.20%) short reads filtered out after trimming by size control 53093 ( 3.78%) empty reads filtered out after trimming by size control 1347896 (96.02%) reads available; of these: 19188 ( 1.42%) trimmed reads available after processing 1328708 (98.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 30 0.00% 19 29 0.00% 20 18 0.00% 21 19 0.00% 22 31 0.00% 23 13 0.00% 24 9 0.00% 25 8 0.00% 26 12 0.00% 27 16 0.00% 28 31 0.00% 29 16 0.00% 30 18 0.00% 31 330 0.02% 32 26 0.00% 33 13 0.00% 34 20 0.00% 35 206 0.02% 36 186 0.01% 37 63 0.00% 38 26 0.00% 39 77 0.01% 40 43 0.00% 41 29 0.00% 42 18 0.00% 43 12 0.00% 44 26 0.00% 45 15 0.00% 46 11 0.00% 47 10 0.00% 48 11 0.00% 49 28 0.00% 50 16 0.00% 51 24 0.00% 52 24 0.00% 53 8 0.00% 54 5 0.00% 55 6 0.00% 56 10 0.00% 57 4 0.00% 58 9 0.00% 59 3 0.00% 60 11 0.00% 61 3 0.00% 62 2 0.00% 63 0 0.00% 64 2 0.00% 65 6 0.00% 66 12 0.00% 67 103 0.01% 68 115 0.01% 69 150 0.01% 70 6857 0.51% 71 5702 0.42% 72 6628 0.49% 73 5613 0.42% 74 5749 0.43% 75 6039 0.45% 76 4965 0.37% 77 6152 0.46% 78 6785 0.50% 79 8329 0.62% 80 6806 0.50% 81 7270 0.54% 82 6763 0.50% 83 8384 0.62% 84 5690 0.42% 85 107 0.01% 86 322 0.02% 87 432 0.03% 88 1122 0.08% 89 2874 0.21% 90 12487 0.93% 91 2881 0.21% 92 14337 1.06% 93 1213689 90.04% criterion=sequence-density sequence-density=1.29 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=32 prefix-density=0.13 prefix-fanout=2.0 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGCGAAGTAGTACCGTGAGGGAAA criterion=fanout-score sequence-density=0.05 sequence-density-rank=18 fanout-score=47.18 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=13.1 sequence=TTTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA Started job on | Dec 07 07:13:20 Started mapping on | Dec 07 07:13:20 Finished on | Dec 07 07:13:25 Mapping speed, Million of reads per hour | 1981.19 Number of input reads | 2751659 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1579385 Uniquely mapped reads % | 57.40% Average mapped length | 91.08 Number of splices: Total | 71622 Number of splices: Annotated (sjdb) | 58254 Number of splices: GT/AG | 68088 Number of splices: GC/AG | 1254 Number of splices: AT/AC | 52 Number of splices: Non-canonical | 2228 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.05% Deletion average length | 1.91 Insertion rate per base | 0.03% Insertion average length | 1.94 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1112184 % of reads mapped to multiple loci | 40.42% Number of reads mapped to too many loci | 14036 % of reads mapped to too many loci | 0.51% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.64% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 60090 60090 60090 N_multimapping 1112184 1112184 1112184 N_noFeature 127549 147748 1508708 N_ambiguous 58734 8098 493 UnstrandedReadsAssigned:1393102 PositiveStrandReadsAssigned:1423539 NegativeStrandReadsAssigned:70184 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133492 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: ERR6133492-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,751,659 reads, 2,185,657 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 929 rounds 52973 ERR6133492.ke.tsv 35125 ERR6133492.se.tsv 88098 total ==> ERR6133492.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 43 19.2874 PNS24243 293 194 0 0 KQK14069 1603 1504 20 8.18354 KQK14071 474 375 0 0 ==> ERR6133492.se.tsv <== BRADI_1g14170v3 20 BRADI_1g53295v3 21 BRADI_1g59795v3 7 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 11 BRADI_1g74790v3 16 BRADI_1g09890v3 0 BRADI_1g77505v3 33 BRADI_1g48960v3 0 ERR6133492 completed mapping pipeline successfully