Starting /dee2/code/volunteer_pipeline.sh ERR6133566 current disk space = 1544477233152 free memory = 1421397044 ERR6133566 SRAfilesize 750c45d5fdb27a89bdaea94f1b56ec33 ERR6133566.sra ERR6133566.sra file validated ERR6133566 is single end ERR6133566 is conventional basespace ERR6133566 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133566_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 35.60725 37.0 33.0 37.0 33.0 37.0 2 36.537 37.0 37.0 37.0 37.0 37.0 3 36.08075 37.0 37.0 37.0 33.0 37.0 4 35.51225 37.0 37.0 37.0 33.0 37.0 5 35.4175 37.0 37.0 37.0 33.0 37.0 6 35.7825 37.0 37.0 37.0 33.0 37.0 7 37.54475 40.0 37.0 40.0 33.0 40.0 8 37.5995 40.0 37.0 40.0 33.0 40.0 9 37.634 40.0 37.0 40.0 33.0 40.0 10-11 37.503874999999994 40.0 37.0 40.0 33.0 40.0 12-13 37.45575 38.5 37.0 40.0 33.0 40.0 14-15 37.456125 37.0 37.0 40.0 33.0 40.0 16-17 37.482124999999996 38.5 37.0 40.0 33.0 40.0 18-19 37.366125 37.0 37.0 40.0 33.0 40.0 20-21 37.206125 37.0 37.0 40.0 33.0 40.0 22-23 37.23975 37.0 37.0 40.0 33.0 40.0 24-25 37.307125 37.0 37.0 40.0 33.0 40.0 26-27 37.198 37.0 37.0 40.0 33.0 40.0 28-29 37.217625 37.0 37.0 40.0 33.0 40.0 30-31 37.11 37.0 37.0 40.0 33.0 40.0 32-33 36.922625 37.0 37.0 40.0 33.0 40.0 34-35 36.893125 37.0 37.0 40.0 33.0 40.0 36-37 36.66275 37.0 37.0 40.0 33.0 40.0 38-39 36.575874999999996 37.0 37.0 40.0 33.0 40.0 40-41 36.424625 37.0 37.0 40.0 33.0 40.0 42-43 36.43025 37.0 37.0 40.0 33.0 40.0 44-45 36.141625 37.0 37.0 40.0 33.0 40.0 46-47 35.833625 37.0 33.0 40.0 33.0 40.0 48-49 35.7145 37.0 33.0 38.5 33.0 40.0 50-51 35.65675 37.0 33.0 37.0 33.0 40.0 52-53 35.34525 37.0 33.0 37.0 33.0 40.0 54-55 35.239875 37.0 33.0 37.0 33.0 40.0 56-57 35.034625 37.0 33.0 37.0 33.0 40.0 58-59 33.9785 37.0 33.0 37.0 27.0 37.0 60-61 34.554375 37.0 33.0 37.0 27.0 37.0 62-63 34.562375 37.0 33.0 37.0 27.0 37.0 64-65 34.46025 37.0 33.0 37.0 27.0 37.0 66-67 34.553125 37.0 33.0 37.0 30.0 37.0 68-69 33.8515 35.0 33.0 37.0 27.0 37.0 70-71 34.017096629425055 37.0 33.0 37.0 27.0 37.0 72-73 34.35577991701351 37.0 33.0 37.0 27.0 37.0 74-75 34.214693097338106 37.0 33.0 37.0 27.0 37.0 76-77 34.183549611481254 37.0 33.0 37.0 27.0 37.0 78-79 34.20097033948011 37.0 33.0 37.0 27.0 37.0 80-81 34.099976991934156 37.0 33.0 37.0 27.0 37.0 82-83 33.961633233020905 37.0 33.0 37.0 27.0 37.0 84-85 33.953672130202136 37.0 33.0 37.0 27.0 37.0 86-87 33.8974560713349 37.0 33.0 37.0 27.0 37.0 88-89 33.853920797272494 37.0 33.0 37.0 27.0 37.0 90-91 33.59900340938893 37.0 33.0 37.0 27.0 37.0 92-93 33.59624967217414 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 13.0 21 15.0 22 16.0 23 23.0 24 24.0 25 22.0 26 36.0 27 42.0 28 49.0 29 62.0 30 63.0 31 112.0 32 136.0 33 159.0 34 242.0 35 409.0 36 852.0 37 931.0 38 755.0 39 39.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 78.64999999999999 6.1 8.05 7.199999999999999 2 68.975 16.3 8.475000000000001 6.25 3 34.4 37.35 17.150000000000002 11.1 4 29.325000000000003 31.874999999999996 20.875 17.925 5 23.35 34.449999999999996 24.675 17.525 6 22.475 39.574999999999996 23.3 14.649999999999999 7 37.675 29.175 19.325 13.825000000000001 8 34.625 29.799999999999997 21.75 13.825000000000001 9 29.525000000000002 27.675 25.874999999999996 16.925 10-11 28.225 29.075 26.2625 16.4375 12-13 29.425 26.087500000000002 28.325 16.162499999999998 14-15 22.375 30.0875 28.925 18.6125 16-17 23.275000000000002 33.0125 27.075 16.6375 18-19 23.5375 27.075 28.499999999999996 20.8875 20-21 24.52806600825103 25.86573321665208 28.653581697712216 20.952619077384675 22-23 25.5375 24.55 29.212500000000002 20.7 24-25 24.706176544136035 26.431607901975497 28.857214303575894 20.005001250312578 26-27 24.2625 25.137500000000003 31.75 18.85 28-29 24.968742185546386 25.03125781445361 29.544886221555387 20.455113778444613 30-31 24.975 24.0125 30.025000000000002 20.9875 32-33 24.1875 26.2125 29.4 20.200000000000003 34-35 25.8625 25.5625 27.800000000000004 20.775 36-37 24.3125 24.9125 30.3 20.474999999999998 38-39 26.3625 24.8625 28.875 19.900000000000002 40-41 25.1 25.5375 29.1625 20.200000000000003 42-43 23.5 27.3 29.5375 19.662499999999998 44-45 23.2875 26.5125 30.3875 19.8125 46-47 24.5375 24.087500000000002 31.0125 20.3625 48-49 24.2375 25.45 30.4375 19.875 50-51 23.400000000000002 26.8 29.7875 20.0125 52-53 24.56777749937359 26.196441994487596 29.353545477323976 19.882235028814836 54-55 23.275000000000002 25.525 31.55 19.650000000000002 56-57 24.95 25.474999999999998 31.05 18.525 58-59 23.6625 25.074999999999996 31.112499999999997 20.150000000000002 60-61 24.425 25.25 31.05 19.275000000000002 62-63 22.725 27.575 30.525000000000002 19.175 64-65 23.974999999999998 25.924999999999997 31.7625 18.337500000000002 66-67 22.912499999999998 27.425 30.7875 18.875 68-69 22.037499999999998 25.912499999999998 31.225 20.825 70-71 22.77339346110485 25.140924464487036 30.590003757985716 21.4956783164224 72-73 26.006309148264982 25.968454258675077 29.21135646687697 18.813880126182966 74-75 23.194109432525075 26.64720071093056 30.176463120477337 19.98222673606703 76-77 21.965539246968728 26.547543075941288 31.01467772814295 20.47223994894703 78-79 24.1840143921871 24.865073245952196 32.52377280904652 18.427139552814186 80-81 21.55317224447603 27.858896498255586 32.43313089546453 18.15480036180385 82-83 22.077753218047068 26.342478221297622 31.647380054609282 19.932388506046028 84-85 22.92676536093279 23.621118826149615 33.355168347962795 20.096947464954802 86-87 22.003671649619722 25.872016784683975 33.044846577498035 19.079464988198268 88-89 21.28245476003147 28.888014686598478 32.20561237870444 17.62391817466562 90-91 23.721479150275375 27.550485182271178 30.81563073695253 17.91240493050092 92-93 21.53160241279832 27.734067663257278 31.628638867033832 19.10569105691057 >>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 1.5 20 0.0 21 0.5 22 1.0 23 3.5 24 6.0 25 5.5 26 5.0 27 8.0 28 23.0 29 35.5 30 32.0 31 33.0 32 51.5 33 88.5 34 110.5 35 120.5 36 137.0 37 167.0 38 205.5 39 218.0 40 232.5 41 252.5 42 248.0 43 235.5 44 214.5 45 192.5 46 178.0 47 174.5 48 180.5 49 169.0 50 160.5 51 132.5 52 96.0 53 100.5 54 87.5 55 58.5 56 56.5 57 60.5 58 53.0 59 37.5 60 28.0 61 22.0 62 24.5 63 26.5 64 22.0 65 18.0 66 12.0 67 11.5 68 8.5 69 5.5 70 5.0 71 3.0 72 2.5 73 2.5 74 3.0 75 1.5 76 1.0 77 1.0 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 0.025 26-27 0.0 28-29 0.025 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 0.22499999999999998 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 17.0 71 13.0 72 15.0 73 9.0 74 15.0 75 6.0 76 15.0 77 14.0 78 10.0 79 12.0 80 9.0 81 11.0 82 17.0 83 17.0 84 7.0 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 3813.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.575 #Duplication Level Percentage of deduplicated Percentage of total 1 90.47471300031027 72.89999999999999 2 5.491777846726652 8.85 3 1.768538628606888 4.275 4 0.8067018305926157 2.6 5 0.40335091529630784 1.625 6 0.12410797393732546 0.6 7 0.18616196090598822 1.05 8 0.12410797393732546 0.8 9 0.12410797393732546 0.8999999999999999 >10 0.49643189574930185 6.4 >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 warn #Sequence Count Percentage Possible Source TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 31 0.775 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 26 0.65 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 24 0.6 No Hit TTCACAAGTCTGGTTCAGGGTGTCCTCCGGTGGAGTTGTCGCGTGTCTGA 18 0.44999999999999996 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 17 0.42500000000000004 No Hit CATTACTGATGGAGTGATGGTCCATAGAGCATTAGTTTCACTACCTTCGC 16 0.4 No Hit CTTTAGCATAATGAGCTGGCCTATTTTGAACGAGGACGTATGATATGATT 15 0.375 No Hit CCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTT 15 0.375 No Hit AGTTCCATCTTGTCTTCTCTTTTTATTTTGTTCGCATCGTCGAAGGCAAC 14 0.35000000000000003 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 13 0.325 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 13 0.325 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 12 0.3 No Hit ACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATG 11 0.27499999999999997 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 11 0.27499999999999997 No Hit GATATCTATCTGAACTGAGAACTGAGTCAGTATATACCAGTCTGTATCAC 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit TCATCGTTCGTCCCCGACATATACATGCATAGAAGATGCAAAGACTAAAA 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GGGGAAGAAGAATGCTGGCAAAATTAATTTGCTTTTTTTGGGGAGAATGG 9 0.22499999999999998 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 9 0.22499999999999998 No Hit TAATTAAGAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAA 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit AAGACTGGTATTCAGTACTCTGCAGATATTTAGCAGAGAACTATGTGTAC 8 0.2 No Hit GGAGATGGTGAATTTGAGAACAGTCCTTGCACTGCCGAGCTGGTGGAAGA 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit TGAGTATGATGAGTCTGGTCCAGCGATTGTTCACAGGAAGTGCTTCTAAG 7 0.17500000000000002 No Hit CTGAGCCGTGCTCTCTTCTGTGTACATCTTCATGTCATTTTAGCGATTCT 7 0.17500000000000002 No Hit GGAGTAAACTAGCATAAATAATTTGTTTGATGCCAGTCATCAAGGTTGAG 7 0.17500000000000002 No Hit TGGTGTGTAGGAAGGGAATAGATCATTAGATTGTACTATGGAACAAGAAC 7 0.17500000000000002 No Hit GGGCAAGTTCATGTAAACATAGATCGATATATGGCGGAGCGCCATTTTAT 7 0.17500000000000002 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 6 0.15 No Hit GGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCGGCACCAGCTGCG 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit CAAAAACATATCTGGAATATATCTGAAACATACTCCTGTACATCTGTGAG 6 0.15 No Hit GGAGGAGAGCGGCGGCGGTCTGTTCAAGATGGCTCAGGGCTTCATGAAGT 5 0.125 No Hit GAGACGCACAAGGAAGAAGAGCTCACCGCCTAAGTTTTTAGTCTTCAGCT 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit TATATGTAAAAACTCAACTCCTTGAGTCTTGCCTGGTCCGATGTAAATAT 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 5 0.125 No Hit GAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAACACAGGG 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACACATATACATGTAATATTATAC 5 0.125 No Hit TTCCATGAATGTATGTATGTACGTATATCTATGATGTAGATACACATTTC 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 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 0.025 0.0 28-29 0.0 0.0 0.0 0.025 0.0 30-31 0.0 0.0 0.0 0.025 0.0 32-33 0.0 0.0 0.0 0.025 0.0 34-35 0.0 0.0 0.0 0.025 0.0 36-37 0.05 0.0 0.0 0.025 0.0 38-39 0.125 0.0 0.0 0.025 0.0 40-41 0.125 0.0 0.0 0.025 0.0 42-43 0.15 0.0 0.0 0.025 0.0 44-45 0.15 0.0 0.0 0.025 0.0 46-47 0.15 0.0 0.0 0.025 0.0 48-49 0.15 0.0 0.0 0.025 0.0 50-51 0.15 0.0 0.0 0.025 0.0 52-53 0.15 0.0 0.0 0.025 0.0 54-55 0.15 0.0 0.0 0.025 0.0 56-57 0.15 0.0 0.0 0.025 0.0 58-59 0.175 0.0 0.0 0.025 0.0 60-61 0.2 0.0 0.0 0.025 0.0 62-63 0.2 0.0 0.0 0.025 0.0 64-65 0.2 0.0 0.0 0.025 0.0 66-67 0.2 0.0 0.0 0.025 0.0 68-69 0.2 0.0 0.0 0.025 0.0 70-71 0.2 0.0 0.0 0.025 0.0 72-73 0.2 0.0 0.0 0.025 0.0 74-75 0.2 0.0 0.0 0.025 0.0 76-77 0.2 0.0 0.0 0.025 0.0 78-79 0.2 0.0 0.0 0.025 0.0 80-81 0.21250000000000002 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14521 READS because READLEN < 1 Read 14521 spots for ERR6133566.sra Written 14521 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra Rejected 14502 READS because READLEN < 1 Read 14502 spots for ERR6133566.sra Written 14502 spots for ERR6133566.sra SRR ids: ['ERR6133566.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_e6y4jrzj ERR6133566.sra spots: 290059 blocks: [[1, 14502], [14503, 29004], [29005, 43506], [43507, 58008], [58009, 72510], [72511, 87012], [87013, 101514], [101515, 116016], [116017, 130518], [130519, 145020], [145021, 159522], [159523, 174024], [174025, 188526], [188527, 203028], [203029, 217530], [217531, 232032], [232033, 246534], [246535, 261036], [261037, 275538], [275539, 290059]] ERR6133566 file size 63384 ERR6133566 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 ERR6133566 ERR6133566_1.fastq Input file: ERR6133566_1.fastq trimmed: ERR6133566-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 08:45:46 2024 >> started Sat Dec 7 08:45:46 2024 >> done (0.238s) 290059 reads processed; of these: 102 ( 0.04%) short reads filtered out after trimming by size control 78 ( 0.03%) empty reads filtered out after trimming by size control 289879 (99.94%) reads available; of these: 6182 ( 2.13%) trimmed reads available after processing 283697 (97.87%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 9 0.00% 20 1 0.00% 21 3 0.00% 22 6 0.00% 23 1 0.00% 24 0 0.00% 25 0 0.00% 26 0 0.00% 27 2 0.00% 28 3 0.00% 29 34 0.01% 30 0 0.00% 31 4 0.00% 32 7 0.00% 33 8 0.00% 34 8 0.00% 35 25 0.01% 36 416 0.14% 37 20 0.01% 38 12 0.00% 39 19 0.01% 40 20 0.01% 41 13 0.00% 42 13 0.00% 43 12 0.00% 44 9 0.00% 45 16 0.01% 46 19 0.01% 47 22 0.01% 48 17 0.01% 49 14 0.00% 50 7 0.00% 51 10 0.00% 52 20 0.01% 53 20 0.01% 54 10 0.00% 55 4 0.00% 56 13 0.00% 57 12 0.00% 58 8 0.00% 59 6 0.00% 60 9 0.00% 61 7 0.00% 62 0 0.00% 63 0 0.00% 64 1 0.00% 65 0 0.00% 66 1 0.00% 67 0 0.00% 68 4 0.00% 69 11 0.00% 70 943 0.33% 71 859 0.30% 72 887 0.31% 73 765 0.26% 74 903 0.31% 75 822 0.28% 76 786 0.27% 77 773 0.27% 78 756 0.26% 79 900 0.31% 80 943 0.33% 81 950 0.33% 82 1126 0.39% 83 1292 0.45% 84 878 0.30% 85 4 0.00% 86 46 0.02% 87 39 0.01% 88 61 0.02% 89 133 0.05% 90 235 0.08% 91 622 0.21% 92 4018 1.39% 93 270257 93.23% 289879 reads passed initial QC criterion=sequence-density sequence-density=0.68 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=22 prefix-density=0.00 prefix-fanout=1.0 sequence=GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACA criterion=fanout-score sequence-density=0.18 sequence-density-rank=17 fanout-score=19.52 fanout-score-rank=1 prefix-density=0.58 prefix-fanout=6.0 sequence=GATGATGATGATCGATCGATGGACTACTTGTAATTTTAAAGTTTCAACGATGGGGATTCAGCGATGATTATATGTACATGTGTAATTAATT Started job on | Dec 07 08:45:57 Started mapping on | Dec 07 08:45:58 Finished on | Dec 07 08:46:01 Mapping speed, Million of reads per hour | 347.85 Number of input reads | 289879 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 251501 Uniquely mapped reads % | 86.76% Average mapped length | 91.89 Number of splices: Total | 6752 Number of splices: Annotated (sjdb) | 5602 Number of splices: GT/AG | 6352 Number of splices: GC/AG | 277 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 123 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 1.90 Insertion rate per base | 0.02% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 31204 % of reads mapped to multiple loci | 10.76% Number of reads mapped to too many loci | 914 % of reads mapped to too many loci | 0.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.12% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7174 7174 7174 N_multimapping 31204 31204 31204 N_noFeature 15056 17341 239987 N_ambiguous 9978 753 20 UnstrandedReadsAssigned:226467 PositiveStrandReadsAssigned:233407 NegativeStrandReadsAssigned:11494 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133566 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: ERR6133566-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 289,879 reads, 248,089 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 819 rounds 52973 ERR6133566.ke.tsv 35125 ERR6133566.se.tsv 88098 total ==> ERR6133566.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 1 6.668 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 0 0 KQK14071 474 375 0 0 ==> ERR6133566.se.tsv <== BRADI_1g14170v3 0 BRADI_1g53295v3 11 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 ERR6133566 completed mapping pipeline successfully