Starting /dee2/code/volunteer_pipeline.sh ERR6133567 current disk space = 1544446353408 free memory = 1597187516 ERR6133567 SRAfilesize 2cec8ac931e6bc2532925b7cdc39ff2c ERR6133567.sra ERR6133567.sra file validated ERR6133567 is single end ERR6133567 is conventional basespace ERR6133567 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133567_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 35.33325 37.0 33.0 37.0 33.0 37.0 2 36.522 37.0 37.0 37.0 37.0 37.0 3 36.08325 37.0 37.0 37.0 33.0 37.0 4 35.6365 37.0 37.0 37.0 33.0 37.0 5 35.4195 37.0 37.0 37.0 33.0 37.0 6 35.7905 37.0 37.0 37.0 33.0 37.0 7 37.6635 40.0 37.0 40.0 33.0 40.0 8 37.64425 40.0 37.0 40.0 33.0 40.0 9 37.69275 40.0 37.0 40.0 33.0 40.0 10-11 37.69775 40.0 37.0 40.0 33.0 40.0 12-13 37.580124999999995 38.5 37.0 40.0 33.0 40.0 14-15 37.533625 37.0 37.0 40.0 33.0 40.0 16-17 37.4375 37.0 37.0 40.0 33.0 40.0 18-19 37.443375 37.0 37.0 40.0 33.0 40.0 20-21 37.381625 37.0 37.0 40.0 33.0 40.0 22-23 37.32725 37.0 37.0 40.0 33.0 40.0 24-25 37.39125 37.0 37.0 40.0 33.0 40.0 26-27 37.343875 37.0 37.0 40.0 33.0 40.0 28-29 37.3045 37.0 37.0 40.0 33.0 40.0 30-31 37.102625 37.0 37.0 40.0 33.0 40.0 32-33 36.977000000000004 37.0 37.0 40.0 33.0 40.0 34-35 36.9045 37.0 37.0 40.0 33.0 40.0 36-37 36.776624999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.515625 37.0 37.0 40.0 33.0 40.0 40-41 36.321 37.0 37.0 40.0 33.0 40.0 42-43 36.2145 37.0 37.0 40.0 33.0 40.0 44-45 35.947125 37.0 37.0 40.0 33.0 40.0 46-47 35.68575 37.0 33.0 37.0 33.0 40.0 48-49 35.542 37.0 33.0 37.0 33.0 40.0 50-51 35.491125 37.0 33.0 37.0 33.0 40.0 52-53 35.166875000000005 37.0 33.0 37.0 33.0 40.0 54-55 35.169250000000005 37.0 33.0 37.0 33.0 40.0 56-57 34.973875 37.0 33.0 37.0 33.0 37.0 58-59 33.699749999999995 35.0 33.0 37.0 27.0 37.0 60-61 34.259874999999994 37.0 33.0 37.0 27.0 37.0 62-63 34.44025 37.0 33.0 37.0 27.0 37.0 64-65 34.364000000000004 37.0 33.0 37.0 27.0 37.0 66-67 34.359875 37.0 33.0 37.0 27.0 37.0 68-69 33.613375000000005 35.0 33.0 37.0 27.0 37.0 70-71 33.762885692846424 35.0 33.0 37.0 27.0 37.0 72-73 34.19065452522597 37.0 33.0 37.0 27.0 37.0 74-75 33.946230397078494 37.0 33.0 37.0 27.0 37.0 76-77 34.014002155765525 37.0 33.0 37.0 27.0 37.0 78-79 34.17616852320604 37.0 33.0 37.0 27.0 37.0 80-81 34.078943986539095 37.0 33.0 37.0 27.0 37.0 82-83 33.956735166187606 37.0 33.0 37.0 27.0 37.0 84-85 33.96285487860827 37.0 33.0 37.0 27.0 37.0 86-87 33.73649859227029 37.0 33.0 37.0 27.0 37.0 88-89 33.93063731763502 37.0 33.0 37.0 27.0 37.0 90-91 33.621960583567954 37.0 33.0 37.0 27.0 37.0 92-93 33.4283337599181 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 9.0 21 11.0 22 16.0 23 14.0 24 28.0 25 32.0 26 27.0 27 39.0 28 55.0 29 65.0 30 78.0 31 99.0 32 144.0 33 152.0 34 254.0 35 425.0 36 930.0 37 1014.0 38 597.0 39 11.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.97500000000001 2.9499999999999997 2.9250000000000003 7.1499999999999995 2 70.025 17.25 7.775 4.95 3 34.475 39.574999999999996 13.600000000000001 12.35 4 34.4 28.075 18.575 18.95 5 24.474999999999998 29.625 26.525 19.375 6 19.75 37.125 25.85 17.275 7 35.575 28.749999999999996 19.925 15.75 8 30.625000000000004 28.425 23.575 17.375 9 26.05 27.6 27.250000000000004 19.1 10-11 25.324999999999996 27.212500000000002 27.0125 20.45 12-13 27.987499999999997 26.275 27.287499999999998 18.45 14-15 22.45 29.525000000000002 28.712500000000002 19.3125 16-17 24.9 31.275 24.3875 19.4375 18-19 24.2 25.2625 28.375 22.162499999999998 20-21 24.79059882485311 25.978247280910118 28.20352544068008 21.027628453556694 22-23 26.650000000000002 23.549999999999997 27.6625 22.1375 24-25 25.890736342042754 25.26565820727591 27.55344418052256 21.29016127015877 26-27 24.675 26.5 30.587500000000002 18.2375 28-29 26.453306663332913 27.29091136392049 26.765845730716343 19.489936242030254 30-31 27.212500000000002 26.437500000000004 25.887500000000003 20.4625 32-33 23.875 26.787499999999998 27.212500000000002 22.125 34-35 24.575 26.437500000000004 27.3875 21.6 36-37 25.8125 24.9 27.6125 21.675 38-39 26.270337922403 24.918648310387987 30.01251564455569 18.798498122653317 40-41 26.81522283425138 25.6885327991988 26.489734601902853 21.00650976464697 42-43 24.862431215607803 28.92696348174087 26.425712856428213 19.78489244622311 44-45 23.3625 26.1625 29.375 21.099999999999998 46-47 24.575 23.7 28.325 23.400000000000002 48-49 25.162499999999998 25.124999999999996 30.175 19.537499999999998 50-51 25.374999999999996 26.437500000000004 27.9125 20.275000000000002 52-53 25.366403607666292 28.18489289740699 26.080420894400604 20.36828260052612 54-55 24.9875 27.224999999999998 28.0625 19.725 56-57 26.387500000000003 25.662499999999998 28.000000000000004 19.950000000000003 58-59 24.4125 25.8 27.700000000000003 22.0875 60-61 24.675 26.275 28.799999999999997 20.25 62-63 22.1375 27.3 32.0375 18.525 64-65 23.5625 27.737499999999997 28.599999999999998 20.1 66-67 25.337500000000002 27.3375 27.6 19.725 68-69 22.4375 27.3 28.449999999999996 21.8125 70-71 24.85621405351338 25.44386096524131 27.74443610902726 21.955488872218055 72-73 25.97695390781563 25.67635270541082 27.667835671342683 20.678857715430862 74-75 24.075936635655015 27.596178023635908 29.129997485541864 19.197887855167213 76-77 24.103987884906612 27.082281675921248 27.612317011610298 21.20141342756184 78-79 23.62463639812824 25.68610092323258 30.567851271025674 20.121411407613508 80-81 23.7509510524981 28.69642404260715 28.937357342125285 18.615267562769464 82-83 23.99439918533605 26.132892057026474 28.373217922606926 21.49949083503055 84-85 23.798568507157462 22.699386503067483 32.016871165644176 21.48517382413088 86-87 21.69183516764781 27.117993345277707 31.136421807013054 20.05374968006143 88-89 21.679037624776043 28.832864090094702 30.176606091630408 19.311492193498847 90-91 24.724852828256974 25.838239058100843 29.651906833887892 19.78500127975429 92-93 22.126951625287944 29.22958791911953 28.986434604555928 19.6570258510366 >>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 0.5 16 2.0 17 12.5 18 14.0 19 4.0 20 1.5 21 1.5 22 1.0 23 3.0 24 6.0 25 6.0 26 8.0 27 11.0 28 17.5 29 23.5 30 28.0 31 32.0 32 42.5 33 62.5 34 69.0 35 70.0 36 91.0 37 131.5 38 158.0 39 175.0 40 191.5 41 180.0 42 207.0 43 248.5 44 210.0 45 181.5 46 212.0 47 206.0 48 175.0 49 180.0 50 176.0 51 154.5 52 147.5 53 155.0 54 147.0 55 94.0 56 57.5 57 59.0 58 58.5 59 47.5 60 42.5 61 38.5 62 29.0 63 25.5 64 27.0 65 29.0 66 23.5 67 19.0 68 13.5 69 12.0 70 9.0 71 4.0 72 7.0 73 6.0 74 2.5 75 3.5 76 2.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.5 82 0.5 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 0.0125 26-27 0.0 28-29 0.0125 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.125 40-41 0.15 42-43 0.05 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.21250000000000002 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 2.0 71 3.0 72 6.0 73 9.0 74 6.0 75 10.0 76 4.0 77 4.0 78 5.0 79 6.0 80 4.0 81 8.0 82 10.0 83 6.0 84 10.0 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 3907.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.025 #Duplication Level Percentage of deduplicated Percentage of total 1 92.31015700096124 72.02499999999999 2 4.1012495994873435 6.4 3 1.0253123998718359 2.4 4 0.8010253123998717 2.5 5 0.4806151874399231 1.875 6 0.25632809996795897 1.2 7 0.16020506247997437 0.8750000000000001 8 0.16020506247997437 1.0 9 0.06408202499198974 0.44999999999999996 >10 0.6408202499198975 11.275 >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 fail #Sequence Count Percentage Possible Source GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 43 1.075 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 40 1.0 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 36 0.8999999999999999 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 36 0.8999999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 32 0.8 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 31 0.775 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 25 0.625 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 24 0.6 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 24 0.6 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 21 0.525 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 18 0.44999999999999996 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 18 0.44999999999999996 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 17 0.42500000000000004 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 17 0.42500000000000004 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 12 0.3 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GGGCCATTCACAGACACACACAACTACACAAGAGCTCTCAGCTGCTGCCC 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 5 0.125 No Hit GGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAAT 5 0.125 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 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 0.0 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 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0125 0.0 0.0 0.0 66-67 0.0 0.025 0.0 0.0 0.0 68-69 0.0 0.025 0.0 0.0 0.0 70-71 0.0 0.025 0.0 0.0 0.0 72-73 0.0 0.025 0.0 0.0 0.0 74-75 0.025 0.025 0.0 0.0 0.0 76-77 0.025 0.025 0.0 0.0 0.0 78-79 0.025 0.025 0.0 0.0 0.0 80-81 0.025 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222350 READS because READLEN < 1 Read 222350 spots for ERR6133567.sra Written 222350 spots for ERR6133567.sra Rejected 222355 READS because READLEN < 1 Read 222355 spots for ERR6133567.sra Written 222355 spots for ERR6133567.sra SRR ids: ['ERR6133567.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jxe3lw98 ERR6133567.sra spots: 4447005 blocks: [[1, 222350], [222351, 444700], [444701, 667050], [667051, 889400], [889401, 1111750], [1111751, 1334100], [1334101, 1556450], [1556451, 1778800], [1778801, 2001150], [2001151, 2223500], [2223501, 2445850], [2445851, 2668200], [2668201, 2890550], [2890551, 3112900], [3112901, 3335250], [3335251, 3557600], [3557601, 3779950], [3779951, 4002300], [4002301, 4224650], [4224651, 4447005]] ERR6133567 file size 984242 ERR6133567 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 ERR6133567 ERR6133567_1.fastq Input file: ERR6133567_1.fastq trimmed: ERR6133567-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 08:46:41 2024 >> started Sat Dec 7 08:46:43 2024 >> done (2.452s) 4447005 reads processed; of these: 64 ( 0.00%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 4446933 (100.00%) reads available; of these: 83794 ( 1.88%) trimmed reads available after processing 4363139 (98.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 23 0.00% 20 10 0.00% 21 3 0.00% 22 5 0.00% 23 1 0.00% 24 1 0.00% 25 2 0.00% 26 2 0.00% 27 0 0.00% 28 9 0.00% 29 20 0.00% 30 2 0.00% 31 7 0.00% 32 14 0.00% 33 5 0.00% 34 5 0.00% 35 33 0.00% 36 459 0.01% 37 17 0.00% 38 14 0.00% 39 30 0.00% 40 53 0.00% 41 8 0.00% 42 7 0.00% 43 12 0.00% 44 13 0.00% 45 6 0.00% 46 7 0.00% 47 7 0.00% 48 5 0.00% 49 6 0.00% 50 4 0.00% 51 36 0.00% 52 15 0.00% 53 5 0.00% 54 5 0.00% 55 5 0.00% 56 7 0.00% 57 13 0.00% 58 10 0.00% 59 4 0.00% 60 13 0.00% 61 9 0.00% 62 2 0.00% 63 3 0.00% 64 8 0.00% 65 7 0.00% 66 8 0.00% 67 11 0.00% 68 27 0.00% 69 62 0.00% 70 7692 0.17% 71 7633 0.17% 72 8109 0.18% 73 7117 0.16% 74 7520 0.17% 75 7550 0.17% 76 6668 0.15% 77 7086 0.16% 78 7990 0.18% 79 9087 0.20% 80 8410 0.19% 81 8365 0.19% 82 10071 0.23% 83 10585 0.24% 84 9111 0.20% 85 155 0.00% 86 354 0.01% 87 524 0.01% 88 971 0.02% 89 1808 0.04% 90 3817 0.09% 91 10803 0.24% 92 62905 1.41% 93 4241549 95.38% 4446933 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=5.86 fanout-score-rank=21 prefix-density=0.72 prefix-fanout=2.6 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGATGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATTATCTTACTGTTTTAAATAAATCTGTTTC criterion=fanout-score sequence-density=0.09 sequence-density-rank=13 fanout-score=38.61 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=6.9 sequence=TGCATGCATGTAAAATTGATTGATGGGACGATATGTCTCTCTAGTTGAAATGGTCGACAATGCACTTAATTTGTGTTGTAAAGTACTACTCCGTGCTAGTGTTATGCATGCTATGTGTATGGATGCATGGTGGATCGAGGAGTGGATGTGATTGGTATGTACATTACAGAGGAAGCTGATGGTTCAGTGCTGTAGTATCTTGTGACGATGATGATCTTTGTTGTGCCTAATAGCATTGTGCTTATTAATTAACT Started job on | Dec 07 08:46:55 Started mapping on | Dec 07 08:46:55 Finished on | Dec 07 08:47:00 Mapping speed, Million of reads per hour | 3201.79 Number of input reads | 4446933 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3078978 Uniquely mapped reads % | 69.24% Average mapped length | 92.23 Number of splices: Total | 136451 Number of splices: Annotated (sjdb) | 112517 Number of splices: GT/AG | 131808 Number of splices: GC/AG | 3839 Number of splices: AT/AC | 92 Number of splices: Non-canonical | 712 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.02% Deletion average length | 1.42 Insertion rate per base | 0.00% Insertion average length | 1.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1292390 % of reads mapped to multiple loci | 29.06% Number of reads mapped to too many loci | 29265 % of reads mapped to too many loci | 0.66% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.00% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 75565 75565 75565 N_multimapping 1292390 1292390 1292390 N_noFeature 207003 235240 2941548 N_ambiguous 121981 12744 430 UnstrandedReadsAssigned:2749994 PositiveStrandReadsAssigned:2830994 NegativeStrandReadsAssigned:137000 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133567 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: ERR6133567-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,446,933 reads, 3,745,016 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,013 rounds 52973 ERR6133567.ke.tsv 35125 ERR6133567.se.tsv 88098 total ==> ERR6133567.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 98 25.2799 PNS24243 293 194 0 0 KQK14069 1603 1504 387 91.0683 KQK14071 474 375 0 0 ==> ERR6133567.se.tsv <== BRADI_1g14170v3 388 BRADI_1g53295v3 55 BRADI_1g59795v3 36 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 25 BRADI_1g74790v3 28 BRADI_1g09890v3 0 BRADI_1g77505v3 74 BRADI_1g48960v3 0 ERR6133567 completed mapping pipeline successfully