Starting /dee2/code/volunteer_pipeline.sh ERR6133517 current disk space = 1544418611200 free memory = 1604101396 ERR6133517 SRAfilesize 915f5fbe933cb573d032adb3b3766dc4 ERR6133517.sra ERR6133517.sra file validated ERR6133517 is single end ERR6133517 is conventional basespace ERR6133517 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133517_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 36.63525 37.0 37.0 37.0 37.0 37.0 2 36.8075 37.0 37.0 37.0 37.0 37.0 3 36.51775 37.0 37.0 37.0 37.0 37.0 4 35.96725 37.0 37.0 37.0 33.0 37.0 5 36.04225 37.0 37.0 37.0 33.0 37.0 6 36.3375 37.0 37.0 37.0 33.0 37.0 7 38.287 40.0 37.0 40.0 37.0 40.0 8 38.38025 40.0 37.0 40.0 37.0 40.0 9 38.39175 40.0 37.0 40.0 37.0 40.0 10-11 38.393125 40.0 37.0 40.0 37.0 40.0 12-13 38.295500000000004 40.0 37.0 40.0 37.0 40.0 14-15 38.277249999999995 40.0 37.0 40.0 37.0 40.0 16-17 38.226 40.0 37.0 40.0 37.0 40.0 18-19 38.146875 40.0 37.0 40.0 37.0 40.0 20-21 38.1725 40.0 37.0 40.0 37.0 40.0 22-23 38.261624999999995 40.0 37.0 40.0 37.0 40.0 24-25 38.182625 40.0 37.0 40.0 37.0 40.0 26-27 38.116125 40.0 37.0 40.0 37.0 40.0 28-29 38.109625 40.0 37.0 40.0 37.0 40.0 30-31 38.147875 40.0 37.0 40.0 37.0 40.0 32-33 38.180375 40.0 37.0 40.0 37.0 40.0 34-35 38.075125 40.0 37.0 40.0 37.0 40.0 36-37 38.038250000000005 38.5 37.0 40.0 37.0 40.0 38-39 37.829625 37.0 37.0 40.0 37.0 40.0 40-41 37.705625 37.0 37.0 40.0 37.0 40.0 42-43 37.674875 37.0 37.0 40.0 37.0 40.0 44-45 37.482124999999996 37.0 37.0 40.0 35.0 40.0 46-47 37.355000000000004 37.0 37.0 40.0 35.0 40.0 48-49 37.174 37.0 37.0 40.0 33.0 40.0 50-51 36.977500000000006 37.0 37.0 37.0 33.0 40.0 52-53 36.582375 37.0 37.0 37.0 33.0 40.0 54-55 36.592375000000004 37.0 37.0 37.0 33.0 40.0 56-57 36.43775 37.0 37.0 37.0 33.0 40.0 58-59 36.045 37.0 37.0 37.0 33.0 37.0 60-61 36.165125 37.0 37.0 37.0 33.0 37.0 62-63 35.9775 37.0 37.0 37.0 33.0 37.0 64-65 35.912375 37.0 37.0 37.0 33.0 37.0 66-67 35.885125 37.0 37.0 37.0 33.0 37.0 68-69 34.982625 35.0 35.0 37.0 33.0 37.0 70-71 35.12913143036387 37.0 33.0 37.0 33.0 37.0 72-73 35.55857428669411 37.0 33.0 37.0 33.0 37.0 74-75 35.59317996166199 37.0 33.0 37.0 33.0 37.0 76-77 35.50191031474672 37.0 33.0 37.0 33.0 37.0 78-79 35.514328290668885 37.0 33.0 37.0 33.0 37.0 80-81 35.36750164224002 37.0 33.0 37.0 33.0 37.0 82-83 35.25150011212993 37.0 33.0 37.0 33.0 37.0 84-85 35.113378723884566 37.0 33.0 37.0 33.0 37.0 86-87 35.10661478599222 37.0 33.0 37.0 33.0 37.0 88-89 35.02178988326848 37.0 33.0 37.0 33.0 37.0 90-91 34.96199740596627 37.0 33.0 37.0 33.0 37.0 92-93 34.93450064850843 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 0.0 23 4.0 24 2.0 25 7.0 26 12.0 27 12.0 28 10.0 29 23.0 30 26.0 31 32.0 32 53.0 33 65.0 34 114.0 35 275.0 36 1079.0 37 1420.0 38 852.0 39 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.625 2.075 3.35 5.949999999999999 2 72.3 15.825 7.6 4.275 3 34.975 40.050000000000004 13.750000000000002 11.225 4 34.150000000000006 26.950000000000003 18.675 20.225 5 24.95 30.725 26.3 18.025 6 19.775000000000002 37.05 26.8 16.375 7 35.825 29.45 19.775000000000002 14.95 8 30.25 31.624999999999996 22.825 15.299999999999999 9 25.724999999999998 28.575 28.625 17.075000000000003 10-11 25.5125 28.6625 27.987499999999997 17.837500000000002 12-13 27.5625 26.875 28.287499999999998 17.275 14-15 22.0 30.8125 29.075 18.1125 16-17 23.65 31.2625 26.775 18.3125 18-19 22.925 28.1125 28.675 20.2875 20-21 23.990498812351543 26.140767595949495 29.216152019002372 20.652581572696587 22-23 27.0875 24.7875 27.762500000000003 20.3625 24-25 25.275 25.825 29.262500000000003 19.6375 26-27 25.025 24.6125 31.65 18.712500000000002 28-29 26.174999999999997 27.05 27.500000000000004 19.275000000000002 30-31 25.112499999999997 27.400000000000002 28.249999999999996 19.2375 32-33 23.150000000000002 27.425 28.525 20.9 34-35 24.2375 27.0875 27.6 21.075 36-37 23.875 25.2875 29.675 21.1625 38-39 26.3125 25.687500000000004 29.599999999999998 18.4 40-41 27.097661623108664 25.184444166562457 27.485306990121295 20.23258722020758 42-43 25.35633908477119 27.53188297074269 28.28207051762941 18.829707426856714 44-45 23.1625 25.7125 30.4 20.724999999999998 46-47 23.7125 24.8 30.4625 21.025 48-49 23.8875 25.525 31.162499999999998 19.425 50-51 24.962500000000002 26.1 29.512500000000003 19.425 52-53 25.37313432835821 26.865671641791046 27.442618838580206 20.31857519127054 54-55 24.54056757094637 28.62857857232154 29.316164520565067 17.514689336167024 56-57 25.75 26.05 28.7375 19.4625 58-59 25.3125 24.7375 29.175 20.775 60-61 24.3875 26.150000000000002 30.362499999999997 19.1 62-63 22.15 27.737499999999997 32.225 17.8875 64-65 23.7 27.450000000000003 29.462500000000002 19.3875 66-67 24.224999999999998 26.6 29.6875 19.4875 68-69 22.3625 27.6375 28.1 21.9 70-71 23.782091421415153 27.388854101440202 28.10269254852849 20.726361928616154 72-73 25.254684945289902 25.896113696390394 27.958747327380202 20.890454030939505 74-75 22.3697521497218 27.9969650986343 30.070814365199798 19.562468386444106 76-77 23.471200202994165 25.666074600355238 29.43415376807917 21.428571428571427 78-79 23.754301006754176 25.079648273225434 31.974002803619218 19.192047916401172 80-81 22.483994878361074 29.871959026888607 29.897567221510883 17.74647887323944 82-83 23.34580162517735 25.82226235005804 29.66593576679995 21.166000257964658 84-85 23.379989631933647 24.624157594608604 31.700362882322448 20.295489891135304 86-87 22.451361867704282 26.1348897535668 31.86770428015564 19.546044098573283 88-89 21.64721141374838 28.378728923476004 30.804150453955902 19.169909208819718 90-91 25.473411154345005 25.979247730220496 29.416342412451364 19.13099870298314 92-93 22.762645914396888 29.234760051880677 30.06485084306096 17.93774319066148 >>END_MODULE >>Per sequence GC content pass #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 4.5 18 5.5 19 1.5 20 1.0 21 2.5 22 2.5 23 3.5 24 4.0 25 5.0 26 5.0 27 6.0 28 20.0 29 30.0 30 36.0 31 40.5 32 43.0 33 55.0 34 70.0 35 83.0 36 118.5 37 150.0 38 187.5 39 205.5 40 210.5 41 213.5 42 213.5 43 235.0 44 223.5 45 212.0 46 230.5 47 204.0 48 180.5 49 189.0 50 164.5 51 157.0 52 159.5 53 150.0 54 131.0 55 89.5 56 59.5 57 57.5 58 51.5 59 33.0 60 17.5 61 12.5 62 11.0 63 15.5 64 14.0 65 7.0 66 5.5 67 8.5 68 8.0 69 5.0 70 3.0 71 1.0 72 0.5 73 1.0 74 1.5 75 1.0 76 0.5 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 0.0125 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 0.0 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 0.3375 54-55 0.0125 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 15.0 71 5.0 72 9.0 73 12.0 74 10.0 75 5.0 76 6.0 77 12.0 78 5.0 79 10.0 80 12.0 81 16.0 82 13.0 83 9.0 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 3855.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.675 #Duplication Level Percentage of deduplicated Percentage of total 1 93.15971132726702 74.225 2 3.6397866331973643 5.800000000000001 3 1.349231251961092 3.225 4 0.3765296517100722 1.2 5 0.2823972387825541 1.125 6 0.25101976780671476 1.2 7 0.12550988390335738 0.7000000000000001 8 0.21964229683087544 1.4000000000000001 9 0.0 0.0 >10 0.5647944775651083 9.75 >50 0.031377470975839344 1.375 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 55 1.375 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 37 0.9249999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 36 0.8999999999999999 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 34 0.8500000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 32 0.8 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 32 0.8 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 25 0.625 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 20 0.5 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 20 0.5 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 20 0.5 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 17 0.42500000000000004 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 16 0.4 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 11 0.27499999999999997 No Hit GGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAG 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 8 0.2 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTT 7 0.17500000000000002 No Hit GGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGAGAGTGTGAGCATATATATTTATACGACGAATAAAAGTCTGCCACGTG 6 0.15 No Hit GGGTGTGAGCTGGAGAGACGATCGGGTCTCTCAGCCGGCGTCTTCATCAG 6 0.15 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 6 0.15 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAACACAGGG 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCA 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 0.0 0.0 0.0 0.0 0.0 40-41 0.0125 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 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGGAGG 15 9.013085E-4 86.262505 2 GGGCGGG 15 9.013085E-4 86.262505 1 CAATTTC 20 0.0028236145 64.69688 6 GGATTCA 20 0.0028236145 64.69688 1 GATTCAA 20 0.0028236145 64.69688 2 GGAGGAG 20 0.0028236145 64.69688 1 ATTCAAT 20 0.0028236145 64.69688 3 TTCAATT 25 0.006833191 51.7575 4 TCAATTT 25 0.006833191 51.7575 5 ATTTCAA 25 0.006833191 51.7575 8 ATCAACC 30 0.0056089875 29.118145 66-67 >>END_MODULE Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79646 READS because READLEN < 1 Read 79646 spots for ERR6133517.sra Written 79646 spots for ERR6133517.sra Rejected 79655 READS because READLEN < 1 Read 79655 spots for ERR6133517.sra Written 79655 spots for ERR6133517.sra SRR ids: ['ERR6133517.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_eo3z7wcs ERR6133517.sra spots: 1592929 blocks: [[1, 79646], [79647, 159292], [159293, 238938], [238939, 318584], [318585, 398230], [398231, 477876], [477877, 557522], [557523, 637168], [637169, 716814], [716815, 796460], [796461, 876106], [876107, 955752], [955753, 1035398], [1035399, 1115044], [1115045, 1194690], [1194691, 1274336], [1274337, 1353982], [1353983, 1433628], [1433629, 1513274], [1513275, 1592929]] ERR6133517 file size 350729 ERR6133517 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 ERR6133517 ERR6133517_1.fastq Input file: ERR6133517_1.fastq trimmed: ERR6133517-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 07:45:12 2024 >> started Sat Dec 7 07:45:13 2024 >> done (0.924s) 1592929 reads processed; of these: 252 ( 0.02%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 1592661 (99.98%) reads available; of these: 7672 ( 0.48%) trimmed reads available after processing 1584989 (99.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 23 0.00% 19 48 0.00% 20 18 0.00% 21 21 0.00% 22 18 0.00% 23 12 0.00% 24 13 0.00% 25 9 0.00% 26 8 0.00% 27 17 0.00% 28 25 0.00% 29 130 0.01% 30 12 0.00% 31 15 0.00% 32 21 0.00% 33 16 0.00% 34 16 0.00% 35 138 0.01% 36 236 0.01% 37 12 0.00% 38 29 0.00% 39 38 0.00% 40 85 0.01% 41 18 0.00% 42 7 0.00% 43 16 0.00% 44 10 0.00% 45 14 0.00% 46 7 0.00% 47 1 0.00% 48 4 0.00% 49 8 0.00% 50 2 0.00% 51 35 0.00% 52 15 0.00% 53 6 0.00% 54 3 0.00% 55 3 0.00% 56 4 0.00% 57 7 0.00% 58 8 0.00% 59 3 0.00% 60 7 0.00% 61 8 0.00% 62 0 0.00% 63 1 0.00% 64 0 0.00% 65 1 0.00% 66 2 0.00% 67 6 0.00% 68 6 0.00% 69 28 0.00% 70 4386 0.28% 71 3734 0.23% 72 3940 0.25% 73 3724 0.23% 74 3633 0.23% 75 3582 0.22% 76 3269 0.21% 77 3228 0.20% 78 3557 0.22% 79 3725 0.23% 80 3554 0.22% 81 4041 0.25% 82 4345 0.27% 83 4182 0.26% 84 3863 0.24% 85 27 0.00% 86 48 0.00% 87 66 0.00% 88 96 0.01% 89 201 0.01% 90 401 0.03% 91 1087 0.07% 92 4273 0.27% 93 1528509 95.97% 1592661 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=36 prefix-density=0.52 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=89.81 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=6.7 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTAT Started job on | Dec 07 07:45:26 Started mapping on | Dec 07 07:45:26 Finished on | Dec 07 07:45:29 Mapping speed, Million of reads per hour | 1911.19 Number of input reads | 1592661 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1126166 Uniquely mapped reads % | 70.71% Average mapped length | 92.01 Number of splices: Total | 65196 Number of splices: Annotated (sjdb) | 55109 Number of splices: GT/AG | 63051 Number of splices: GC/AG | 1157 Number of splices: AT/AC | 38 Number of splices: Non-canonical | 950 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.04% Deletion average length | 1.88 Insertion rate per base | 0.03% Insertion average length | 1.53 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 420833 % of reads mapped to multiple loci | 26.42% Number of reads mapped to too many loci | 12705 % of reads mapped to too many loci | 0.80% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.03% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 45662 45662 45662 N_multimapping 420833 420833 420833 N_noFeature 80326 90128 1078841 N_ambiguous 42777 5243 145 UnstrandedReadsAssigned:1003063 PositiveStrandReadsAssigned:1030795 NegativeStrandReadsAssigned:47180 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133517 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: ERR6133517-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,592,661 reads, 1,340,198 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 962 rounds 52973 ERR6133517.ke.tsv 35125 ERR6133517.se.tsv 88098 total ==> ERR6133517.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 52 36.8434 PNS24243 293 194 0 0 KQK14069 1603 1504 16 10.3415 KQK14071 474 375 0 0 ==> ERR6133517.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 5 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 28 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 44 BRADI_1g48960v3 0 ERR6133517 completed mapping pipeline successfully