Starting /dee2/code/volunteer_pipeline.sh ERR6133431 current disk space = 1546490544128 free memory = 1603453492 ERR6133431 SRAfilesize 7fbc631e9f98f6a7c3b56a8acd931f47 ERR6133431.sra ERR6133431.sra file validated ERR6133431 is single end ERR6133431 is conventional basespace ERR6133431 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133431_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.35325 37.0 33.0 37.0 33.0 37.0 2 36.375 37.0 37.0 37.0 37.0 37.0 3 35.69725 37.0 37.0 37.0 33.0 37.0 4 35.368 37.0 37.0 37.0 33.0 37.0 5 35.27125 37.0 37.0 37.0 33.0 37.0 6 35.595 37.0 37.0 37.0 33.0 37.0 7 37.17875 37.0 37.0 40.0 33.0 40.0 8 37.19225 37.0 37.0 40.0 33.0 40.0 9 37.20475 37.0 37.0 40.0 33.0 40.0 10-11 37.09375 37.0 37.0 40.0 33.0 40.0 12-13 36.976749999999996 37.0 37.0 40.0 33.0 40.0 14-15 36.981125 37.0 37.0 40.0 33.0 40.0 16-17 36.922375 37.0 37.0 40.0 33.0 40.0 18-19 37.181625 37.0 37.0 40.0 33.0 40.0 20-21 37.312250000000006 37.0 37.0 40.0 33.0 40.0 22-23 37.23975 37.0 37.0 40.0 33.0 40.0 24-25 37.1495 37.0 37.0 40.0 33.0 40.0 26-27 36.987 37.0 37.0 40.0 33.0 40.0 28-29 37.110625 37.0 37.0 40.0 33.0 40.0 30-31 37.09925 37.0 37.0 40.0 33.0 40.0 32-33 36.996875 37.0 37.0 40.0 33.0 40.0 34-35 36.857375000000005 37.0 37.0 40.0 33.0 40.0 36-37 36.761125 37.0 37.0 40.0 33.0 40.0 38-39 36.588125 37.0 37.0 40.0 33.0 40.0 40-41 36.416624999999996 37.0 37.0 40.0 33.0 40.0 42-43 36.3875 37.0 37.0 40.0 33.0 40.0 44-45 36.12949999999999 37.0 37.0 40.0 33.0 40.0 46-47 36.109625 37.0 37.0 37.0 33.0 40.0 48-49 35.877250000000004 37.0 35.0 37.0 33.0 40.0 50-51 35.69525 37.0 33.0 37.0 33.0 40.0 52-53 35.558375 37.0 33.0 37.0 33.0 40.0 54-55 35.507374999999996 37.0 33.0 37.0 33.0 40.0 56-57 35.357875 37.0 33.0 37.0 33.0 37.0 58-59 34.920500000000004 37.0 33.0 37.0 33.0 37.0 60-61 34.802125000000004 37.0 33.0 37.0 33.0 37.0 62-63 34.78025 37.0 33.0 37.0 33.0 37.0 64-65 34.3815 37.0 33.0 37.0 30.0 37.0 66-67 34.2855 37.0 33.0 37.0 27.0 37.0 68-69 33.105000000000004 35.0 33.0 35.0 27.0 37.0 70-71 33.418121462559476 35.0 33.0 37.0 27.0 37.0 72-73 34.116840854363126 37.0 33.0 37.0 27.0 37.0 74-75 34.33274590958037 37.0 33.0 37.0 33.0 37.0 76-77 34.282986441112584 37.0 33.0 37.0 33.0 37.0 78-79 34.215699423187154 37.0 33.0 37.0 30.0 37.0 80-81 34.214794186448884 37.0 33.0 37.0 33.0 37.0 82-83 33.994536796219265 37.0 33.0 37.0 30.0 37.0 84-85 34.03581046360491 37.0 33.0 37.0 27.0 37.0 86-87 33.94662058371736 37.0 33.0 37.0 30.0 37.0 88-89 33.92677931387608 37.0 33.0 37.0 27.0 37.0 90-91 33.7721454173067 37.0 33.0 37.0 27.0 37.0 92-93 33.687403993855604 35.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 13.0 22 11.0 23 12.0 24 20.0 25 23.0 26 33.0 27 34.0 28 50.0 29 52.0 30 75.0 31 108.0 32 136.0 33 171.0 34 271.0 35 469.0 36 994.0 37 1052.0 38 463.0 39 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.97500000000001 2.375 2.55 5.1 2 76.45145145145145 13.613613613613614 6.231231231231231 3.7037037037037033 3 36.675000000000004 40.075 13.075000000000001 10.174999999999999 4 33.85 29.475 17.75 18.925 5 26.775 31.324999999999996 23.875 18.025 6 21.2 37.25 25.05 16.5 7 39.2 28.199999999999996 17.525 15.075 8 32.4 32.425 22.375 12.8 9 26.875 27.375 27.925 17.825 10-11 26.087500000000002 28.000000000000004 28.199999999999996 17.712500000000002 12-13 28.9375 26.5375 27.700000000000003 16.825000000000003 14-15 22.037499999999998 29.95 29.1875 18.825 16-17 22.975 30.9625 28.0625 18.0 18-19 22.875 27.6875 28.462500000000002 20.974999999999998 20-21 25.55 25.5375 28.462500000000002 20.45 22-23 27.400000000000002 23.075000000000003 28.549999999999997 20.974999999999998 24-25 25.1875 24.762500000000003 28.9 21.15 26-27 24.95 25.3 30.912499999999998 18.8375 28-29 24.7875 27.075 27.6375 20.5 30-31 26.237500000000004 25.424999999999997 27.987499999999997 20.349999999999998 32-33 23.9875 27.400000000000002 28.7 19.9125 34-35 24.3125 25.587500000000002 29.262500000000003 20.837500000000002 36-37 23.962500000000002 25.8125 27.962500000000002 22.2625 38-39 26.05 24.725 29.825000000000003 19.400000000000002 40-41 26.087500000000002 24.837500000000002 27.3 21.775 42-43 23.875 26.200000000000003 28.475 21.45 44-45 23.125 24.875 30.4375 21.5625 46-47 24.2625 24.45 29.325000000000003 21.9625 48-49 24.1125 25.887500000000003 30.5 19.5 50-51 24.962500000000002 25.5625 29.7375 19.7375 52-53 24.8625 26.987499999999997 28.5625 19.5875 54-55 23.849999999999998 26.6125 30.5125 19.025 56-57 25.112499999999997 24.95 30.599999999999998 19.3375 58-59 24.075 24.875 29.612500000000004 21.4375 60-61 23.2625 24.9 31.2875 20.549999999999997 62-63 22.4875 27.250000000000004 31.6 18.6625 64-65 23.3 25.3125 30.887500000000003 20.5 66-67 23.5125 26.087500000000002 30.4375 19.9625 68-69 23.075000000000003 26.887499999999996 29.525000000000002 20.5125 70-71 24.78418616289253 25.197047416489426 29.563367946953583 20.455398473664456 72-73 26.243718592964825 24.34673366834171 29.032663316582912 20.376884422110553 74-75 22.89855072463768 25.305608065532454 31.44297416509137 20.352867044738502 76-77 22.43711288079889 26.58323852863102 30.552395398811782 20.42725319175831 78-79 22.654665314401623 24.226673427991887 32.2261663286004 20.892494929006087 80-81 22.715139189017414 28.48608109825855 30.621583831193593 18.177195881530444 82-83 22.68264694632156 26.23995919928599 30.677036848144844 20.40035700624761 84-85 23.356357124584292 23.816832949603477 32.27168073676132 20.55512918905091 86-87 23.259088581669225 25.640040962621608 32.74449564772146 18.35637480798771 88-89 21.249359959037378 27.8673835125448 31.426011264720945 19.457245263696876 90-91 24.628776241679468 25.857654889912958 30.837173579109063 18.676395289298515 92-93 21.915002560163853 28.417818740399387 30.312339989759344 19.35483870967742 >>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 0.0 16 0.5 17 6.0 18 7.5 19 2.5 20 1.0 21 0.5 22 1.5 23 5.5 24 4.0 25 1.5 26 3.5 27 8.5 28 27.0 29 41.0 30 37.5 31 49.5 32 62.0 33 67.0 34 81.5 35 104.0 36 120.0 37 122.0 38 161.5 39 185.0 40 184.5 41 200.0 42 225.5 43 248.5 44 226.5 45 208.0 46 228.0 47 210.0 48 159.5 49 151.5 50 158.5 51 152.5 52 126.5 53 115.5 54 108.0 55 80.5 56 63.0 57 56.0 58 59.0 59 54.0 60 38.5 61 27.0 62 27.0 63 29.0 64 28.5 65 26.0 66 21.0 67 18.0 68 12.5 69 10.0 70 7.5 71 4.0 72 3.5 73 2.5 74 1.0 75 0.0 76 0.0 77 0.0 78 0.0 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 0.1 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 0.01278935925310142 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 7.0 71 9.0 72 8.0 73 6.0 74 5.0 75 7.0 76 5.0 77 7.0 78 4.0 79 4.0 80 9.0 81 5.0 82 5.0 83 6.0 84 7.0 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 3906.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 93.73501199040767 78.175 2 3.597122302158273 6.0 3 0.9292565947242206 2.325 4 0.38968824940047964 1.3 5 0.3597122302158274 1.5 6 0.1798561151079137 0.8999999999999999 7 0.05995203836930455 0.35000000000000003 8 0.1798561151079137 1.2 9 0.05995203836930455 0.44999999999999996 >10 0.5095923261390888 7.8 >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 warn #Sequence Count Percentage Possible Source GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 38 0.95 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 36 0.8999999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 33 0.8250000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 32 0.8 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 24 0.6 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 21 0.525 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 17 0.42500000000000004 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 14 0.35000000000000003 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 11 0.27499999999999997 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 10 0.25 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GGAGAGTGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTG 8 0.2 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGGAATTGCTATTCTTTCTACTTCTCGAGGGATAATGACAGATCGAGAGG 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 6 0.15 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 6 0.15 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGGTCAACTAGAGAGATCGAGAGATCGGCCGTCTTCTCCGGCTCCGGCGC 5 0.125 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GGAGAAGGGTCACATATATGCTGCAGGATTCGGTTGAGCACGTTGTAGTA 5 0.125 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit TCATCGTTCGTCCCCGACATATACATGCATAGAAGATGCAAAGACTAAAA 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGAGGAGATCGAGTTGTTACTTGAGAGTTTGTAACCCTTTATCATGCCAT 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 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 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 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 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234573 READS because READLEN < 1 Read 234573 spots for ERR6133431.sra Written 234573 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra Rejected 234572 READS because READLEN < 1 Read 234572 spots for ERR6133431.sra Written 234572 spots for ERR6133431.sra SRR ids: ['ERR6133431.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v8mt40_0 ERR6133431.sra spots: 4691441 blocks: [[1, 234572], [234573, 469144], [469145, 703716], [703717, 938288], [938289, 1172860], [1172861, 1407432], [1407433, 1642004], [1642005, 1876576], [1876577, 2111148], [2111149, 2345720], [2345721, 2580292], [2580293, 2814864], [2814865, 3049436], [3049437, 3284008], [3284009, 3518580], [3518581, 3753152], [3753153, 3987724], [3987725, 4222296], [4222297, 4456868], [4456869, 4691441]] ERR6133431 file size 1038818 ERR6133431 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 ERR6133431 ERR6133431_1.fastq Input file: ERR6133431_1.fastq trimmed: ERR6133431-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 05:13:17 2024 >> started Sat Dec 7 05:13:20 2024 >> done (2.565s) 4691441 reads processed; of these: 1611 ( 0.03%) short reads filtered out after trimming by size control 26 ( 0.00%) empty reads filtered out after trimming by size control 4689804 (99.97%) reads available; of these: 59217 ( 1.26%) trimmed reads available after processing 4630587 (98.74%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 29 0.00% 19 39 0.00% 20 27 0.00% 21 16 0.00% 22 14 0.00% 23 17 0.00% 24 12 0.00% 25 15 0.00% 26 12 0.00% 27 10 0.00% 28 4 0.00% 29 25 0.00% 30 7 0.00% 31 7 0.00% 32 15 0.00% 33 15 0.00% 34 6 0.00% 35 12 0.00% 36 10 0.00% 37 12 0.00% 38 18 0.00% 39 24 0.00% 40 27 0.00% 41 15 0.00% 42 18 0.00% 43 18 0.00% 44 23 0.00% 45 25 0.00% 46 21 0.00% 47 20 0.00% 48 20 0.00% 49 23 0.00% 50 24 0.00% 51 26 0.00% 52 24 0.00% 53 29 0.00% 54 28 0.00% 55 16 0.00% 56 21 0.00% 57 22 0.00% 58 13 0.00% 59 19 0.00% 60 26 0.00% 61 13 0.00% 62 2 0.00% 63 3 0.00% 64 7 0.00% 65 4 0.00% 66 8 0.00% 67 11 0.00% 68 26 0.00% 69 84 0.00% 70 7372 0.16% 71 7562 0.16% 72 7388 0.16% 73 6859 0.15% 74 7379 0.16% 75 7181 0.15% 76 6712 0.14% 77 7073 0.15% 78 7529 0.16% 79 8502 0.18% 80 7772 0.17% 81 8184 0.17% 82 8943 0.19% 83 9553 0.20% 84 8050 0.17% 85 101 0.00% 86 207 0.00% 87 368 0.01% 88 692 0.01% 89 1378 0.03% 90 3173 0.07% 91 9717 0.21% 92 41177 0.88% 93 4515970 96.29% 4689804 reads passed initial QC criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=5.17 fanout-score-rank=26 prefix-density=0.75 prefix-fanout=3.8 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=147.19 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=8.4 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTAT Started job on | Dec 07 05:13:34 Started mapping on | Dec 07 05:13:34 Finished on | Dec 07 05:13:41 Mapping speed, Million of reads per hour | 2411.90 Number of input reads | 4689804 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3604019 Uniquely mapped reads % | 76.85% Average mapped length | 92.16 Number of splices: Total | 172658 Number of splices: Annotated (sjdb) | 144019 Number of splices: GT/AG | 163569 Number of splices: GC/AG | 5050 Number of splices: AT/AC | 72 Number of splices: Non-canonical | 3967 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.05% Deletion average length | 1.88 Insertion rate per base | 0.03% Insertion average length | 1.86 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 987909 % of reads mapped to multiple loci | 21.07% Number of reads mapped to too many loci | 21537 % of reads mapped to too many loci | 0.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.60% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 97876 97876 97876 N_multimapping 987909 987909 987909 N_noFeature 228189 260382 3438110 N_ambiguous 148731 15034 511 UnstrandedReadsAssigned:3227099 PositiveStrandReadsAssigned:3328603 NegativeStrandReadsAssigned:165398 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133431 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: ERR6133431-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,689,804 reads, 4,022,826 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,099 rounds 52973 ERR6133431.ke.tsv 35125 ERR6133431.se.tsv 88098 total ==> ERR6133431.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 101 24.6453 PNS24243 293 194 0 0 KQK14069 1603 1504 62 13.801 KQK14071 474 375 0 0 ==> ERR6133431.se.tsv <== BRADI_1g14170v3 62 BRADI_1g53295v3 138 BRADI_1g59795v3 11 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 123 BRADI_1g74790v3 43 BRADI_1g09890v3 0 BRADI_1g77505v3 116 BRADI_1g48960v3 0 ERR6133431 completed mapping pipeline successfully