Starting /dee2/code/volunteer_pipeline.sh ERR6133306 current disk space = 1548421771264 free memory = 1400758936 ERR6133306 SRAfilesize 2abd5367992221bf75628c1e60020302 ERR6133306.sra ERR6133306.sra file validated ERR6133306 is single end ERR6133306 is conventional basespace ERR6133306 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133306_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 35.20325 37.0 33.0 37.0 33.0 37.0 2 36.394 37.0 37.0 37.0 33.0 37.0 3 36.015 37.0 37.0 37.0 33.0 37.0 4 35.5065 37.0 37.0 37.0 33.0 37.0 5 35.42 37.0 37.0 37.0 33.0 37.0 6 35.87825 37.0 37.0 37.0 33.0 37.0 7 37.60875 40.0 37.0 40.0 33.0 40.0 8 37.656 40.0 37.0 40.0 33.0 40.0 9 37.713 40.0 37.0 40.0 33.0 40.0 10-11 37.647625000000005 40.0 37.0 40.0 33.0 40.0 12-13 37.62125 40.0 37.0 40.0 33.0 40.0 14-15 37.633624999999995 40.0 37.0 40.0 33.0 40.0 16-17 37.51525 40.0 37.0 40.0 33.0 40.0 18-19 37.416375 37.0 37.0 40.0 33.0 40.0 20-21 37.2675 37.0 37.0 40.0 33.0 40.0 22-23 37.10625 37.0 37.0 40.0 33.0 40.0 24-25 37.30525 37.0 37.0 40.0 33.0 40.0 26-27 37.2345 37.0 37.0 40.0 33.0 40.0 28-29 37.035624999999996 37.0 37.0 40.0 33.0 40.0 30-31 37.049375 37.0 37.0 40.0 33.0 40.0 32-33 36.877875 37.0 37.0 40.0 33.0 40.0 34-35 36.824875 37.0 37.0 40.0 33.0 40.0 36-37 36.708375000000004 37.0 37.0 40.0 33.0 40.0 38-39 36.384875 37.0 37.0 40.0 33.0 40.0 40-41 36.159125 37.0 37.0 40.0 33.0 40.0 42-43 36.003875 37.0 37.0 40.0 33.0 40.0 44-45 35.57425 37.0 33.0 40.0 33.0 40.0 46-47 35.357625 37.0 33.0 38.5 30.0 40.0 48-49 35.261125 37.0 33.0 37.0 30.0 40.0 50-51 35.099125 37.0 33.0 37.0 27.0 40.0 52-53 34.826 37.0 33.0 37.0 27.0 40.0 54-55 34.705124999999995 37.0 33.0 37.0 27.0 40.0 56-57 34.470124999999996 37.0 33.0 37.0 27.0 40.0 58-59 32.138125 33.0 30.0 37.0 24.5 37.0 60-61 33.660125 37.0 33.0 37.0 27.0 37.0 62-63 33.9015 37.0 33.0 37.0 27.0 37.0 64-65 33.800875 37.0 33.0 37.0 27.0 37.0 66-67 33.558125 37.0 33.0 37.0 27.0 37.0 68-69 32.919 35.0 33.0 37.0 27.0 37.0 70-71 33.0437396225232 35.0 33.0 37.0 27.0 37.0 72-73 33.27414136104258 37.0 33.0 37.0 27.0 37.0 74-75 33.36794068919237 37.0 33.0 37.0 27.0 37.0 76-77 33.35287440979137 37.0 33.0 37.0 27.0 37.0 78-79 33.23634169397588 37.0 33.0 37.0 27.0 37.0 80-81 33.248554342042596 37.0 33.0 37.0 27.0 37.0 82-83 33.04761006572064 33.0 33.0 37.0 27.0 37.0 84-85 32.81794968595206 33.0 33.0 37.0 27.0 37.0 86-87 32.75052687038989 33.0 33.0 37.0 27.0 37.0 88-89 32.99986828240253 33.0 33.0 37.0 27.0 37.0 90-91 32.69006849315068 33.0 33.0 37.0 27.0 37.0 92-93 32.64001580611169 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 17.0 21 12.0 22 18.0 23 25.0 24 26.0 25 51.0 26 51.0 27 53.0 28 74.0 29 75.0 30 89.0 31 122.0 32 155.0 33 202.0 34 263.0 35 453.0 36 795.0 37 897.0 38 609.0 39 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.6 4.075 5.4 8.924999999999999 2 62.824999999999996 21.05 10.35 5.775 3 30.85 38.45 16.575 14.124999999999998 4 32.0 25.3 21.15 21.55 5 20.95 28.925 31.374999999999996 18.75 6 19.7 36.625 27.925 15.75 7 34.050000000000004 28.499999999999996 22.025 15.425 8 28.625 28.475 25.650000000000002 17.25 9 23.075000000000003 26.924999999999997 29.4 20.599999999999998 10-11 22.925 27.762500000000003 29.3875 19.925 12-13 24.45 26.474999999999998 28.675 20.4 14-15 20.3125 28.812500000000004 31.2 19.675 16-17 23.775 31.825 25.424999999999997 18.975 18-19 22.5625 27.9375 28.5875 20.9125 20-21 23.625 25.912499999999998 30.1875 20.275000000000002 22-23 26.987499999999997 22.2625 28.375 22.375 24-25 24.8625 26.7625 29.325000000000003 19.05 26-27 25.637500000000003 25.874999999999996 30.2125 18.275 28-29 24.75 27.200000000000003 28.6875 19.3625 30-31 24.95 26.937499999999996 27.987499999999997 20.125 32-33 23.150000000000002 27.125 30.575000000000003 19.15 34-35 23.0 27.675 27.6125 21.712500000000002 36-37 25.2875 25.137500000000003 28.487499999999997 21.087500000000002 38-39 25.912499999999998 24.587500000000002 31.225 18.275 40-41 24.7 26.6625 26.924999999999997 21.712500000000002 42-43 23.9875 28.287499999999998 27.9375 19.787499999999998 44-45 22.0125 27.3375 30.1875 20.4625 46-47 23.625 25.374999999999996 29.9 21.099999999999998 48-49 23.625 25.324999999999996 30.75 20.3 50-51 23.1625 26.637499999999996 29.775000000000002 20.424999999999997 52-53 24.69367341835459 27.306826706676667 27.881970492623154 20.117529382345587 54-55 24.3625 26.724999999999998 30.2875 18.625 56-57 26.025 26.150000000000002 29.025000000000002 18.8 58-59 23.925 26.187500000000004 30.075000000000003 19.8125 60-61 23.974999999999998 27.1125 30.2625 18.65 62-63 21.0625 30.2 31.5375 17.2 64-65 22.3 28.4375 30.725 18.5375 66-67 23.2375 29.612500000000004 28.625 18.525 68-69 21.837500000000002 27.287499999999998 28.7 22.175 70-71 22.649305120821335 27.469638162013272 29.172405158382368 20.70865155878302 72-73 25.35637693957361 25.6465245363946 28.573230730415037 20.423867793616754 74-75 23.51746031746032 28.29206349206349 29.16825396825397 19.022222222222222 76-77 22.393970362800207 27.388860500766484 28.219213081246806 21.99795605518651 78-79 23.994345199845778 25.767896157306257 30.510217195733198 19.727541447114767 80-81 23.096841015018125 28.987571206628687 30.33402382185396 17.581563956499224 82-83 22.745660968289183 26.751924833616076 30.56244290747749 19.93997129061725 84-85 22.429660794109914 23.218511701288456 34.012621614514856 20.339205890086774 86-87 21.153846153846153 26.84404636459431 31.282929399367752 20.71917808219178 88-89 20.29768177028451 29.596944151738676 30.927291886195995 19.17808219178082 90-91 24.196522655426765 27.14699683877766 30.756059009483668 17.900421496311907 92-93 21.325079030558484 30.65068493150685 29.05690200210748 18.967334035827186 >>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 0.5 16 1.5 17 16.0 18 17.5 19 3.5 20 1.5 21 2.0 22 5.5 23 9.5 24 10.5 25 12.0 26 14.0 27 18.0 28 24.5 29 26.0 30 32.5 31 53.5 32 67.0 33 81.5 34 93.5 35 100.0 36 128.5 37 180.5 38 203.0 39 184.0 40 184.5 41 210.5 42 232.5 43 240.0 44 210.5 45 165.5 46 179.0 47 181.0 48 160.0 49 167.5 50 175.5 51 152.5 52 120.0 53 125.0 54 121.5 55 85.0 56 51.0 57 40.0 58 36.0 59 30.0 60 27.5 61 28.0 62 25.5 63 17.0 64 14.5 65 14.0 66 13.0 67 11.5 68 7.0 69 6.0 70 3.5 71 1.0 72 3.5 73 5.5 74 3.5 75 2.0 76 1.5 77 0.5 78 0.0 79 0.5 80 0.5 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 0.5 92 0.5 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 0.025 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 13.0 71 13.0 72 21.0 73 11.0 74 9.0 75 14.0 76 10.0 77 10.0 78 17.0 79 14.0 80 12.0 81 16.0 82 17.0 83 13.0 84 14.0 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 3796.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.775 #Duplication Level Percentage of deduplicated Percentage of total 1 91.61992741669415 69.425 2 4.519960409105906 6.8500000000000005 3 1.3526888815572418 3.075 4 0.5608709996700759 1.7000000000000002 5 0.4618937644341801 1.7500000000000002 6 0.3629165291982844 1.6500000000000001 7 0.06598482349059716 0.35000000000000003 8 0.13196964698119432 0.8 9 0.1979544704717915 1.35 >10 0.6928406466512702 11.600000000000001 >50 0.03299241174529858 1.4500000000000002 >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 58 1.4500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 45 1.125 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 39 0.975 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 38 0.95 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 37 0.9249999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 34 0.8500000000000001 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 32 0.8 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 26 0.65 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 24 0.6 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 20 0.5 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 20 0.5 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 17 0.42500000000000004 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 17 0.42500000000000004 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 16 0.4 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 14 0.35000000000000003 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 11 0.27499999999999997 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 11 0.27499999999999997 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 11 0.27499999999999997 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 10 0.25 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 9 0.22499999999999998 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 8 0.2 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 8 0.2 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 8 0.2 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit GGATCGGTCGATCATCGGAGAAGAACACTTCCTCCGTGCATATGCGTGTA 6 0.15 No Hit GGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAAT 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGC 6 0.15 No Hit TCATCGTTCGTCCCCGACATATACATGCATAGAAGATGCAAAGACTAAAA 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 6 0.15 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 5 0.125 No Hit GATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGG 5 0.125 No Hit CAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTAT 5 0.125 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 5 0.125 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 5 0.125 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 5 0.125 No Hit GGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAA 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit GGCCGATTAATCTTCCAATATGCTAGTTTCAACAACTCTCGTTCTTTACA 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 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 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.025 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 0.0125 0.0 62-63 0.075 0.0 0.0 0.025 0.0 64-65 0.075 0.0 0.0 0.025 0.0 66-67 0.1 0.0125 0.0 0.025 0.0 68-69 0.1 0.025 0.0 0.025 0.0 70-71 0.1 0.025 0.0 0.025 0.0 72-73 0.1 0.025 0.0 0.025 0.0 74-75 0.1 0.025 0.0 0.025 0.0 76-77 0.1125 0.025 0.0 0.025 0.0 78-79 0.125 0.025 0.0 0.025 0.0 80-81 0.15 0.025 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATTCA 25 0.00679027 51.84 1 TTTCAAC 25 0.00679027 51.84 9 GATTCAA 25 0.00679027 51.84 2 >>END_MODULE Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101042 READS because READLEN < 1 Read 101042 spots for ERR6133306.sra Written 101042 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra Rejected 101025 READS because READLEN < 1 Read 101025 spots for ERR6133306.sra Written 101025 spots for ERR6133306.sra SRR ids: ['ERR6133306.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0384n85e ERR6133306.sra spots: 2020517 blocks: [[1, 101025], [101026, 202050], [202051, 303075], [303076, 404100], [404101, 505125], [505126, 606150], [606151, 707175], [707176, 808200], [808201, 909225], [909226, 1010250], [1010251, 1111275], [1111276, 1212300], [1212301, 1313325], [1313326, 1414350], [1414351, 1515375], [1515376, 1616400], [1616401, 1717425], [1717426, 1818450], [1818451, 1919475], [1919476, 2020517]] ERR6133306 file size 444321 ERR6133306 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 ERR6133306 ERR6133306_1.fastq Input file: ERR6133306_1.fastq trimmed: ERR6133306-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 00:18:33 2024 >> started Sat Dec 7 00:18:35 2024 >> done (1.765s) 2020517 reads processed; of these: 201 ( 0.01%) short reads filtered out after trimming by size control 25 ( 0.00%) empty reads filtered out after trimming by size control 2020291 (99.99%) reads available; of these: 33466 ( 1.66%) trimmed reads available after processing 1986825 (98.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 39 0.00% 19 57 0.00% 20 49 0.00% 21 71 0.00% 22 56 0.00% 23 13 0.00% 24 19 0.00% 25 6 0.00% 26 16 0.00% 27 25 0.00% 28 47 0.00% 29 43 0.00% 30 28 0.00% 31 61 0.00% 32 24 0.00% 33 29 0.00% 34 31 0.00% 35 144 0.01% 36 263 0.01% 37 39 0.00% 38 45 0.00% 39 230 0.01% 40 71 0.00% 41 90 0.00% 42 6 0.00% 43 10 0.00% 44 18 0.00% 45 12 0.00% 46 8 0.00% 47 9 0.00% 48 11 0.00% 49 11 0.00% 50 8 0.00% 51 28 0.00% 52 19 0.00% 53 4 0.00% 54 3 0.00% 55 2 0.00% 56 6 0.00% 57 9 0.00% 58 16 0.00% 59 7 0.00% 60 12 0.00% 61 12 0.00% 62 3 0.00% 63 1 0.00% 64 2 0.00% 65 3 0.00% 66 3 0.00% 67 9 0.00% 68 18 0.00% 69 91 0.00% 70 7422 0.37% 71 6566 0.33% 72 7600 0.38% 73 6469 0.32% 74 7001 0.35% 75 7375 0.37% 76 6042 0.30% 77 6157 0.30% 78 7226 0.36% 79 8051 0.40% 80 7157 0.35% 81 7809 0.39% 82 9016 0.45% 83 9008 0.45% 84 7335 0.36% 85 107 0.01% 86 161 0.01% 87 272 0.01% 88 481 0.02% 89 989 0.05% 90 1928 0.10% 91 5558 0.28% 92 20928 1.04% 93 1877796 92.95% 2020291 reads passed initial QC criterion=sequence-density sequence-density=0.73 sequence-density-rank=1 fanout-score=2.32 fanout-score-rank=33 prefix-density=0.82 prefix-fanout=2.1 sequence=TGTACATTTGAACCCTGACTACACATATACACACATATACATGTAATATTATACAATCTGTCGAGTATGTGTTGGTTCATACT criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=78.70 fanout-score-rank=1 prefix-density=0.45 prefix-fanout=1.0 sequence=GGCATTTTGGATTTCAGGGCTTTTAGCCCCGATTAGTGAAGGACCCGAAAAGCTTTCTAGTTATGAATCGGGTATAGAACCCATGGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTTGTTGTTTTTGATGTGGAAACCGTCTTTCTCTACCCTTGGGCAATGAGTTTCGACGTATTGGGTGTATCCGTTTTTATCGAAGCTTTCATTTTCGTGCTTATCCTAGTTGTTGGTTTAGTTTATGCATGGCGAAAAGGAGCCTTGGAATGGTCTTAACTGAATATTTA Started job on | Dec 07 00:18:50 Started mapping on | Dec 07 00:18:51 Finished on | Dec 07 00:18:56 Mapping speed, Million of reads per hour | 1454.61 Number of input reads | 2020291 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1258564 Uniquely mapped reads % | 62.30% Average mapped length | 91.53 Number of splices: Total | 39686 Number of splices: Annotated (sjdb) | 31312 Number of splices: GT/AG | 37683 Number of splices: GC/AG | 1000 Number of splices: AT/AC | 21 Number of splices: Non-canonical | 982 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.05% Deletion average length | 1.74 Insertion rate per base | 0.02% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 692404 % of reads mapped to multiple loci | 34.27% Number of reads mapped to too many loci | 37954 % of reads mapped to too many loci | 1.88% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.41% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 69323 69323 69323 N_multimapping 692404 692404 692404 N_noFeature 115921 128509 1203433 N_ambiguous 48826 6223 247 UnstrandedReadsAssigned:1093817 PositiveStrandReadsAssigned:1123832 NegativeStrandReadsAssigned:54884 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133306 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: ERR6133306-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,020,291 reads, 1,600,968 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 898 rounds 52973 ERR6133306.ke.tsv 35125 ERR6133306.se.tsv 88098 total ==> ERR6133306.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 27 16.5871 PNS24243 293 194 0 0 KQK14069 1603 1504 20 11.2084 KQK14071 474 375 0 0 ==> ERR6133306.se.tsv <== BRADI_1g14170v3 20 BRADI_1g53295v3 3 BRADI_1g59795v3 14 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 63 BRADI_1g48960v3 0 ERR6133306 completed mapping pipeline successfully