Starting /dee2/code/volunteer_pipeline.sh ERR6133458 current disk space = 1545491107840 free memory = 1596405696 ERR6133458 SRAfilesize 99de989a04a6b43f29802d49b41d8de7 ERR6133458.sra ERR6133458.sra file validated ERR6133458 is single end ERR6133458 is conventional basespace ERR6133458 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133458_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.82675 37.0 33.0 37.0 33.0 37.0 2 36.13925 37.0 37.0 37.0 33.0 37.0 3 35.157 37.0 33.0 37.0 33.0 37.0 4 34.6765 37.0 33.0 37.0 27.0 37.0 5 34.62275 37.0 33.0 37.0 27.0 37.0 6 34.95075 37.0 33.0 37.0 33.0 37.0 7 36.5025 37.0 37.0 40.0 33.0 40.0 8 36.69825 37.0 37.0 40.0 33.0 40.0 9 36.91025 37.0 37.0 40.0 33.0 40.0 10-11 36.844875 37.0 37.0 40.0 33.0 40.0 12-13 36.75075 37.0 37.0 40.0 33.0 40.0 14-15 36.69525 37.0 37.0 40.0 33.0 40.0 16-17 36.528 37.0 37.0 40.0 33.0 40.0 18-19 36.111625000000004 37.0 37.0 40.0 33.0 40.0 20-21 36.004875 37.0 33.0 40.0 33.0 40.0 22-23 35.683875 37.0 33.0 40.0 30.0 40.0 24-25 35.958124999999995 37.0 33.0 40.0 33.0 40.0 26-27 36.18675 37.0 35.0 40.0 33.0 40.0 28-29 36.08775 37.0 33.0 40.0 33.0 40.0 30-31 36.115375 37.0 35.0 40.0 33.0 40.0 32-33 35.954375 37.0 33.0 40.0 33.0 40.0 34-35 35.867875 37.0 33.0 40.0 33.0 40.0 36-37 35.86925 37.0 33.0 40.0 33.0 40.0 38-39 35.720749999999995 37.0 33.0 40.0 33.0 40.0 40-41 35.620000000000005 37.0 33.0 40.0 33.0 40.0 42-43 35.623374999999996 37.0 33.0 40.0 33.0 40.0 44-45 35.235125 37.0 33.0 37.0 30.0 40.0 46-47 35.322125 37.0 33.0 37.0 30.0 40.0 48-49 35.409875 37.0 33.0 37.0 33.0 40.0 50-51 35.231625 37.0 33.0 37.0 33.0 40.0 52-53 35.027 37.0 33.0 37.0 27.0 40.0 54-55 35.014375 37.0 33.0 37.0 33.0 40.0 56-57 34.825874999999996 37.0 33.0 37.0 33.0 38.5 58-59 34.224000000000004 37.0 33.0 37.0 27.0 37.0 60-61 34.46675 37.0 33.0 37.0 27.0 37.0 62-63 34.371125000000006 37.0 33.0 37.0 27.0 37.0 64-65 34.104749999999996 37.0 33.0 37.0 27.0 37.0 66-67 33.951375 37.0 33.0 37.0 27.0 37.0 68-69 33.181250000000006 35.0 33.0 37.0 27.0 37.0 70-71 33.35006119889641 33.0 33.0 37.0 27.0 37.0 72-73 33.72159257634924 37.0 33.0 37.0 27.0 37.0 74-75 33.732760759093985 37.0 33.0 37.0 27.0 37.0 76-77 33.87380211867614 37.0 33.0 37.0 27.0 37.0 78-79 33.645819531543054 37.0 33.0 37.0 27.0 37.0 80-81 33.691371294687514 37.0 33.0 37.0 27.0 37.0 82-83 33.48458230958231 37.0 33.0 37.0 27.0 37.0 84-85 33.35371830726562 35.0 33.0 37.0 27.0 37.0 86-87 33.26991150442478 33.0 33.0 37.0 27.0 37.0 88-89 33.34552316501822 35.0 33.0 37.0 27.0 37.0 90-91 32.95926600728787 33.0 33.0 37.0 27.0 37.0 92-93 32.98529411764706 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 16.0 21 14.0 22 14.0 23 24.0 24 36.0 25 39.0 26 48.0 27 61.0 28 77.0 29 67.0 30 126.0 31 136.0 32 171.0 33 226.0 34 293.0 35 491.0 36 868.0 37 858.0 38 417.0 39 18.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.39999999999999 4.6 3.3000000000000003 6.7 2 69.89999999999999 17.875 7.9 4.324999999999999 3 39.875 34.675 13.975000000000001 11.475 4 28.025 34.699999999999996 18.25 19.025 5 31.15 26.5 25.575 16.775000000000002 6 17.675 43.1 23.875 15.35 7 41.375 26.224999999999998 18.3 14.099999999999998 8 26.424999999999997 27.525 21.85 24.2 9 23.05 34.050000000000004 25.224999999999998 17.675 10-11 23.1875 30.375000000000004 29.675 16.7625 12-13 24.075 29.349999999999998 24.725 21.85 14-15 19.5875 37.475 25.412499999999998 17.525 16-17 27.075 28.299999999999997 22.7125 21.912499999999998 18-19 25.728216027003377 24.515564445555693 30.97887235904488 18.777347168396048 20-21 26.691682301438398 23.639774859287055 31.294559099437148 18.3739837398374 22-23 29.925 20.474999999999998 29.812499999999996 19.787499999999998 24-25 23.400000000000002 23.425 30.0 23.175 26-27 26.987499999999997 22.6875 27.8875 22.4375 28-29 23.0125 29.2875 29.3375 18.3625 30-31 33.5 22.825 24.9 18.775 32-33 27.6875 23.95 25.1875 23.175 34-35 21.8875 34.0375 24.837500000000002 19.2375 36-37 27.928491061382672 23.252906613326665 24.54056757094637 24.278034754344294 38-39 32.96662082760345 23.35291911488936 27.040880110013752 16.639579947493438 40-41 23.674999999999997 23.3125 33.0875 19.925 42-43 27.49248496993988 30.723947895791582 24.561623246492985 17.221943887775552 44-45 25.218804701175294 24.706176544136035 31.04526131532883 19.02975743935984 46-47 27.025 23.3 25.362499999999997 24.3125 48-49 26.924999999999997 23.7375 27.0125 22.325 50-51 21.925 29.049999999999997 25.724999999999998 23.3 52-53 23.14142678347935 23.992490613266586 24.505632040050063 28.360450563204004 54-55 23.202900362545318 24.1780222527816 30.653831728966118 21.965245655706962 56-57 27.575 28.1375 27.1125 17.175 58-59 21.55 28.3375 31.2875 18.825 60-61 31.4625 23.962500000000002 27.0125 17.5625 62-63 19.8375 26.5625 32.425 21.175 64-65 21.5375 34.35 26.974999999999998 17.1375 66-67 25.825 29.95 25.650000000000002 18.575 68-69 20.652581572696587 25.403175396924617 30.05375671958995 23.89048631078885 70-71 21.873043696006008 28.68411168148241 25.666708401151872 23.77613622135971 72-73 27.339126054653068 23.69978592116862 30.57549427024304 18.38559375393527 74-75 25.85291887793783 29.403588577204953 27.621935809957037 17.121556734900174 76-77 20.782023613050654 23.866954424273203 25.860099022470486 29.49092294020566 78-79 26.683673469387752 26.926020408163264 27.512755102040813 18.877551020408163 80-81 20.420728578758336 36.87788609543355 26.064648537711648 16.63673678809646 82-83 24.84207812298569 24.90653603197112 26.363284775041894 23.888101070001287 84-85 21.14835022083658 25.863860743050143 33.3203429462198 19.667446089893478 86-87 18.7532535137949 29.11244143675169 28.38365434669443 23.75065070275898 88-89 19.31285788651744 26.78292555960437 31.337844872462263 22.566371681415927 90-91 26.67881311816762 29.580947423217076 26.171264966163456 17.568974492451847 92-93 19.963560645497136 27.40760020822488 30.986465382613222 21.642373763664757 >>END_MODULE >>Per sequence GC content fail #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 0.5 17 7.0 18 7.0 19 1.0 20 1.0 21 3.0 22 4.5 23 5.5 24 7.0 25 8.0 26 12.0 27 15.5 28 23.5 29 32.5 30 28.0 31 28.5 32 48.0 33 61.5 34 68.0 35 83.0 36 114.0 37 146.0 38 173.5 39 173.5 40 164.0 41 171.5 42 201.5 43 230.0 44 190.0 45 159.5 46 184.0 47 164.0 48 132.5 49 144.0 50 147.5 51 144.5 52 131.5 53 129.5 54 282.5 55 265.5 56 84.0 57 61.0 58 50.5 59 36.0 60 31.0 61 27.0 62 27.5 63 30.5 64 25.5 65 18.0 66 12.5 67 11.0 68 11.0 69 11.5 70 8.5 71 5.0 72 3.0 73 2.0 74 2.5 75 1.5 76 1.0 77 0.5 78 0.0 79 0.0 80 1.0 81 1.0 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 0.0125 20-21 0.0625 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 0.0125 38-39 0.0125 40-41 0.0 42-43 0.2 44-45 0.025 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.125 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 0.0125 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 7.0 73 5.0 74 10.0 75 9.0 76 9.0 77 8.0 78 12.0 79 14.0 80 4.0 81 11.0 82 13.0 83 16.0 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 3842.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.95 #Duplication Level Percentage of deduplicated Percentage of total 1 92.46058944482523 67.45 2 4.249485949280329 6.2 3 1.439342015078821 3.15 4 0.2741603838245374 0.8 5 0.3084304318026045 1.125 6 0.23989033584647018 1.05 7 0.205620287868403 1.05 8 0.06854009595613435 0.4 9 0.1370801919122687 0.8999999999999999 >10 0.5825908156271419 8.475000000000001 >50 0.0 0.0 >100 0.034270047978067174 9.4 >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 376 9.4 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 40 1.0 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 40 1.0 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 39 0.975 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 32 0.8 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 25 0.625 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 23 0.575 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 18 0.44999999999999996 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 17 0.42500000000000004 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 14 0.35000000000000003 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 12 0.3 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 12 0.3 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 10 0.25 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 10 0.25 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 7 0.17500000000000002 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 7 0.17500000000000002 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 5 0.125 No Hit GGGCAATGGGGGATGTGAAGGCTTGTGGTGCCTGTGTGGGCTTGGTGTAG 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 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 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 45 3.8198777E-11 76.54445 1 GGAGAGC 40 1.4588295E-9 75.348434 2 GCAATAC 40 1.4588295E-9 75.348434 7 CAATACA 40 1.4588295E-9 75.348434 8 AGCAATA 40 1.4588295E-9 75.348434 6 GAGCAAT 45 3.7071004E-9 66.97639 5 GAGAGCA 45 3.7071004E-9 66.97639 3 AGAGCAA 50 8.53106E-9 60.278748 4 AATACAA 50 8.53106E-9 60.278748 9 ATGATTC 25 0.006880399 51.6675 4 TGATTCT 25 0.006880399 51.6675 5 GGGATGA 25 0.006880399 51.6675 1 CATCACT 35 1.0643271E-7 44.73377 82-83 ATCACTA 35 1.0643271E-7 44.73377 84-85 AGCATCA 35 1.0643271E-7 44.73377 80-81 CACTAGC 35 1.0643271E-7 44.73377 86-87 TCACTAG 35 1.0643271E-7 44.73377 84-85 ACTAGCT 35 1.0643271E-7 44.73377 86-87 GCATCAC 40 3.0397314E-7 39.142044 82-83 AAGCATC 40 3.0397314E-7 39.142044 80-81 >>END_MODULE Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162257 READS because READLEN < 1 Read 162257 spots for ERR6133458.sra Written 162257 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra Rejected 162238 READS because READLEN < 1 Read 162238 spots for ERR6133458.sra Written 162238 spots for ERR6133458.sra SRR ids: ['ERR6133458.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ytyf1vp3 ERR6133458.sra spots: 3244779 blocks: [[1, 162238], [162239, 324476], [324477, 486714], [486715, 648952], [648953, 811190], [811191, 973428], [973429, 1135666], [1135667, 1297904], [1297905, 1460142], [1460143, 1622380], [1622381, 1784618], [1784619, 1946856], [1946857, 2109094], [2109095, 2271332], [2271333, 2433570], [2433571, 2595808], [2595809, 2758046], [2758047, 2920284], [2920285, 3082522], [3082523, 3244779]] ERR6133458 file size 716348 ERR6133458 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 ERR6133458 ERR6133458_1.fastq Input file: ERR6133458_1.fastq trimmed: ERR6133458-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 06:26:37 2024 >> started Sat Dec 7 06:26:40 2024 >> done (2.720s) 3244779 reads processed; of these: 240 ( 0.01%) short reads filtered out after trimming by size control 12 ( 0.00%) empty reads filtered out after trimming by size control 3244527 (99.99%) reads available; of these: 47974 ( 1.48%) trimmed reads available after processing 3196553 (98.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 30 0.00% 19 49 0.00% 20 23 0.00% 21 33 0.00% 22 34 0.00% 23 19 0.00% 24 15 0.00% 25 19 0.00% 26 20 0.00% 27 27 0.00% 28 211 0.01% 29 42 0.00% 30 24 0.00% 31 32 0.00% 32 36 0.00% 33 42 0.00% 34 30 0.00% 35 80 0.00% 36 651 0.02% 37 19 0.00% 38 22 0.00% 39 92 0.00% 40 48 0.00% 41 51 0.00% 42 11 0.00% 43 18 0.00% 44 30 0.00% 45 16 0.00% 46 22 0.00% 47 15 0.00% 48 13 0.00% 49 15 0.00% 50 18 0.00% 51 31 0.00% 52 14 0.00% 53 10 0.00% 54 11 0.00% 55 15 0.00% 56 23 0.00% 57 31 0.00% 58 14 0.00% 59 17 0.00% 60 9 0.00% 61 9 0.00% 62 2 0.00% 63 4 0.00% 64 4 0.00% 65 4 0.00% 66 6 0.00% 67 13 0.00% 68 27 0.00% 69 94 0.00% 70 9325 0.29% 71 8787 0.27% 72 8598 0.27% 73 7951 0.25% 74 8319 0.26% 75 8594 0.26% 76 7390 0.23% 77 7381 0.23% 78 7660 0.24% 79 8314 0.26% 80 7985 0.25% 81 8956 0.28% 82 10018 0.31% 83 9159 0.28% 84 8260 0.25% 85 118 0.00% 86 239 0.01% 87 327 0.01% 88 671 0.02% 89 1203 0.04% 90 2623 0.08% 91 8347 0.26% 92 30760 0.95% 93 3071397 94.66% 3244527 reads passed initial QC criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=0.63 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=160.76 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=8.2 sequence=AGGAAGAGGAGGATGCAGTCAGGGCTCACAAACAACCTGCCACTGCCGCCATTGGCCTTCTAAAACAGGAGAGGAGGGGTTAGATAGTTTCGATCTGCAAGGGGGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACAGTAGCGTACTTGAGGTGTTGTATTTTTATTTATTT Started job on | Dec 07 06:26:53 Started mapping on | Dec 07 06:26:53 Finished on | Dec 07 06:27:00 Mapping speed, Million of reads per hour | 1668.61 Number of input reads | 3244527 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1885463 Uniquely mapped reads % | 58.11% Average mapped length | 92.05 Number of splices: Total | 95359 Number of splices: Annotated (sjdb) | 78435 Number of splices: GT/AG | 92078 Number of splices: GC/AG | 1895 Number of splices: AT/AC | 69 Number of splices: Non-canonical | 1317 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.04% Deletion average length | 1.80 Insertion rate per base | 0.01% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1223411 % of reads mapped to multiple loci | 37.71% Number of reads mapped to too many loci | 31218 % of reads mapped to too many loci | 0.96% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.13% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 135653 135653 135653 N_multimapping 1223411 1223411 1223411 N_noFeature 140311 157199 1802599 N_ambiguous 75973 10016 268 UnstrandedReadsAssigned:1669179 PositiveStrandReadsAssigned:1718248 NegativeStrandReadsAssigned:82596 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133458 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: ERR6133458-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,244,527 reads, 2,315,195 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 972 rounds 52973 ERR6133458.ke.tsv 35125 ERR6133458.se.tsv 88098 total ==> ERR6133458.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 58 23.9791 PNS24243 293 194 0 0 KQK14069 1603 1504 52 19.6116 KQK14071 474 375 0 0 ==> ERR6133458.se.tsv <== BRADI_1g14170v3 52 BRADI_1g53295v3 11 BRADI_1g59795v3 16 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 33 BRADI_1g74790v3 19 BRADI_1g09890v3 0 BRADI_1g77505v3 60 BRADI_1g48960v3 0 ERR6133458 completed mapping pipeline successfully