Starting /dee2/code/volunteer_pipeline.sh ERR6133513 current disk space = 1544355926016 free memory = 1443586832 ERR6133513 SRAfilesize 249bde726676426b26a8b653e2be3b08 ERR6133513.sra ERR6133513.sra file validated ERR6133513 is single end ERR6133513 is conventional basespace ERR6133513 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133513_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 35.175 37.0 33.0 37.0 33.0 37.0 2 36.461 37.0 37.0 37.0 37.0 37.0 3 36.16825 37.0 37.0 37.0 33.0 37.0 4 35.73875 37.0 37.0 37.0 33.0 37.0 5 35.6895 37.0 37.0 37.0 33.0 37.0 6 35.9175 37.0 37.0 37.0 33.0 37.0 7 37.748 40.0 37.0 40.0 33.0 40.0 8 37.73425 40.0 37.0 40.0 33.0 40.0 9 37.88975 40.0 37.0 40.0 33.0 40.0 10-11 37.78525 40.0 37.0 40.0 33.0 40.0 12-13 37.759625 40.0 37.0 40.0 33.0 40.0 14-15 37.694500000000005 40.0 37.0 40.0 33.0 40.0 16-17 37.591625 40.0 37.0 40.0 33.0 40.0 18-19 37.547125 40.0 37.0 40.0 33.0 40.0 20-21 37.41925 38.5 37.0 40.0 33.0 40.0 22-23 37.363625 37.0 37.0 40.0 33.0 40.0 24-25 37.441625 38.5 37.0 40.0 33.0 40.0 26-27 37.363125 38.5 37.0 40.0 33.0 40.0 28-29 37.256375 37.0 37.0 40.0 33.0 40.0 30-31 37.255875 37.0 37.0 40.0 33.0 40.0 32-33 37.0625 37.0 37.0 40.0 33.0 40.0 34-35 36.977875 37.0 37.0 40.0 33.0 40.0 36-37 36.863749999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.651250000000005 37.0 37.0 40.0 33.0 40.0 40-41 36.416375 37.0 37.0 40.0 33.0 40.0 42-43 36.135125 37.0 37.0 40.0 33.0 40.0 44-45 35.821 37.0 33.0 40.0 33.0 40.0 46-47 35.347125000000005 37.0 33.0 40.0 30.0 40.0 48-49 35.4435 37.0 33.0 37.0 30.0 40.0 50-51 35.295500000000004 37.0 33.0 37.0 27.0 40.0 52-53 35.04025 37.0 33.0 37.0 27.0 40.0 54-55 34.90625 37.0 33.0 37.0 27.0 40.0 56-57 34.5485 37.0 33.0 37.0 27.0 40.0 58-59 32.218875 33.0 30.0 37.0 24.5 37.0 60-61 33.858 37.0 33.0 37.0 27.0 37.0 62-63 34.10025 37.0 33.0 37.0 27.0 37.0 64-65 33.9785 37.0 33.0 37.0 27.0 37.0 66-67 33.687125 37.0 33.0 37.0 27.0 37.0 68-69 33.16125 35.0 33.0 37.0 27.0 37.0 70-71 33.24568375344871 35.0 33.0 37.0 27.0 37.0 72-73 33.481532910278524 37.0 33.0 37.0 27.0 37.0 74-75 33.37941929044844 37.0 33.0 37.0 27.0 37.0 76-77 33.56132824293083 37.0 33.0 37.0 27.0 37.0 78-79 33.46173177626372 37.0 33.0 37.0 27.0 37.0 80-81 33.44848261423231 37.0 33.0 37.0 27.0 37.0 82-83 33.196506880697676 37.0 33.0 37.0 27.0 37.0 84-85 33.026255277667204 33.0 33.0 37.0 27.0 37.0 86-87 32.98242135871002 33.0 33.0 37.0 27.0 37.0 88-89 33.12450436161777 33.0 33.0 37.0 27.0 37.0 90-91 32.87020882897171 33.0 33.0 37.0 27.0 37.0 92-93 32.865450700502244 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 15.0 21 15.0 22 17.0 23 28.0 24 22.0 25 28.0 26 37.0 27 55.0 28 59.0 29 80.0 30 85.0 31 103.0 32 150.0 33 201.0 34 255.0 35 460.0 36 837.0 37 903.0 38 624.0 39 26.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.175 5.25 6.2 7.375 2 60.550000000000004 21.2 12.65 5.6000000000000005 3 29.9 36.65 17.25 16.2 4 30.2 27.224999999999998 21.75 20.825 5 23.3 28.425 31.7 16.575 6 17.9 39.525 25.45 17.125 7 34.425 29.15 21.775 14.649999999999999 8 28.725 26.35 26.150000000000002 18.775 9 22.25 28.775000000000002 29.4 19.575 10-11 23.0375 28.525 30.4375 18.0 12-13 25.0625 26.6625 27.5125 20.7625 14-15 20.8 30.662499999999998 29.049999999999997 19.4875 16-17 23.6625 30.912499999999998 25.2875 20.1375 18-19 22.45 27.675 29.1125 20.7625 20-21 24.775 26.2625 28.8625 20.1 22-23 27.825 22.625 28.762500000000003 20.7875 24-25 24.6875 27.175 28.125 20.0125 26-27 25.85 25.575 30.9875 17.5875 28-29 24.5625 28.3125 27.825 19.3 30-31 28.237499999999997 26.0625 27.0625 18.637500000000003 32-33 23.8125 27.525 28.787499999999998 19.875 34-35 23.724999999999998 28.525 26.887499999999996 20.8625 36-37 24.975 26.2125 27.3875 21.425 38-39 27.953494186773348 24.065508188523566 30.678834854356797 17.302162770346293 40-41 25.25 25.974999999999998 28.212500000000002 20.5625 42-43 24.7 29.3875 26.8375 19.075 44-45 23.5 26.6625 30.412499999999998 19.425 46-47 24.275 24.95 28.8875 21.8875 48-49 24.3625 26.3625 28.462500000000002 20.8125 50-51 22.823911955977987 27.201100550275136 28.73936968484242 21.235617808904454 52-53 24.01151151151151 27.38988988988989 25.93843843843844 22.66016016016016 54-55 24.425 27.250000000000004 29.4375 18.8875 56-57 25.575 27.650000000000002 27.6625 19.112499999999997 58-59 23.625 26.437500000000004 30.612499999999997 19.325 60-61 24.9875 26.8625 29.262500000000003 18.8875 62-63 21.462500000000002 29.549999999999997 31.0125 17.974999999999998 64-65 22.35 30.25 28.9 18.5 66-67 23.2125 29.612500000000004 28.1625 19.0125 68-69 21.025 27.700000000000003 28.875 22.400000000000002 70-71 21.848003004882933 28.05809440340553 28.6465506447978 21.447351946913734 72-73 25.875976808671542 23.392992185530627 29.9092513234182 20.82177968237963 74-75 23.98017537171178 28.351760071165334 29.609861481763883 18.058203075359003 76-77 21.880604663079684 25.749423520368946 27.747886241352802 24.622085575198565 78-79 26.005673027333675 26.405363589479116 29.203197524497167 18.385765858690046 80-81 22.832294911734163 30.711318795430948 28.93302180685358 17.523364485981308 82-83 22.8676085818943 26.02040816326531 30.20669806384092 20.905285190999475 84-85 21.984692531010822 23.700184745315386 34.41541303774083 19.899709685932965 86-87 21.292624900872323 27.650013217023528 30.650277557494054 20.407084324610096 88-89 20.182394924662965 30.385937086968013 29.63256674596881 19.799101242400212 90-91 25.918583135077984 28.403383558022732 27.95400475812847 17.724028548770818 92-93 21.808088818398097 31.98519693365054 27.623579169970924 18.58313507798044 >>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 17.5 18 20.5 19 5.5 20 3.5 21 4.0 22 4.0 23 9.0 24 15.0 25 12.0 26 16.5 27 19.5 28 19.5 29 23.0 30 23.5 31 38.0 32 58.5 33 75.0 34 85.5 35 94.5 36 125.0 37 182.5 38 227.5 39 210.5 40 197.0 41 200.5 42 195.0 43 201.0 44 196.5 45 179.5 46 177.0 47 151.0 48 133.0 49 158.0 50 178.0 51 161.0 52 122.0 53 118.5 54 147.0 55 117.0 56 59.5 57 54.5 58 50.5 59 40.0 60 32.5 61 25.5 62 19.5 63 18.0 64 14.0 65 16.5 66 16.0 67 9.5 68 8.0 69 5.5 70 4.0 71 4.0 72 3.0 73 5.5 74 5.5 75 2.0 76 2.0 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 0.0125 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.05 52-53 0.1 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 9.0 72 22.0 73 12.0 74 19.0 75 16.0 76 12.0 77 13.0 78 12.0 79 13.0 80 14.0 81 14.0 82 18.0 83 18.0 84 12.0 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 3783.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.8 #Duplication Level Percentage of deduplicated Percentage of total 1 92.31283422459893 69.05 2 3.8770053475935833 5.800000000000001 3 1.1697860962566844 2.625 4 0.9358288770053476 2.8000000000000003 5 0.2339572192513369 0.8750000000000001 6 0.2339572192513369 1.05 7 0.1336898395721925 0.7000000000000001 8 0.2005347593582888 1.2 9 0.06684491978609625 0.44999999999999996 >10 0.7352941176470588 9.875 >50 0.1002673796791444 5.575 >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 99 2.475 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 67 1.675 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 57 1.425 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 39 0.975 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 33 0.8250000000000001 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 32 0.8 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 31 0.775 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 28 0.7000000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 24 0.6 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 20 0.5 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 20 0.5 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 17 0.42500000000000004 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 17 0.42500000000000004 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 12 0.3 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 11 0.27499999999999997 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 10 0.25 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 10 0.25 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 10 0.25 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit GAAATCTTTGGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGG 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 7 0.17500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTTTTAA 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 7 0.17500000000000002 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 6 0.15 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGTTTCAGTATATTGAAATAGAAAGATAAAATAGAAGAGAGAGGATAGGC 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit TTAGACTTAGAACACTAACAGGTAAAATGTGAGATTTTTATTAAGTAAAA 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.0125 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.037500000000000006 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 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.175 0.0 0.0 0.0 0.0 80-81 0.1875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 35 0.0094002485 26.179049 86-87 >>END_MODULE Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196585 READS because READLEN < 1 Read 196585 spots for ERR6133513.sra Written 196585 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra Rejected 196571 READS because READLEN < 1 Read 196571 spots for ERR6133513.sra Written 196571 spots for ERR6133513.sra SRR ids: ['ERR6133513.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yxbbogwj ERR6133513.sra spots: 3931434 blocks: [[1, 196571], [196572, 393142], [393143, 589713], [589714, 786284], [786285, 982855], [982856, 1179426], [1179427, 1375997], [1375998, 1572568], [1572569, 1769139], [1769140, 1965710], [1965711, 2162281], [2162282, 2358852], [2358853, 2555423], [2555424, 2751994], [2751995, 2948565], [2948566, 3145136], [3145137, 3341707], [3341708, 3538278], [3538279, 3734849], [3734850, 3931434]] ERR6133513 file size 866134 ERR6133513 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 ERR6133513 ERR6133513_1.fastq Input file: ERR6133513_1.fastq trimmed: ERR6133513-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 07:41:23 2024 >> started Sat Dec 7 07:41:25 2024 >> done (2.052s) 3931434 reads processed; of these: 470 ( 0.01%) short reads filtered out after trimming by size control 53 ( 0.00%) empty reads filtered out after trimming by size control 3930911 (99.99%) reads available; of these: 60182 ( 1.53%) trimmed reads available after processing 3870729 (98.47%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 51 0.00% 19 137 0.00% 20 91 0.00% 21 153 0.00% 22 140 0.00% 23 31 0.00% 24 40 0.00% 25 29 0.00% 26 32 0.00% 27 54 0.00% 28 124 0.00% 29 89 0.00% 30 91 0.00% 31 144 0.00% 32 57 0.00% 33 58 0.00% 34 78 0.00% 35 800 0.02% 36 408 0.01% 37 65 0.00% 38 90 0.00% 39 474 0.01% 40 167 0.00% 41 213 0.01% 42 11 0.00% 43 20 0.00% 44 28 0.00% 45 25 0.00% 46 13 0.00% 47 21 0.00% 48 21 0.00% 49 33 0.00% 50 27 0.00% 51 82 0.00% 52 23 0.00% 53 15 0.00% 54 15 0.00% 55 17 0.00% 56 13 0.00% 57 48 0.00% 58 35 0.00% 59 10 0.00% 60 33 0.00% 61 22 0.00% 62 4 0.00% 63 8 0.00% 64 5 0.00% 65 10 0.00% 66 10 0.00% 67 14 0.00% 68 48 0.00% 69 132 0.00% 70 14778 0.38% 71 13856 0.35% 72 16752 0.43% 73 13589 0.35% 74 14211 0.36% 75 14270 0.36% 76 12332 0.31% 77 12772 0.32% 78 14992 0.38% 79 16099 0.41% 80 15494 0.39% 81 17716 0.45% 82 19137 0.49% 83 18323 0.47% 84 15732 0.40% 85 193 0.00% 86 325 0.01% 87 527 0.01% 88 868 0.02% 89 1612 0.04% 90 3327 0.08% 91 9731 0.25% 92 36880 0.94% 93 3643036 92.68% 3930911 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=4.93 fanout-score-rank=23 prefix-density=0.92 prefix-fanout=1.9 sequence=AGGCTAAATACTCCTGGGTGACCGATAGCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=45 fanout-score=34.99 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=1.1 sequence=GGCATTTTGGATTTCAGGGCTTTTAGCCCCGATTAGTGAAGGACCCGAAAAGCTTTCTAGTTATGAATCGGGTATAGAACCCATGGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTTGTTGTTTTTGATGTGGAAACCGTCTTTCTCTACCCTTGGGCAATGAGTTTCGACGTATTGGGTGTATCCGTTTTTATCGAAGCTTTCATTTTCGTGCTTATCCTAGTTGTTGGTTTAGTTTATGCATGGCGAAAAGGAGCCTTGGAATGGTCTTAACTGAATATT Started job on | Dec 07 07:41:41 Started mapping on | Dec 07 07:41:41 Finished on | Dec 07 07:41:48 Mapping speed, Million of reads per hour | 2021.61 Number of input reads | 3930911 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 2320134 Uniquely mapped reads % | 59.02% Average mapped length | 91.36 Number of splices: Total | 97898 Number of splices: Annotated (sjdb) | 75028 Number of splices: GT/AG | 91984 Number of splices: GC/AG | 1871 Number of splices: AT/AC | 74 Number of splices: Non-canonical | 3969 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.05% Deletion average length | 1.70 Insertion rate per base | 0.03% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1457736 % of reads mapped to multiple loci | 37.08% Number of reads mapped to too many loci | 82744 % of reads mapped to too many loci | 2.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.63% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 153041 153041 153041 N_multimapping 1457736 1457736 1457736 N_noFeature 211196 239754 2218460 N_ambiguous 85446 12060 659 UnstrandedReadsAssigned:2023492 PositiveStrandReadsAssigned:2068320 NegativeStrandReadsAssigned:101015 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133513 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: ERR6133513-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,930,911 reads, 3,035,132 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 964 rounds 52973 ERR6133513.ke.tsv 35125 ERR6133513.se.tsv 88098 total ==> ERR6133513.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 77 24.9349 PNS24243 293 194 0 0 KQK14069 1603 1504 126 37.2214 KQK14071 474 375 0 0 ==> ERR6133513.se.tsv <== BRADI_1g14170v3 126 BRADI_1g53295v3 16 BRADI_1g59795v3 17 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 17 BRADI_1g74790v3 20 BRADI_1g09890v3 0 BRADI_1g77505v3 71 BRADI_1g48960v3 0 ERR6133513 completed mapping pipeline successfully