Starting /dee2/code/volunteer_pipeline.sh ERR6133539 current disk space = 1544470872064 free memory = 1597293456 ERR6133539 SRAfilesize 0b66dd34bda20b674c16859564b25e25 ERR6133539.sra ERR6133539.sra file validated ERR6133539 is single end ERR6133539 is conventional basespace ERR6133539 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133539_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 34.233 37.0 33.0 37.0 33.0 37.0 2 36.11075 37.0 37.0 37.0 33.0 37.0 3 35.15975 37.0 33.0 37.0 33.0 37.0 4 35.33375 37.0 37.0 37.0 33.0 37.0 5 35.25625 37.0 37.0 37.0 33.0 37.0 6 35.60375 37.0 37.0 37.0 33.0 37.0 7 37.334 37.0 37.0 40.0 33.0 40.0 8 37.3075 37.0 37.0 40.0 33.0 40.0 9 37.4145 37.0 37.0 40.0 33.0 40.0 10-11 37.445125 37.0 37.0 40.0 33.0 40.0 12-13 37.378125 37.0 37.0 40.0 33.0 40.0 14-15 37.3795 37.0 37.0 40.0 33.0 40.0 16-17 37.253125 37.0 37.0 40.0 33.0 40.0 18-19 37.194874999999996 37.0 37.0 40.0 33.0 40.0 20-21 37.152625 37.0 37.0 40.0 33.0 40.0 22-23 36.987625 37.0 37.0 40.0 33.0 40.0 24-25 37.07625 37.0 37.0 40.0 33.0 40.0 26-27 37.08125 37.0 37.0 40.0 33.0 40.0 28-29 37.059250000000006 37.0 37.0 40.0 33.0 40.0 30-31 37.0055 37.0 37.0 40.0 33.0 40.0 32-33 36.76225 37.0 37.0 40.0 33.0 40.0 34-35 36.679125 37.0 37.0 40.0 33.0 40.0 36-37 36.4815 37.0 37.0 40.0 33.0 40.0 38-39 36.403999999999996 37.0 37.0 40.0 33.0 40.0 40-41 36.19775 37.0 37.0 40.0 33.0 40.0 42-43 36.146125 37.0 37.0 40.0 33.0 40.0 44-45 35.794624999999996 37.0 35.0 38.5 33.0 40.0 46-47 35.48524999999999 37.0 33.0 37.0 33.0 40.0 48-49 35.569125 37.0 33.0 37.0 33.0 40.0 50-51 35.44 37.0 33.0 37.0 33.0 40.0 52-53 35.180625 37.0 33.0 37.0 33.0 40.0 54-55 35.161875 37.0 33.0 37.0 33.0 40.0 56-57 34.93875 37.0 33.0 37.0 33.0 37.0 58-59 34.241375000000005 37.0 33.0 37.0 27.0 37.0 60-61 34.49575 37.0 33.0 37.0 27.0 37.0 62-63 34.36625 37.0 33.0 37.0 27.0 37.0 64-65 34.3825 37.0 33.0 37.0 27.0 37.0 66-67 34.442750000000004 37.0 33.0 37.0 27.0 37.0 68-69 33.73375 35.0 33.0 37.0 30.0 37.0 70-71 33.66492807961943 35.0 33.0 37.0 27.0 37.0 72-73 34.01120467922793 37.0 33.0 37.0 27.0 37.0 74-75 34.037547605872206 37.0 33.0 37.0 27.0 37.0 76-77 34.00244211692316 37.0 33.0 37.0 27.0 37.0 78-79 34.05131361336017 37.0 33.0 37.0 27.0 37.0 80-81 33.92383543194026 37.0 33.0 37.0 27.0 37.0 82-83 33.781596325339066 37.0 33.0 37.0 27.0 37.0 84-85 33.74987153243866 37.0 33.0 37.0 27.0 37.0 86-87 33.66460268317853 37.0 33.0 37.0 27.0 37.0 88-89 33.69891640866873 37.0 33.0 37.0 27.0 37.0 90-91 33.48477812177502 37.0 33.0 37.0 27.0 37.0 92-93 33.420923632610936 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 7.0 22 23.0 23 23.0 24 24.0 25 43.0 26 31.0 27 48.0 28 55.0 29 74.0 30 82.0 31 112.0 32 142.0 33 179.0 34 252.0 35 434.0 36 908.0 37 916.0 38 631.0 39 9.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.55 2.125 2.125 6.2 2 74.575 15.2 6.75 3.4750000000000005 3 37.325 37.1 14.249999999999998 11.325000000000001 4 34.525 29.099999999999998 17.5 18.875 5 25.650000000000002 30.75 25.025 18.575 6 20.599999999999998 37.824999999999996 24.875 16.7 7 35.4 30.875000000000004 19.025 14.7 8 30.7 31.75 22.400000000000002 15.15 9 27.025 27.800000000000004 28.199999999999996 16.975 10-11 26.1 27.375 27.775 18.75 12-13 28.199999999999996 25.424999999999997 27.962500000000002 18.4125 14-15 22.45 29.4 30.162499999999998 17.9875 16-17 24.4875 31.374999999999996 26.087500000000002 18.05 18-19 23.9875 26.487500000000004 27.575 21.95 20-21 25.015626953369168 26.328291036379547 28.316039504938118 20.340042505313164 22-23 27.675 23.8875 27.224999999999998 21.212500000000002 24-25 26.737499999999997 25.162499999999998 28.275 19.825 26-27 25.112499999999997 25.662499999999998 29.975 19.25 28-29 26.0 27.1 27.187499999999996 19.7125 30-31 27.1 25.6 26.575 20.724999999999998 32-33 23.4375 28.037499999999998 27.950000000000003 20.575 34-35 24.90301589287949 26.1419096483544 28.26930296583657 20.685771492929543 36-37 24.75 24.4125 28.1875 22.650000000000002 38-39 25.4875 25.575 30.562499999999996 18.375 40-41 27.251125562781393 24.79989994997499 27.688844422211105 20.260130065032516 42-43 25.21597596093652 27.532239889820957 27.419556779767124 19.832227369475397 44-45 24.024512256128062 25.26263131565783 29.48974487243622 21.223111555777887 46-47 24.95 23.849999999999998 27.9125 23.2875 48-49 25.17814726840855 24.928116014501814 30.60382547818477 19.289911238904864 50-51 24.975 26.650000000000002 28.799999999999997 19.575 52-53 25.468867216804203 26.944236059014752 27.781945486371594 19.80495123780945 54-55 23.825 28.175 28.775000000000002 19.225 56-57 26.025 24.6875 28.849999999999998 20.4375 58-59 24.1125 24.025 29.612500000000004 22.25 60-61 24.95 24.587500000000002 29.425 21.0375 62-63 22.4375 27.825 30.675 19.0625 64-65 24.1625 26.637499999999996 29.575000000000003 19.625 66-67 25.2 26.087500000000002 29.3875 19.325 68-69 23.4125 26.450000000000003 28.8375 21.3 70-71 25.519139354515886 25.369026770077557 28.233675256442332 20.878158618964225 72-73 25.48994974874372 24.547738693467338 29.070351758793972 20.891959798994975 74-75 24.10489157841654 26.853252647503783 28.93343419062027 20.108421583459403 76-77 23.041882829305326 26.30646589902569 30.22902695179046 20.422624319878526 78-79 23.306646333714575 25.238276782310333 30.855254797305886 20.59982208666921 80-81 23.596938775510203 29.272959183673468 29.03061224489796 18.099489795918366 82-83 24.692465402357765 26.67862634546386 28.639159405433112 19.989748846745258 84-85 24.652061855670105 24.40721649484536 30.76030927835052 20.18041237113402 86-87 23.400412796697626 26.418988648090814 31.746646026831787 18.433952528379773 88-89 21.658926728586174 28.934468524251805 30.58565531475748 18.82094943240454 90-91 26.922084623323013 25.96749226006192 28.753869969040245 18.356553147574818 92-93 23.03921568627451 29.282765737874094 28.689370485036118 18.988648090815275 >>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 0.0 17 8.5 18 9.5 19 2.5 20 2.0 21 1.0 22 1.0 23 3.0 24 3.5 25 3.5 26 6.0 27 9.0 28 17.0 29 23.0 30 23.5 31 31.0 32 38.5 33 55.5 34 75.5 35 94.5 36 104.0 37 128.5 38 176.5 39 188.5 40 191.0 41 193.5 42 207.0 43 224.5 44 197.0 45 189.5 46 235.5 47 217.0 48 168.0 49 178.0 50 165.5 51 159.5 52 144.5 53 140.5 54 140.0 55 93.0 56 73.5 57 69.5 58 54.0 59 37.0 60 36.5 61 29.0 62 26.5 63 31.5 64 29.5 65 23.0 66 15.0 67 13.5 68 13.5 69 13.5 70 11.0 71 8.0 72 5.0 73 2.0 74 2.0 75 2.5 76 2.0 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 0.0125 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 0.11249999999999999 36-37 0.0 38-39 0.0 40-41 0.05 42-43 0.1625 44-45 0.05 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.025 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 6.0 71 11.0 72 6.0 73 9.0 74 4.0 75 7.0 76 11.0 77 8.0 78 7.0 79 7.0 80 8.0 81 8.0 82 12.0 83 12.0 84 8.0 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 3876.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.425 #Duplication Level Percentage of deduplicated Percentage of total 1 93.67516119128032 76.275 2 3.653669020571078 5.949999999999999 3 0.9517961314092724 2.325 4 0.49124961621123736 1.6 5 0.24562480810561868 1.0 6 0.030703101013202335 0.15 7 0.15351550506601166 0.8750000000000001 8 0.092109303039607 0.6 9 0.030703101013202335 0.22499999999999998 >10 0.644765121277249 9.5 >50 0.030703101013202335 1.5 >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 60 1.5 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 40 1.0 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 35 0.8750000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 31 0.775 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 24 0.6 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 23 0.575 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 22 0.5499999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 21 0.525 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 17 0.42500000000000004 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 17 0.42500000000000004 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 16 0.4 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 16 0.4 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGAGCACAACAAGGTAATTTGCCCGTCCCAGAAGGTTGCACTGACCGGAA 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 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 0.025 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 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra Rejected 393561 READS because READLEN < 1 Read 393561 spots for ERR6133539.sra Written 393561 spots for ERR6133539.sra Rejected 393542 READS because READLEN < 1 Read 393542 spots for ERR6133539.sra Written 393542 spots for ERR6133539.sra SRR ids: ['ERR6133539.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_coempo2f ERR6133539.sra spots: 7870859 blocks: [[1, 393542], [393543, 787084], [787085, 1180626], [1180627, 1574168], [1574169, 1967710], [1967711, 2361252], [2361253, 2754794], [2754795, 3148336], [3148337, 3541878], [3541879, 3935420], [3935421, 4328962], [4328963, 4722504], [4722505, 5116046], [5116047, 5509588], [5509589, 5903130], [5903131, 6296672], [6296673, 6690214], [6690215, 7083756], [7083757, 7477298], [7477299, 7870859]] ERR6133539 file size 1741916 ERR6133539 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 ERR6133539 ERR6133539_1.fastq Input file: ERR6133539_1.fastq trimmed: ERR6133539-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 08:14:01 2024 >> started Sat Dec 7 08:14:05 2024 >> done (3.643s) 7870859 reads processed; of these: 214 ( 0.00%) short reads filtered out after trimming by size control 91 ( 0.00%) empty reads filtered out after trimming by size control 7870554 (100.00%) reads available; of these: 142080 ( 1.81%) trimmed reads available after processing 7728474 (98.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 41 0.00% 20 13 0.00% 21 6 0.00% 22 9 0.00% 23 2 0.00% 24 3 0.00% 25 7 0.00% 26 2 0.00% 27 6 0.00% 28 5 0.00% 29 14 0.00% 30 5 0.00% 31 11 0.00% 32 22 0.00% 33 13 0.00% 34 21 0.00% 35 58 0.00% 36 1178 0.01% 37 24 0.00% 38 24 0.00% 39 55 0.00% 40 91 0.00% 41 30 0.00% 42 34 0.00% 43 24 0.00% 44 32 0.00% 45 23 0.00% 46 20 0.00% 47 23 0.00% 48 25 0.00% 49 19 0.00% 50 24 0.00% 51 61 0.00% 52 28 0.00% 53 14 0.00% 54 14 0.00% 55 15 0.00% 56 12 0.00% 57 21 0.00% 58 16 0.00% 59 10 0.00% 60 14 0.00% 61 21 0.00% 62 9 0.00% 63 6 0.00% 64 7 0.00% 65 18 0.00% 66 19 0.00% 67 35 0.00% 68 75 0.00% 69 209 0.00% 70 16679 0.21% 71 16325 0.21% 72 17518 0.22% 73 16351 0.21% 74 16921 0.21% 75 17296 0.22% 76 15560 0.20% 77 16125 0.20% 78 18374 0.23% 79 20862 0.27% 80 18340 0.23% 81 20253 0.26% 82 22499 0.29% 83 23955 0.30% 84 20153 0.26% 85 317 0.00% 86 604 0.01% 87 998 0.01% 88 1756 0.02% 89 3695 0.05% 90 8131 0.10% 91 23682 0.30% 92 96559 1.23% 93 7455123 94.72% 7870554 reads passed initial QC criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=4.58 fanout-score-rank=25 prefix-density=1.02 prefix-fanout=3.5 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=251.73 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=7.4 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 08:14:18 Started mapping on | Dec 07 08:14:18 Finished on | Dec 07 08:14:26 Mapping speed, Million of reads per hour | 3541.75 Number of input reads | 7870554 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 5745569 Uniquely mapped reads % | 73.00% Average mapped length | 92.04 Number of splices: Total | 233584 Number of splices: Annotated (sjdb) | 188740 Number of splices: GT/AG | 222362 Number of splices: GC/AG | 7080 Number of splices: AT/AC | 119 Number of splices: Non-canonical | 4023 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.03% Deletion average length | 1.75 Insertion rate per base | 0.02% Insertion average length | 2.06 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1949531 % of reads mapped to multiple loci | 24.77% Number of reads mapped to too many loci | 72829 % of reads mapped to too many loci | 0.93% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.25% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 175454 175454 175454 N_multimapping 1949531 1949531 1949531 N_noFeature 347482 398261 5488836 N_ambiguous 232298 26311 670 UnstrandedReadsAssigned:5165789 PositiveStrandReadsAssigned:5320997 NegativeStrandReadsAssigned:256063 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133539 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: ERR6133539-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,870,554 reads, 6,764,060 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,106 rounds 52973 ERR6133539.ke.tsv 35125 ERR6133539.se.tsv 88098 total ==> ERR6133539.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 187 26.9666 PNS24243 293 194 0 0 KQK14069 1603 1504 91 11.971 KQK14071 474 375 0 0 ==> ERR6133539.se.tsv <== BRADI_1g14170v3 92 BRADI_1g53295v3 87 BRADI_1g59795v3 41 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 100 BRADI_1g74790v3 67 BRADI_1g09890v3 0 BRADI_1g77505v3 173 BRADI_1g48960v3 1 ERR6133539 completed mapping pipeline successfully