Starting /dee2/code/volunteer_pipeline.sh ERR6133312 current disk space = 1548136198144 free memory = 1425381628 ERR6133312 SRAfilesize 35902c7306187cafce2684f67aac691b ERR6133312.sra ERR6133312.sra file validated ERR6133312 is single end ERR6133312 is conventional basespace ERR6133312 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133312_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 35.24325 37.0 33.0 37.0 33.0 37.0 2 36.378 37.0 37.0 37.0 33.0 37.0 3 36.00775 37.0 37.0 37.0 33.0 37.0 4 35.55075 37.0 37.0 37.0 33.0 37.0 5 35.48075 37.0 37.0 37.0 33.0 37.0 6 35.79025 37.0 37.0 37.0 33.0 37.0 7 37.42375 37.0 37.0 40.0 33.0 40.0 8 37.502 37.0 37.0 40.0 33.0 40.0 9 37.5905 40.0 37.0 40.0 33.0 40.0 10-11 37.48925 37.0 37.0 40.0 33.0 40.0 12-13 37.45625 37.0 37.0 40.0 33.0 40.0 14-15 37.43675 37.0 37.0 40.0 33.0 40.0 16-17 37.461 37.0 37.0 40.0 33.0 40.0 18-19 37.304249999999996 37.0 37.0 40.0 33.0 40.0 20-21 37.060875 37.0 37.0 40.0 33.0 40.0 22-23 36.941874999999996 37.0 37.0 40.0 33.0 40.0 24-25 37.13475 37.0 37.0 40.0 33.0 40.0 26-27 36.94575 37.0 37.0 40.0 33.0 40.0 28-29 36.811875 37.0 37.0 40.0 33.0 40.0 30-31 36.887 37.0 37.0 40.0 33.0 40.0 32-33 36.736125 37.0 37.0 40.0 33.0 40.0 34-35 36.548874999999995 37.0 37.0 40.0 33.0 40.0 36-37 36.535624999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.20975 37.0 37.0 40.0 33.0 40.0 40-41 36.12075 37.0 37.0 40.0 33.0 40.0 42-43 36.011875 37.0 37.0 40.0 33.0 40.0 44-45 35.562375 37.0 33.0 40.0 30.0 40.0 46-47 35.180875 37.0 33.0 38.5 27.0 40.0 48-49 35.174 37.0 33.0 37.0 27.0 40.0 50-51 35.004375 37.0 33.0 37.0 27.0 40.0 52-53 34.729625 37.0 33.0 37.0 27.0 40.0 54-55 34.58625 37.0 33.0 37.0 27.0 40.0 56-57 34.44125 37.0 33.0 37.0 27.0 40.0 58-59 32.0605 33.0 30.0 37.0 24.5 37.0 60-61 33.66275 37.0 33.0 37.0 27.0 37.0 62-63 33.714125 37.0 33.0 37.0 27.0 37.0 64-65 33.56 37.0 33.0 37.0 27.0 37.0 66-67 33.404624999999996 37.0 33.0 37.0 27.0 37.0 68-69 32.807625 35.0 33.0 37.0 27.0 37.0 70-71 32.92055263489662 33.0 33.0 37.0 27.0 37.0 72-73 33.25586383061703 37.0 33.0 37.0 27.0 37.0 74-75 33.308611219955495 37.0 33.0 37.0 27.0 37.0 76-77 33.1577408560827 37.0 33.0 37.0 27.0 37.0 78-79 33.140317240861336 37.0 33.0 37.0 27.0 37.0 80-81 32.96548456888909 35.0 33.0 37.0 27.0 37.0 82-83 32.821746938302496 33.0 33.0 37.0 27.0 37.0 84-85 32.61286280832445 33.0 33.0 37.0 27.0 37.0 86-87 32.42597968069666 33.0 33.0 37.0 22.0 37.0 88-89 32.66603773584906 33.0 33.0 37.0 27.0 37.0 90-91 32.50682148040639 33.0 33.0 37.0 22.0 37.0 92-93 32.47314949201741 33.0 33.0 37.0 24.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 16.0 21 21.0 22 20.0 23 37.0 24 39.0 25 43.0 26 45.0 27 46.0 28 61.0 29 95.0 30 87.0 31 132.0 32 154.0 33 207.0 34 239.0 35 479.0 36 799.0 37 862.0 38 589.0 39 29.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.65 4.15 3.675 7.5249999999999995 2 65.225 18.45 10.825 5.5 3 33.025 38.75 17.05 11.175 4 30.775000000000002 28.825 20.9 19.5 5 22.7 31.0 29.599999999999998 16.7 6 19.45 35.775 27.1 17.675 7 33.125 28.199999999999996 22.75 15.925 8 26.35 27.224999999999998 27.750000000000004 18.675 9 24.975 27.1 30.599999999999998 17.325 10-11 24.9 26.4125 30.337500000000002 18.35 12-13 23.75 26.8625 30.775000000000002 18.6125 14-15 19.35 29.375 31.7 19.575 16-17 23.474999999999998 29.9375 25.275 21.3125 18-19 23.8375 25.05 31.162499999999998 19.950000000000003 20-21 24.975 23.35 29.425 22.25 22-23 25.662499999999998 23.474999999999998 28.6375 22.225 24-25 24.825 26.625 29.512500000000003 19.037499999999998 26-27 24.2625 24.7875 30.662499999999998 20.2875 28-29 25.162499999999998 27.437499999999996 28.1 19.3 30-31 24.462500000000002 26.1 28.287499999999998 21.15 32-33 25.124999999999996 24.5125 30.612499999999997 19.75 34-35 23.0625 28.037499999999998 28.6875 20.2125 36-37 24.525 26.674999999999997 26.75 22.05 38-39 26.887499999999996 23.6875 30.312499999999996 19.112499999999997 40-41 25.162499999999998 23.9875 29.675 21.175 42-43 23.5375 28.675 29.775000000000002 18.0125 44-45 21.840230028753595 27.315914489311165 31.341417677209648 19.50243780472559 46-47 22.7625 27.625 28.1125 21.5 48-49 24.725 25.412499999999998 30.162499999999998 19.7 50-51 22.95573893473368 26.481620405101275 29.80745186296574 20.7551887971993 52-53 23.72838887496868 29.128038085692808 26.710097719869708 20.433475319468805 54-55 23.5 28.375 29.7875 18.337500000000002 56-57 23.5375 29.4 28.575 18.4875 58-59 23.724999999999998 26.8 29.212500000000002 20.2625 60-61 25.124999999999996 26.25 28.999999999999996 19.625 62-63 21.825 29.45 30.612499999999997 18.1125 64-65 23.3625 31.137500000000003 27.625 17.875 66-67 24.275 29.575000000000003 27.500000000000004 18.65 68-69 20.837500000000002 27.425 29.725 22.0125 70-71 24.742656289229224 26.813959327140346 28.897815716796384 19.545568666834047 72-73 24.588069996168095 25.827053263507473 31.02567377698301 18.559202963341423 74-75 24.79885803270179 25.629379704126652 28.808720477549958 20.763041785621596 76-77 22.503627489777074 27.265532251681833 28.24165677351273 21.98918348502836 78-79 23.356980323919156 28.095301833757198 29.152723865613705 19.394993976709944 80-81 22.59910093992644 30.704263724288243 28.2250374608364 18.471597874948916 82-83 24.50266181003082 27.038386102549733 29.153824600728495 19.30512748669095 84-85 21.554209919261822 25.08650519031142 33.52076124567474 19.83852364475202 86-87 20.9288824383164 29.14368650217707 28.867924528301884 21.059506531204644 88-89 21.01596516690856 28.88243831640058 29.796806966618288 20.30478955007257 90-91 23.55587808417997 30.362844702467346 28.026124818577646 18.055152394775035 92-93 20.058055152394775 33.32365747460087 28.18577648766328 18.432510885341074 >>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 0.0 17 3.0 18 3.5 19 0.5 20 0.0 21 0.0 22 0.5 23 5.0 24 9.0 25 12.5 26 14.5 27 16.0 28 28.5 29 39.5 30 46.5 31 52.5 32 67.5 33 89.5 34 96.5 35 124.0 36 177.5 37 230.0 38 251.0 39 222.5 40 198.5 41 192.5 42 214.0 43 245.0 44 219.0 45 182.0 46 174.5 47 148.5 48 129.0 49 133.5 50 118.0 51 99.5 52 111.5 53 127.0 54 132.0 55 104.5 56 84.5 57 98.0 58 73.5 59 33.5 60 20.0 61 23.0 62 22.0 63 18.5 64 17.5 65 15.0 66 10.5 67 9.0 68 8.0 69 10.5 70 11.0 71 7.0 72 11.5 73 11.0 74 4.5 75 3.5 76 3.0 77 1.5 78 0.5 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 0.0 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 0.0125 46-47 0.0 48-49 0.0 50-51 0.025 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 34.0 71 34.0 72 35.0 73 28.0 74 32.0 75 29.0 76 35.0 77 21.0 78 33.0 79 31.0 80 35.0 81 46.0 82 76.0 83 40.0 84 46.0 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 3445.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.125 #Duplication Level Percentage of deduplicated Percentage of total 1 92.38249594813614 71.25 2 3.9222042139384112 6.05 3 1.2317666126418152 2.85 4 0.5834683954619124 1.7999999999999998 5 0.45380875202593196 1.7500000000000002 6 0.22690437601296598 1.05 7 0.2593192868719611 1.4000000000000001 8 0.12965964343598055 0.8 9 0.0972447325769854 0.675 >10 0.6158833063209076 8.15 >50 0.0972447325769854 4.2250000000000005 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 61 1.525 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 56 1.4000000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 52 1.3 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 42 1.05 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 32 0.8 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 31 0.775 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 22 0.5499999999999999 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 19 0.475 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 17 0.42500000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 15 0.375 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 14 0.35000000000000003 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 12 0.3 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 12 0.3 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 10 0.25 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 10 0.25 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 9 0.22499999999999998 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 9 0.22499999999999998 No Hit GGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGA 8 0.2 No Hit GGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAA 8 0.2 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 8 0.2 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 8 0.2 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 7 0.17500000000000002 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 7 0.17500000000000002 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 7 0.17500000000000002 No Hit GGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGAC 7 0.17500000000000002 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 7 0.17500000000000002 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 7 0.17500000000000002 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 6 0.15 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 6 0.15 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGCTATTAA 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit CAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGG 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 5 0.125 No Hit TATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAA 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.0875 0.0 0.0 0.0 0.0 30-31 0.1375 0.0 0.0 0.0 0.0 32-33 0.16249999999999998 0.0 0.0 0.0 0.0 34-35 0.175 0.0 0.0 0.0 0.0 36-37 0.2 0.0 0.0 0.0 0.0 38-39 0.25 0.0 0.0 0.0 0.0 40-41 0.275 0.0 0.0 0.0 0.0 42-43 0.325 0.0 0.0 0.0 0.0 44-45 0.325 0.0 0.0 0.0 0.0 46-47 0.325 0.0 0.0 0.0 0.0 48-49 0.325 0.0 0.0 0.0 0.0 50-51 0.325 0.0 0.0 0.0 0.0 52-53 0.35 0.0 0.0 0.0 0.0 54-55 0.35 0.0 0.0 0.0 0.0 56-57 0.35 0.0 0.0 0.0 0.0 58-59 0.35 0.0 0.0 0.0 0.0 60-61 0.35 0.0 0.0 0.0 0.0 62-63 0.35 0.0 0.0 0.0 0.0 64-65 0.35 0.0 0.0 0.0 0.0 66-67 0.35 0.0 0.0 0.0 0.0 68-69 0.35 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.3625 0.0 0.0 0.0 0.0 78-79 0.4125 0.0 0.0 0.0 0.0 80-81 0.44999999999999996 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCAATT 15 9.325893E-4 85.524994 4 AATTTCA 15 9.325893E-4 85.524994 7 CAATTTC 15 9.325893E-4 85.524994 6 GGATTCA 15 9.325893E-4 85.524994 1 TTTCAAC 15 9.325893E-4 85.524994 9 TCAATTT 15 9.325893E-4 85.524994 5 GATTCAA 15 9.325893E-4 85.524994 2 ATTTCAA 15 9.325893E-4 85.524994 8 ATTCAAT 15 9.325893E-4 85.524994 3 AAGAGAC 15 0.009905079 47.513885 80-81 GACAACC 15 0.009905079 47.513885 84-85 AGAGACA 15 0.009905079 47.513885 80-81 AGACAAC 15 0.009905079 47.513885 82-83 ACAACCT 15 0.009905079 47.513885 84-85 GAGACAA 15 0.009905079 47.513885 82-83 ATTAATA 25 0.0023948788 34.643036 46-47 >>END_MODULE Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109522 READS because READLEN < 1 Read 109522 spots for ERR6133312.sra Written 109522 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra Rejected 109513 READS because READLEN < 1 Read 109513 spots for ERR6133312.sra Written 109513 spots for ERR6133312.sra SRR ids: ['ERR6133312.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v4eyfq54 ERR6133312.sra spots: 2190269 blocks: [[1, 109513], [109514, 219026], [219027, 328539], [328540, 438052], [438053, 547565], [547566, 657078], [657079, 766591], [766592, 876104], [876105, 985617], [985618, 1095130], [1095131, 1204643], [1204644, 1314156], [1314157, 1423669], [1423670, 1533182], [1533183, 1642695], [1642696, 1752208], [1752209, 1861721], [1861722, 1971234], [1971235, 2080747], [2080748, 2190269]] ERR6133312 file size 476002 ERR6133312 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 ERR6133312 ERR6133312_1.fastq Input file: ERR6133312_1.fastq trimmed: ERR6133312-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 00:26:14 2024 >> started Sat Dec 7 00:26:15 2024 >> done (1.775s) 2190269 reads processed; of these: 833 ( 0.04%) short reads filtered out after trimming by size control 42 ( 0.00%) empty reads filtered out after trimming by size control 2189394 (99.96%) reads available; of these: 42636 ( 1.95%) trimmed reads available after processing 2146758 (98.05%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 115 0.01% 19 316 0.01% 20 199 0.01% 21 234 0.01% 22 307 0.01% 23 85 0.00% 24 114 0.01% 25 62 0.00% 26 61 0.00% 27 91 0.00% 28 224 0.01% 29 192 0.01% 30 159 0.01% 31 282 0.01% 32 209 0.01% 33 89 0.00% 34 167 0.01% 35 1513 0.07% 36 544 0.02% 37 154 0.01% 38 172 0.01% 39 933 0.04% 40 405 0.02% 41 353 0.02% 42 36 0.00% 43 39 0.00% 44 46 0.00% 45 30 0.00% 46 17 0.00% 47 19 0.00% 48 29 0.00% 49 30 0.00% 50 29 0.00% 51 182 0.01% 52 38 0.00% 53 25 0.00% 54 31 0.00% 55 17 0.00% 56 25 0.00% 57 60 0.00% 58 64 0.00% 59 29 0.00% 60 84 0.00% 61 31 0.00% 62 2 0.00% 63 3 0.00% 64 3 0.00% 65 5 0.00% 66 9 0.00% 67 29 0.00% 68 55 0.00% 69 249 0.01% 70 19824 0.91% 71 18541 0.85% 72 21674 0.99% 73 18069 0.83% 74 18582 0.85% 75 18829 0.86% 76 16927 0.77% 77 17239 0.79% 78 18653 0.85% 79 20014 0.91% 80 19793 0.90% 81 26145 1.19% 82 28219 1.29% 83 23550 1.08% 84 26928 1.23% 85 107 0.00% 86 193 0.01% 87 256 0.01% 88 623 0.03% 89 948 0.04% 90 1894 0.09% 91 6102 0.28% 92 20706 0.95% 93 1837382 83.92% 2189394 reads passed initial QC criterion=sequence-density sequence-density=1.54 sequence-density-rank=1 fanout-score=5.56 fanout-score-rank=20 prefix-density=4.78 prefix-fanout=1.8 sequence=AGGCTAAATACTCCTGGGTGACCGATAGCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=237.30 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=8.7 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 00:26:42 Started mapping on | Dec 07 00:26:42 Finished on | Dec 07 00:26:47 Mapping speed, Million of reads per hour | 1576.36 Number of input reads | 2189394 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 1330485 Uniquely mapped reads % | 60.77% Average mapped length | 89.80 Number of splices: Total | 38933 Number of splices: Annotated (sjdb) | 31402 Number of splices: GT/AG | 36660 Number of splices: GC/AG | 784 Number of splices: AT/AC | 26 Number of splices: Non-canonical | 1463 Mismatch rate per base, % | 0.46% Deletion rate per base | 0.04% Deletion average length | 1.57 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 645706 % of reads mapped to multiple loci | 29.49% Number of reads mapped to too many loci | 154931 % of reads mapped to too many loci | 7.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.22% % of reads unmapped: other | 0.44% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 213203 213203 213203 N_multimapping 645706 645706 645706 N_noFeature 123965 138914 1272035 N_ambiguous 51079 7280 498 UnstrandedReadsAssigned:1155441 PositiveStrandReadsAssigned:1184291 NegativeStrandReadsAssigned:57952 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133312 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: ERR6133312-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,189,394 reads, 1,545,722 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 980 rounds 52973 ERR6133312.ke.tsv 35125 ERR6133312.se.tsv 88098 total ==> ERR6133312.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 35 22.6725 PNS24243 293 194 0 0 KQK14069 1603 1504 9 5.31839 KQK14071 474 375 0 0 ==> ERR6133312.se.tsv <== BRADI_1g14170v3 9 BRADI_1g53295v3 34 BRADI_1g59795v3 15 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 32 BRADI_1g74790v3 20 BRADI_1g09890v3 0 BRADI_1g77505v3 39 BRADI_1g48960v3 0 ERR6133312 completed mapping pipeline successfully