Starting /dee2/code/volunteer_pipeline.sh ERR6133412 current disk space = 1547272044544 free memory = 1457594100 ERR6133412 SRAfilesize 250460496c7e576a7f70249b710ef2bb ERR6133412.sra ERR6133412.sra file validated ERR6133412 is single end ERR6133412 is conventional basespace ERR6133412 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133412_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.38875 33.0 27.0 33.0 15.0 37.0 2 33.56975 33.0 33.0 37.0 27.0 37.0 3 33.7315 37.0 33.0 37.0 27.0 37.0 4 33.82075 37.0 33.0 37.0 27.0 37.0 5 33.97875 37.0 33.0 37.0 27.0 37.0 6 33.917 37.0 33.0 37.0 27.0 37.0 7 35.2895 37.0 33.0 40.0 27.0 40.0 8 35.36825 37.0 33.0 40.0 27.0 40.0 9 35.506 37.0 33.0 40.0 33.0 40.0 10-11 35.40575 37.0 33.0 40.0 33.0 40.0 12-13 35.235125 37.0 33.0 37.0 30.0 40.0 14-15 35.22475 37.0 33.0 38.5 27.0 40.0 16-17 34.929 37.0 33.0 37.0 27.0 40.0 18-19 34.87025 37.0 33.0 37.0 27.0 40.0 20-21 33.925125 37.0 33.0 37.0 24.5 40.0 22-23 33.70825 37.0 33.0 37.0 24.5 40.0 24-25 33.569125 37.0 33.0 37.0 22.0 40.0 26-27 33.342375000000004 37.0 33.0 37.0 22.0 40.0 28-29 32.938500000000005 37.0 33.0 37.0 22.0 40.0 30-31 32.828625 35.0 33.0 37.0 22.0 40.0 32-33 32.309625 33.0 33.0 37.0 22.0 40.0 34-35 31.392375 33.0 27.0 37.0 15.0 40.0 36-37 30.88925 33.0 27.0 37.0 15.0 37.0 38-39 31.447375 33.0 27.0 37.0 22.0 40.0 40-41 31.156374999999997 33.0 27.0 37.0 22.0 40.0 42-43 31.05525 33.0 27.0 37.0 15.0 40.0 44-45 30.68775 33.0 27.0 37.0 18.5 38.5 46-47 30.077625 33.0 27.0 37.0 15.0 37.0 48-49 30.023375 33.0 27.0 37.0 15.0 37.0 50-51 29.544249999999998 33.0 27.0 37.0 15.0 37.0 52-53 29.41225 33.0 27.0 37.0 15.0 37.0 54-55 29.3545 33.0 27.0 37.0 15.0 37.0 56-57 28.434375000000003 33.0 24.5 35.0 15.0 37.0 58-59 28.060625 33.0 24.5 33.0 15.0 37.0 60-61 28.05775 33.0 27.0 33.0 15.0 37.0 62-63 27.749499999999998 33.0 22.0 33.0 15.0 37.0 64-65 27.23075 33.0 22.0 33.0 10.5 37.0 66-67 26.81525 33.0 22.0 33.0 6.0 37.0 68-69 26.094 27.0 22.0 33.0 10.5 35.0 70-71 28.294260771543087 33.0 27.0 33.0 15.0 37.0 72-73 28.645850156174255 33.0 27.0 33.0 15.0 37.0 74-75 28.59712984366949 33.0 27.0 33.0 15.0 37.0 76-77 28.489928539505016 33.0 27.0 33.0 15.0 37.0 78-79 27.491153672162994 33.0 24.5 33.0 10.5 37.0 80-81 26.69300328359128 33.0 22.0 33.0 6.0 37.0 82-83 25.98462550227997 33.0 22.0 33.0 4.0 37.0 84-85 25.586155417278412 33.0 22.0 33.0 2.0 37.0 86-87 24.71456386292835 33.0 15.0 33.0 2.0 37.0 88-89 23.91588785046729 30.0 15.0 33.0 2.0 35.0 90-91 22.594626168224302 27.0 2.0 33.0 2.0 37.0 92-93 21.357606438213914 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 99.0 21 101.0 22 137.0 23 159.0 24 198.0 25 221.0 26 217.0 27 221.0 28 241.0 29 249.0 30 252.0 31 279.0 32 304.0 33 281.0 34 313.0 35 297.0 36 239.0 37 170.0 38 22.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.875 8.375 10.424999999999999 12.325 2 49.125 25.75 15.024999999999999 10.100000000000001 3 32.300000000000004 33.650000000000006 17.825 16.225 4 23.95 34.225 19.775000000000002 22.05 5 30.125 23.974999999999998 27.55 18.35 6 14.625 45.800000000000004 24.025 15.55 7 40.475 26.674999999999997 18.05 14.799999999999999 8 23.925 25.825 23.125 27.125 9 19.625 36.1 25.5 18.775 10-11 19.925 31.175000000000004 31.4625 17.4375 12-13 18.337500000000002 32.275 25.3 24.087500000000002 14-15 21.0 37.175000000000004 24.6875 17.1375 16-17 26.5125 26.924999999999997 22.0625 24.5 18-19 24.775 23.075000000000003 33.862500000000004 18.2875 20-21 27.075 22.375 32.45 18.099999999999998 22-23 31.424999999999997 19.950000000000003 31.612499999999997 17.0125 24-25 22.6375 24.6125 29.275000000000002 23.474999999999998 26-27 27.575 22.475 27.525 22.425 28-29 22.037499999999998 29.375 28.875 19.7125 30-31 33.4375 23.400000000000002 24.9875 18.175 32-33 28.549999999999997 23.0375 25.937500000000004 22.475 34-35 19.650000000000002 38.675 22.037499999999998 19.6375 36-37 27.3125 25.374999999999996 22.325 24.9875 38-39 35.1875 20.6625 24.587500000000002 19.5625 40-41 22.537499999999998 24.0375 35.35 18.075 42-43 29.049999999999997 31.674999999999997 23.9125 15.3625 44-45 25.55 25.6125 30.925000000000004 17.9125 46-47 29.7875 22.912499999999998 25.7375 21.5625 48-49 27.287499999999998 22.112499999999997 25.6125 24.9875 50-51 19.0625 31.724999999999998 24.5625 24.65 52-53 23.5625 23.3125 23.0125 30.112499999999997 54-55 22.0625 22.425 31.2875 24.224999999999998 56-57 29.4875 29.262500000000003 24.474999999999998 16.775000000000002 58-59 20.875 30.5 30.975 17.65 60-61 32.6375 25.587500000000002 24.625 17.150000000000002 62-63 19.7125 27.1 31.374999999999996 21.8125 64-65 18.95 38.824999999999996 24.95 17.275 66-67 24.8625 33.5125 23.549999999999997 18.075 68-69 19.8125 24.224999999999998 29.312500000000004 26.650000000000002 70-71 19.61961961961962 32.62012012012012 24.737237237237235 23.023023023023022 72-73 27.61306532663317 22.889447236180903 32.21105527638191 17.28643216080402 74-75 27.296853279413625 29.104006065967397 26.60179451535448 16.9973461392645 76-77 19.736174530695077 21.182141045154744 25.34246575342466 33.73921867072552 78-79 31.088478676002545 27.803946530872054 24.32845321451305 16.77912157861235 80-81 21.96339434276206 39.45987456802765 23.76807884295405 14.80865224625624 82-83 25.17374517374517 25.135135135135133 24.491634491634493 25.1994851994852 84-85 19.409173360974346 26.224410469033426 35.24229074889868 19.124125421093545 86-87 19.39252336448598 30.63343717549325 23.61111111111111 26.36292834890966 88-89 17.61422637590862 28.400830737279335 30.257009345794394 23.727933541017656 90-91 26.038421599169265 31.775700934579437 25.038940809968846 17.14693665628245 92-93 18.87331256490135 30.062305295950154 28.595534787123572 22.468847352024923 >>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 1.5 17 8.5 18 8.0 19 2.0 20 3.5 21 4.5 22 2.5 23 2.0 24 5.5 25 7.5 26 9.5 27 15.0 28 17.0 29 16.0 30 21.5 31 34.0 32 44.0 33 43.0 34 48.5 35 71.0 36 117.0 37 201.0 38 234.5 39 197.0 40 205.0 41 205.0 42 181.5 43 185.0 44 172.0 45 147.5 46 141.0 47 130.5 48 99.5 49 99.0 50 136.5 51 174.5 52 150.0 53 130.0 54 298.0 55 308.5 56 124.5 57 78.5 58 60.0 59 36.5 60 24.5 61 20.0 62 20.5 63 15.0 64 7.5 65 5.5 66 5.5 67 4.5 68 7.0 69 7.0 70 4.5 71 4.0 72 3.0 73 1.5 74 0.5 75 0.5 76 0.5 77 0.5 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 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 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 8.0 71 3.0 72 18.0 73 12.0 74 5.0 75 9.0 76 6.0 77 5.0 78 13.0 79 11.0 80 7.0 81 11.0 82 14.0 83 12.0 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 3852.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 63.3 #Duplication Level Percentage of deduplicated Percentage of total 1 91.58767772511848 57.975 2 4.265402843601896 5.4 3 0.9478672985781991 1.7999999999999998 4 0.9083728278041073 2.3 5 0.3949447077409162 1.25 6 0.47393364928909953 1.7999999999999998 7 0.1579778830963665 0.7000000000000001 8 0.1579778830963665 0.8 9 0.0 0.0 >10 0.9478672985781991 11.5 >50 0.11848341232227488 5.6000000000000005 >100 0.03949447077409163 10.875 >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 435 10.875 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 84 2.1 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 84 2.1 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 56 1.4000000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 36 0.8999999999999999 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 32 0.8 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 30 0.75 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 29 0.7250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 26 0.65 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 24 0.6 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 24 0.6 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 24 0.6 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 22 0.5499999999999999 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 21 0.525 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 20 0.5 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 18 0.44999999999999996 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 18 0.44999999999999996 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 16 0.4 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 15 0.375 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 15 0.375 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 14 0.35000000000000003 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 13 0.325 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 11 0.27499999999999997 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 11 0.27499999999999997 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 10 0.25 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 10 0.25 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGGGCCGC 10 0.25 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 8 0.2 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 8 0.2 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 8 0.2 No Hit GTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCA 7 0.17500000000000002 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 7 0.17500000000000002 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 7 0.17500000000000002 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit CACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATT 6 0.15 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 6 0.15 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGACGC 6 0.15 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 6 0.15 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 6 0.15 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 5 0.125 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGAGGTTGAGTGCCGC 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTACAAACATGGGTTATTGTAA 5 0.125 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 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 0.0 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 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 60 5.456968E-12 64.79063 2 GCAATAC 60 5.456968E-12 64.79063 7 GGGAGAG 60 5.456968E-12 64.79063 1 CAATACA 60 5.456968E-12 64.79063 8 GAGCAAT 60 5.456968E-12 64.79063 5 GAGAGCA 60 5.456968E-12 64.79063 3 AATACAA 60 5.456968E-12 64.79063 9 AGCAATA 60 5.456968E-12 64.79063 6 AGAGCAA 65 1.2732926E-11 59.806736 4 GGCACCC 30 1.8401393E-4 57.591667 7 CTAGGCA 30 1.8401393E-4 57.591667 4 GCACCCA 30 1.8401393E-4 57.591667 8 TACCTAG 30 1.8401393E-4 57.591667 1 ACCTAGG 30 1.8401393E-4 57.591667 2 CCTAGGC 30 1.8401393E-4 57.591667 3 TAGGCAC 30 1.8401393E-4 57.591667 5 CACCCAG 35 3.941491E-4 49.364285 9 AGGCACC 35 3.941491E-4 49.364285 6 ACTAGCT 45 2.9649527E-10 44.876625 86-87 GAAAGCA 55 0.0 44.876625 78-79 >>END_MODULE Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46901 READS because READLEN < 1 Read 46901 spots for ERR6133412.sra Written 46901 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra Rejected 46890 READS because READLEN < 1 Read 46890 spots for ERR6133412.sra Written 46890 spots for ERR6133412.sra SRR ids: ['ERR6133412.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd___jsdkbi ERR6133412.sra spots: 937811 blocks: [[1, 46890], [46891, 93780], [93781, 140670], [140671, 187560], [187561, 234450], [234451, 281340], [281341, 328230], [328231, 375120], [375121, 422010], [422011, 468900], [468901, 515790], [515791, 562680], [562681, 609570], [609571, 656460], [656461, 703350], [703351, 750240], [750241, 797130], [797131, 844020], [844021, 890910], [890911, 937811]] ERR6133412 file size 205810 ERR6133412 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 ERR6133412 ERR6133412_1.fastq Input file: ERR6133412_1.fastq trimmed: ERR6133412-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 03:57:16 2024 >> started Sat Dec 7 03:57:17 2024 >> done (0.832s) 937811 reads processed; of these: 8 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 937803 (100.00%) reads available; of these: 249008 (26.55%) trimmed reads available after processing 688795 (73.45%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 3 0.00% 20 1 0.00% 21 1 0.00% 22 1 0.00% 23 0 0.00% 24 1 0.00% 25 0 0.00% 26 1 0.00% 27 1 0.00% 28 10 0.00% 29 42 0.00% 30 3 0.00% 31 1 0.00% 32 3 0.00% 33 3 0.00% 34 0 0.00% 35 2 0.00% 36 2 0.00% 37 1 0.00% 38 1 0.00% 39 2 0.00% 40 8 0.00% 41 1 0.00% 42 4 0.00% 43 13 0.00% 44 1 0.00% 45 13 0.00% 46 14 0.00% 47 26 0.00% 48 48 0.01% 49 60 0.01% 50 76 0.01% 51 139 0.01% 52 146 0.02% 53 243 0.03% 54 393 0.04% 55 553 0.06% 56 726 0.08% 57 1013 0.11% 58 707 0.08% 59 827 0.09% 60 1014 0.11% 61 1211 0.13% 62 1378 0.15% 63 1509 0.16% 64 1722 0.18% 65 1780 0.19% 66 1769 0.19% 67 1843 0.20% 68 1637 0.17% 69 1419 0.15% 70 3471 0.37% 71 4085 0.44% 72 5060 0.54% 73 5161 0.55% 74 5890 0.63% 75 6498 0.69% 76 7106 0.76% 77 8443 0.90% 78 8903 0.95% 79 8984 0.96% 80 9745 1.04% 81 11168 1.19% 82 11124 1.19% 83 11950 1.27% 84 13750 1.47% 85 12326 1.31% 86 12841 1.37% 87 14355 1.53% 88 18314 1.95% 89 18995 2.03% 90 19655 2.10% 91 20957 2.23% 92 18624 1.99% 93 660025 70.38% 937803 reads passed initial QC criterion=sequence-density sequence-density=13.79 sequence-density-rank=1 fanout-score=1.29 fanout-score-rank=27 prefix-density=0.65 prefix-fanout=1.3 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT criterion=fanout-score sequence-density=0.13 sequence-density-rank=21 fanout-score=108.88 fanout-score-rank=1 prefix-density=13.08 prefix-fanout=1.1 sequence=CTAGATGGCTACAGTCCAGTAGC Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT -o ERR6133412 - Input file: STDIN trimmed: ERR6133412-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sat Dec 7 03:57:21 2024 >> started Sat Dec 7 03:57:22 2024 >> done (0.996s) 803831 reads processed; of these: 7902 ( 0.98%) short reads filtered out after trimming by size control 106151 (13.21%) empty reads filtered out after trimming by size control 689778 (85.81%) reads available; of these: 15564 ( 2.26%) trimmed reads available after processing 674214 (97.74%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 14 0.00% 20 33 0.00% 21 23 0.00% 22 309 0.04% 23 59 0.01% 24 14 0.00% 25 6 0.00% 26 23 0.00% 27 27 0.00% 28 48 0.01% 29 42 0.01% 30 35 0.01% 31 291 0.04% 32 107 0.02% 33 22 0.00% 34 6 0.00% 35 5 0.00% 36 25 0.00% 37 335 0.05% 38 56 0.01% 39 33 0.00% 40 26 0.00% 41 49 0.01% 42 126 0.02% 43 29 0.00% 44 69 0.01% 45 76 0.01% 46 33 0.00% 47 23 0.00% 48 47 0.01% 49 182 0.03% 50 95 0.01% 51 201 0.03% 52 323 0.05% 53 234 0.03% 54 267 0.04% 55 416 0.06% 56 607 0.09% 57 831 0.12% 58 563 0.08% 59 704 0.10% 60 842 0.12% 61 992 0.14% 62 1075 0.16% 63 1209 0.18% 64 1339 0.19% 65 1365 0.20% 66 1364 0.20% 67 1409 0.20% 68 1503 0.22% 69 1303 0.19% 70 2961 0.43% 71 3257 0.47% 72 3728 0.54% 73 4035 0.58% 74 4782 0.69% 75 5194 0.75% 76 5396 0.78% 77 7609 1.10% 78 7686 1.11% 79 7487 1.09% 80 7158 1.04% 81 8587 1.24% 82 8370 1.21% 83 9016 1.31% 84 9833 1.43% 85 9203 1.33% 86 9880 1.43% 87 10573 1.53% 88 12019 1.74% 89 14400 2.09% 90 17846 2.59% 91 15072 2.19% 92 13139 1.90% 93 473722 68.68% criterion=sequence-density sequence-density=2.24 sequence-density-rank=1 fanout-score=1.27 fanout-score-rank=25 prefix-density=0.11 prefix-fanout=1.3 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT criterion=fanout-score sequence-density=0.16 sequence-density-rank=14 fanout-score=90.85 fanout-score-rank=1 prefix-density=14.07 prefix-fanout=1.0 sequence=GATAGTCAAGGGCGCGTTATTAA Started job on | Dec 07 03:57:36 Started mapping on | Dec 07 03:57:36 Finished on | Dec 07 03:57:41 Mapping speed, Million of reads per hour | 593.10 Number of input reads | 823750 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 328381 Uniquely mapped reads % | 39.86% Average mapped length | 88.90 Number of splices: Total | 19300 Number of splices: Annotated (sjdb) | 15711 Number of splices: GT/AG | 18626 Number of splices: GC/AG | 292 Number of splices: AT/AC | 17 Number of splices: Non-canonical | 365 Mismatch rate per base, % | 0.81% Deletion rate per base | 0.03% Deletion average length | 1.72 Insertion rate per base | 0.01% Insertion average length | 1.65 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 443869 % of reads mapped to multiple loci | 53.88% Number of reads mapped to too many loci | 15654 % of reads mapped to too many loci | 1.90% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.99% % of reads unmapped: other | 0.36% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 51500 51500 51500 N_multimapping 443869 443869 443869 N_noFeature 28260 32338 313691 N_ambiguous 12423 1778 73 UnstrandedReadsAssigned:287698 PositiveStrandReadsAssigned:294265 NegativeStrandReadsAssigned:14617 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=87 echo kmer=83 ERR6133412 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: ERR6133412-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 823,750 reads, 572,009 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 904 rounds 52973 ERR6133412.ke.tsv 35125 ERR6133412.se.tsv 88098 total ==> ERR6133412.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 7 11.4677 PNS24243 293 194 0 0 KQK14069 1603 1504 16 23.9113 KQK14071 474 375 0 0 ==> ERR6133412.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 6 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 2 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 5 BRADI_1g48960v3 0 ERR6133412 completed mapping pipeline successfully