Starting /dee2/code/volunteer_pipeline.sh ERR6133516 current disk space = 1544435429376 free memory = 1429208580 ERR6133516 SRAfilesize 1ac186272524cc466528b11f205e90d5 ERR6133516.sra ERR6133516.sra file validated ERR6133516 is single end ERR6133516 is conventional basespace ERR6133516 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133516_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 36.63175 37.0 37.0 37.0 37.0 37.0 2 36.8435 37.0 37.0 37.0 37.0 37.0 3 36.512 37.0 37.0 37.0 37.0 37.0 4 35.857 37.0 37.0 37.0 33.0 37.0 5 35.9625 37.0 37.0 37.0 33.0 37.0 6 36.19825 37.0 37.0 37.0 33.0 37.0 7 38.14125 40.0 37.0 40.0 37.0 40.0 8 38.2085 40.0 37.0 40.0 37.0 40.0 9 38.201 40.0 37.0 40.0 37.0 40.0 10-11 38.19475 40.0 37.0 40.0 37.0 40.0 12-13 38.1225 40.0 37.0 40.0 37.0 40.0 14-15 38.068125 40.0 37.0 40.0 37.0 40.0 16-17 38.016000000000005 40.0 37.0 40.0 37.0 40.0 18-19 37.959625 40.0 37.0 40.0 37.0 40.0 20-21 37.86525 40.0 37.0 40.0 33.0 40.0 22-23 38.0975 40.0 37.0 40.0 37.0 40.0 24-25 37.96225 40.0 37.0 40.0 37.0 40.0 26-27 37.843375 38.5 37.0 40.0 37.0 40.0 28-29 37.778875 37.0 37.0 40.0 35.0 40.0 30-31 37.884875 37.0 37.0 40.0 37.0 40.0 32-33 37.92575 37.0 37.0 40.0 37.0 40.0 34-35 37.893249999999995 37.0 37.0 40.0 37.0 40.0 36-37 37.777375 37.0 37.0 40.0 37.0 40.0 38-39 37.689499999999995 37.0 37.0 40.0 37.0 40.0 40-41 37.492000000000004 37.0 37.0 40.0 35.0 40.0 42-43 37.474875 37.0 37.0 40.0 35.0 40.0 44-45 37.196625 37.0 37.0 40.0 35.0 40.0 46-47 37.067499999999995 37.0 37.0 40.0 33.0 40.0 48-49 36.93775 37.0 37.0 37.0 33.0 40.0 50-51 36.714749999999995 37.0 37.0 37.0 33.0 40.0 52-53 36.354124999999996 37.0 37.0 37.0 33.0 40.0 54-55 36.397625000000005 37.0 37.0 37.0 33.0 40.0 56-57 36.2385 37.0 37.0 37.0 33.0 37.0 58-59 35.838750000000005 37.0 37.0 37.0 33.0 37.0 60-61 35.981750000000005 37.0 37.0 37.0 33.0 37.0 62-63 35.823 37.0 37.0 37.0 33.0 37.0 64-65 35.712625 37.0 35.0 37.0 33.0 37.0 66-67 35.721000000000004 37.0 37.0 37.0 33.0 37.0 68-69 34.854 35.0 35.0 37.0 33.0 37.0 70-71 35.03836403508772 37.0 33.0 37.0 33.0 37.0 72-73 35.545252021503146 37.0 33.0 37.0 33.0 37.0 74-75 35.43347239460893 37.0 33.0 37.0 33.0 37.0 76-77 35.426766197291045 37.0 33.0 37.0 33.0 37.0 78-79 35.43145186494338 37.0 33.0 37.0 33.0 37.0 80-81 35.290762765159904 37.0 33.0 37.0 33.0 37.0 82-83 35.08527041819788 37.0 33.0 37.0 33.0 37.0 84-85 34.94277023967692 37.0 33.0 37.0 33.0 37.0 86-87 34.99352667011911 37.0 33.0 37.0 33.0 37.0 88-89 34.95183842568618 37.0 33.0 37.0 33.0 37.0 90-91 34.83117555670637 37.0 33.0 37.0 33.0 37.0 92-93 34.8081305023304 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 4.0 22 3.0 23 10.0 24 4.0 25 11.0 26 12.0 27 14.0 28 13.0 29 21.0 30 30.0 31 39.0 32 52.0 33 54.0 34 116.0 35 317.0 36 1201.0 37 1415.0 38 666.0 39 14.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.0 2.8000000000000003 3.025 5.175 2 74.6 15.174999999999999 6.175 4.05 3 38.85 38.1 12.025 11.025 4 33.800000000000004 30.15 17.8 18.25 5 26.150000000000002 32.7 23.925 17.224999999999998 6 22.225 38.875 23.7 15.2 7 36.875 30.575000000000003 18.475 14.075 8 29.95 29.849999999999998 23.1 17.1 9 26.075 29.349999999999998 27.450000000000003 17.125 10-11 25.937500000000004 28.5625 27.275 18.224999999999998 12-13 28.475 26.575 26.924999999999997 18.025 14-15 21.462500000000002 32.9125 28.0625 17.5625 16-17 23.375 32.6875 25.162499999999998 18.775 18-19 22.6875 28.675 27.450000000000003 21.1875 20-21 25.4875 26.05 28.212500000000002 20.25 22-23 26.687499999999996 23.275000000000002 29.4125 20.625 24-25 27.187499999999996 24.212500000000002 27.1625 21.4375 26-27 27.3375 25.6125 28.1125 18.9375 28-29 26.1 27.725 26.825 19.35 30-31 29.4 25.0 26.075 19.525000000000002 32-33 25.412499999999998 27.712500000000002 25.8 21.075 34-35 25.174999999999997 27.224999999999998 27.1625 20.4375 36-37 24.2375 25.424999999999997 29.2875 21.05 38-39 28.050000000000004 25.45 28.449999999999996 18.05 40-41 27.487499999999997 25.3 26.8375 20.375 42-43 24.637500000000003 29.7875 25.324999999999996 20.25 44-45 24.725 26.275 28.237499999999997 20.7625 46-47 25.2375 23.7 27.5125 23.549999999999997 48-49 25.3 24.8125 29.5 20.3875 50-51 26.875 26.6125 27.05 19.4625 52-53 25.257085527965888 28.304489591171304 25.70855279658891 20.72987208427389 54-55 23.85596399099775 29.40735183795949 26.79419854963741 19.94248562140535 56-57 26.9125 27.775 26.900000000000002 18.4125 58-59 23.2875 26.525 28.925 21.2625 60-61 25.7625 25.374999999999996 27.500000000000004 21.3625 62-63 23.2375 26.474999999999998 31.025000000000002 19.2625 64-65 24.725 28.762500000000003 27.962500000000002 18.55 66-67 24.8125 27.950000000000003 27.187499999999996 20.05 68-69 23.5375 27.5625 26.950000000000003 21.95 70-71 24.55569461827284 27.246558197747184 27.02127659574468 21.176470588235293 72-73 26.894034734457588 24.075006292474203 28.580417820286936 20.450541152781273 74-75 23.627624588919808 28.396154819124714 29.15507209714141 18.821148494814068 76-77 22.517145034290067 27.254254508509018 27.978155956311912 22.250444500889003 78-79 24.815003827507017 25.835672365399336 29.0635366164838 20.28578719060985 80-81 24.393997691419777 29.61395408490445 28.04924971142747 17.942798512248302 82-83 25.470239628961604 24.942025251223914 29.502705488276217 20.085029631538262 84-85 23.66412213740458 24.776814594384785 30.40496830120326 21.154094967007374 86-87 21.892801657172452 27.019678922837908 31.796996374935265 19.290523045054375 88-89 21.116002071465562 28.935784567581564 29.854997410668048 20.093215950284826 90-91 26.191092698083896 30.010357327809423 26.178146038322115 17.620403935784566 92-93 24.029000517866393 29.207664422578976 27.80942516830658 18.95390989124806 >>END_MODULE >>Per sequence GC content pass #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 1.0 17 1.5 18 3.0 19 3.5 20 3.0 21 2.5 22 2.0 23 3.5 24 5.0 25 4.5 26 8.0 27 10.0 28 15.5 29 23.5 30 25.5 31 31.0 32 33.0 33 42.5 34 57.0 35 73.5 36 100.0 37 116.0 38 137.0 39 158.5 40 175.5 41 187.0 42 194.5 43 202.5 44 193.0 45 199.5 46 276.0 47 280.0 48 199.5 49 188.0 50 192.5 51 190.5 52 170.0 53 147.5 54 165.5 55 129.0 56 66.5 57 57.0 58 50.0 59 37.0 60 30.0 61 20.5 62 17.0 63 18.0 64 14.5 65 14.5 66 10.0 67 6.0 68 7.0 69 6.5 70 3.5 71 1.0 72 0.5 73 0.0 74 1.5 75 2.0 76 1.0 77 0.5 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 0.0 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 0.325 54-55 0.025 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 10.0 71 9.0 72 16.0 73 10.0 74 4.0 75 10.0 76 8.0 77 9.0 78 10.0 79 11.0 80 9.0 81 10.0 82 6.0 83 11.0 84 5.0 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 3862.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.05 #Duplication Level Percentage of deduplicated Percentage of total 1 93.63193174893357 76.825 2 4.021937842778794 6.6000000000000005 3 1.0054844606946984 2.475 4 0.3656307129798903 1.2 5 0.2742230347349177 1.125 6 0.1218769043266301 0.6 7 0.030469226081657527 0.17500000000000002 8 0.0 0.0 9 0.06093845216331505 0.44999999999999996 >10 0.42656916514320536 6.4 >50 0.06093845216331505 4.15 >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 85 2.125 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 81 2.025 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 35 0.8750000000000001 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 27 0.675 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 24 0.6 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 22 0.5499999999999999 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 20 0.5 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 18 0.44999999999999996 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 16 0.4 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 14 0.35000000000000003 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 14 0.35000000000000003 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 14 0.35000000000000003 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCA 5 0.125 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 5 0.125 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGACAACTGCACCTGCAACCCGTGCACCTGCAAGTGAAACTCAACTTGAG 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 30 1.8640274E-4 57.44166 2 GGGAGAG 40 1.1178736E-5 53.851566 1 GCAATAC 35 3.9925636E-4 49.235714 7 CAATACA 35 3.9925636E-4 49.235714 8 AATACAA 35 3.9925636E-4 49.235714 9 AGCAATA 35 3.9925636E-4 49.235714 6 GAGCAAT 40 7.713967E-4 43.081253 5 AGAGCAA 40 7.713967E-4 43.081253 4 GAGAGCA 40 7.713967E-4 43.081253 3 CATCACT 25 0.0019048193 36.278946 82-83 ATCACTA 25 0.0019048193 36.278946 84-85 CGAAAGC 25 0.0019048193 36.278946 76-77 CACTAGC 25 0.0019048193 36.278946 86-87 TCACTAG 25 0.0019048193 36.278946 84-85 ACTAGCT 25 0.0019048193 36.278946 86-87 GCATCAC 25 0.0019048193 36.278946 82-83 CCGAAAG 25 0.0019048193 36.278946 76-77 TAGCCGA 25 0.0020327973 35.807793 72-73 AGCCGAA 25 0.0020327973 35.807793 74-75 GCCGAAA 25 0.0020327973 35.807793 74-75 >>END_MODULE Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53209 READS because READLEN < 1 Read 53209 spots for ERR6133516.sra Written 53209 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra Rejected 53197 READS because READLEN < 1 Read 53197 spots for ERR6133516.sra Written 53197 spots for ERR6133516.sra SRR ids: ['ERR6133516.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_m91e4t44 ERR6133516.sra spots: 1063952 blocks: [[1, 53197], [53198, 106394], [106395, 159591], [159592, 212788], [212789, 265985], [265986, 319182], [319183, 372379], [372380, 425576], [425577, 478773], [478774, 531970], [531971, 585167], [585168, 638364], [638365, 691561], [691562, 744758], [744759, 797955], [797956, 851152], [851153, 904349], [904350, 957546], [957547, 1010743], [1010744, 1063952]] ERR6133516 file size 233361 ERR6133516 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 ERR6133516 ERR6133516_1.fastq Input file: ERR6133516_1.fastq trimmed: ERR6133516-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 07:44:14 2024 >> started Sat Dec 7 07:44:15 2024 >> done (0.772s) 1063952 reads processed; of these: 169 ( 0.02%) short reads filtered out after trimming by size control 13 ( 0.00%) empty reads filtered out after trimming by size control 1063770 (99.98%) reads available; of these: 5666 ( 0.53%) trimmed reads available after processing 1058104 (99.47%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 38 0.00% 20 23 0.00% 21 14 0.00% 22 32 0.00% 23 8 0.00% 24 7 0.00% 25 7 0.00% 26 3 0.00% 27 11 0.00% 28 21 0.00% 29 35 0.00% 30 16 0.00% 31 19 0.00% 32 18 0.00% 33 18 0.00% 34 18 0.00% 35 93 0.01% 36 184 0.02% 37 12 0.00% 38 25 0.00% 39 51 0.00% 40 55 0.01% 41 21 0.00% 42 6 0.00% 43 7 0.00% 44 11 0.00% 45 9 0.00% 46 5 0.00% 47 4 0.00% 48 4 0.00% 49 7 0.00% 50 13 0.00% 51 19 0.00% 52 6 0.00% 53 4 0.00% 54 1 0.00% 55 7 0.00% 56 7 0.00% 57 8 0.00% 58 6 0.00% 59 6 0.00% 60 8 0.00% 61 4 0.00% 62 1 0.00% 63 1 0.00% 64 1 0.00% 65 0 0.00% 66 0 0.00% 67 2 0.00% 68 5 0.00% 69 27 0.00% 70 3384 0.32% 71 2900 0.27% 72 3051 0.29% 73 2761 0.26% 74 2833 0.27% 75 2768 0.26% 76 2553 0.24% 77 2610 0.25% 78 2697 0.25% 79 3019 0.28% 80 2588 0.24% 81 3056 0.29% 82 3304 0.31% 83 3148 0.30% 84 2756 0.26% 85 13 0.00% 86 36 0.00% 87 45 0.00% 88 77 0.01% 89 150 0.01% 90 326 0.03% 91 843 0.08% 92 3057 0.29% 93 1014866 95.40% 1063770 reads passed initial QC criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=22 prefix-density=0.54 prefix-fanout=2.1 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=115.68 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=7.2 sequence=AGGAAGAGGAGGATGCAGTCAGGGCTCACAAACAACCTGCCACTGCCGCCATTGGCCTTCTAAAACAGGAGAGGAGGGGTTAGATAGTTTCGATCTGCAAGGGGGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGCAGAAGCTGTATGCTTATGAGCAGCTATGGTACTTATCGAGGACAGTAGCGTACT Started job on | Dec 07 07:44:33 Started mapping on | Dec 07 07:44:33 Finished on | Dec 07 07:44:37 Mapping speed, Million of reads per hour | 957.39 Number of input reads | 1063770 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 760111 Uniquely mapped reads % | 71.45% Average mapped length | 91.87 Number of splices: Total | 63441 Number of splices: Annotated (sjdb) | 54131 Number of splices: GT/AG | 61437 Number of splices: GC/AG | 1162 Number of splices: AT/AC | 30 Number of splices: Non-canonical | 812 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.05% Deletion average length | 1.87 Insertion rate per base | 0.02% Insertion average length | 1.75 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 263438 % of reads mapped to multiple loci | 24.76% Number of reads mapped to too many loci | 6511 % of reads mapped to too many loci | 0.61% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.14% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 40221 40221 40221 N_multimapping 263438 263438 263438 N_noFeature 46027 53696 726598 N_ambiguous 30144 4336 111 UnstrandedReadsAssigned:683940 PositiveStrandReadsAssigned:702079 NegativeStrandReadsAssigned:33402 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133516 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: ERR6133516-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,063,770 reads, 882,183 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 871 rounds 52973 ERR6133516.ke.tsv 35125 ERR6133516.se.tsv 88098 total ==> ERR6133516.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 20 21.9431 PNS24243 293 194 0 0 KQK14069 1603 1504 56 56.0483 KQK14071 474 375 0 0 ==> ERR6133516.se.tsv <== BRADI_1g14170v3 57 BRADI_1g53295v3 13 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 16 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 11 BRADI_1g48960v3 0 ERR6133516 completed mapping pipeline successfully