Starting /dee2/code/volunteer_pipeline.sh ERR6133504 current disk space = 1544364544000 free memory = 1466939808 ERR6133504 SRAfilesize 6c1b03f771b3abad8cb9b8d671cc670b ERR6133504.sra ERR6133504.sra file validated ERR6133504 is single end ERR6133504 is conventional basespace ERR6133504 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133504_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 36.62975 37.0 37.0 37.0 37.0 37.0 2 36.82675 37.0 37.0 37.0 37.0 37.0 3 36.49075 37.0 37.0 37.0 37.0 37.0 4 35.86075 37.0 37.0 37.0 33.0 37.0 5 35.96475 37.0 37.0 37.0 33.0 37.0 6 36.221 37.0 37.0 37.0 33.0 37.0 7 38.1415 40.0 37.0 40.0 37.0 40.0 8 38.194 40.0 37.0 40.0 37.0 40.0 9 38.249 40.0 37.0 40.0 37.0 40.0 10-11 38.194374999999994 40.0 37.0 40.0 37.0 40.0 12-13 38.090625 40.0 37.0 40.0 37.0 40.0 14-15 38.079375 40.0 37.0 40.0 37.0 40.0 16-17 38.04 40.0 37.0 40.0 37.0 40.0 18-19 37.957875 40.0 37.0 40.0 35.0 40.0 20-21 37.8945 40.0 37.0 40.0 33.0 40.0 22-23 38.048125 40.0 37.0 40.0 37.0 40.0 24-25 37.93475 40.0 37.0 40.0 35.0 40.0 26-27 37.8965 38.5 37.0 40.0 33.0 40.0 28-29 37.863625 37.0 37.0 40.0 37.0 40.0 30-31 37.916 37.0 37.0 40.0 37.0 40.0 32-33 37.930625 38.5 37.0 40.0 37.0 40.0 34-35 37.879125 37.0 37.0 40.0 37.0 40.0 36-37 37.79125 37.0 37.0 40.0 37.0 40.0 38-39 37.668625000000006 37.0 37.0 40.0 37.0 40.0 40-41 37.508375 37.0 37.0 40.0 33.0 40.0 42-43 37.44325 37.0 37.0 40.0 37.0 40.0 44-45 37.283 37.0 37.0 40.0 35.0 40.0 46-47 37.132875 37.0 37.0 40.0 33.0 40.0 48-49 37.0245 37.0 37.0 37.0 33.0 40.0 50-51 36.7645 37.0 37.0 37.0 33.0 40.0 52-53 36.475624999999994 37.0 37.0 37.0 33.0 40.0 54-55 36.421 37.0 37.0 37.0 33.0 40.0 56-57 36.25175 37.0 37.0 37.0 33.0 37.0 58-59 35.941 37.0 37.0 37.0 33.0 37.0 60-61 35.994 37.0 37.0 37.0 33.0 37.0 62-63 35.896249999999995 37.0 37.0 37.0 33.0 37.0 64-65 35.82575 37.0 37.0 37.0 33.0 37.0 66-67 35.760999999999996 37.0 37.0 37.0 33.0 37.0 68-69 34.932625 35.0 35.0 37.0 33.0 37.0 70-71 35.14749423847695 37.0 33.0 37.0 33.0 37.0 72-73 35.57790931386735 37.0 33.0 37.0 33.0 37.0 74-75 35.546663058432244 37.0 33.0 37.0 33.0 37.0 76-77 35.56301947904379 37.0 33.0 37.0 33.0 37.0 78-79 35.502547183004296 37.0 33.0 37.0 33.0 37.0 80-81 35.373209220932054 37.0 33.0 37.0 33.0 37.0 82-83 35.19897785323552 37.0 33.0 37.0 33.0 37.0 84-85 34.99586297691288 37.0 33.0 37.0 33.0 37.0 86-87 34.98366769547325 37.0 33.0 37.0 33.0 37.0 88-89 35.00604423868313 37.0 33.0 37.0 33.0 37.0 90-91 34.92296810699588 37.0 33.0 37.0 33.0 37.0 92-93 34.94753086419753 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 5.0 22 4.0 23 4.0 24 4.0 25 6.0 26 8.0 27 11.0 28 22.0 29 16.0 30 35.0 31 36.0 32 41.0 33 68.0 34 123.0 35 318.0 36 1186.0 37 1432.0 38 667.0 39 14.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 90.75 2.35 2.275 4.625 2 78.14999999999999 13.325000000000001 4.9 3.6249999999999996 3 37.7 39.074999999999996 12.7 10.525 4 37.075 28.849999999999998 16.85 17.224999999999998 5 26.924999999999997 33.625 22.8 16.650000000000002 6 21.45 41.3 23.025000000000002 14.224999999999998 7 38.675 30.599999999999998 18.15 12.575 8 31.25 31.825 22.375 14.549999999999999 9 27.875 28.199999999999996 26.900000000000002 17.025000000000002 10-11 26.825 27.3625 27.537499999999998 18.275 12-13 29.037499999999998 26.700000000000003 27.875 16.3875 14-15 22.7625 31.674999999999997 28.487499999999997 17.075000000000003 16-17 23.375 33.0125 25.7 17.9125 18-19 22.8 29.1375 27.025 21.0375 20-21 24.34054256782098 26.840855106888363 28.9536192024003 19.86498312289036 22-23 26.387500000000003 23.3125 29.2 21.099999999999998 24-25 28.125 24.85 26.987499999999997 20.0375 26-27 25.324999999999996 25.825 30.6375 18.212500000000002 28-29 26.487500000000004 27.3625 26.25 19.900000000000002 30-31 28.325 26.237500000000004 25.7375 19.7 32-33 24.425 28.512500000000003 26.6625 20.4 34-35 25.5 24.462500000000002 28.575 21.462500000000002 36-37 24.224999999999998 24.9 29.8875 20.9875 38-39 26.2782847855982 26.59082385298162 29.22865358169771 17.902237779722466 40-41 28.114057028514257 25.937968984492244 24.899949974987493 21.048024012006003 42-43 25.49387346836709 28.719679919979995 26.081520380095025 19.70492623155789 44-45 24.025 25.937500000000004 28.7375 21.3 46-47 24.099999999999998 23.7875 29.049999999999997 23.0625 48-49 26.05 24.1625 31.2 18.587500000000002 50-51 26.903362920365048 25.87823477934742 27.94099262407801 19.277409676209526 52-53 25.91803484145883 28.763002882566735 25.755107156285252 19.563855119689183 54-55 24.318579644911228 30.23255813953488 27.719429857464366 17.72943235808952 56-57 26.0375 25.5625 28.812500000000004 19.5875 58-59 24.0 25.025 28.762500000000003 22.2125 60-61 23.962500000000002 25.2375 29.25 21.55 62-63 23.1375 27.325 31.525 18.0125 64-65 24.4125 26.5 29.7 19.3875 66-67 24.85 26.637499999999996 28.9125 19.6 68-69 23.45 26.987499999999997 27.987499999999997 21.575 70-71 25.175175175175173 25.675675675675674 27.715215215215217 21.433933933933936 72-73 26.45323289391086 23.741368487131197 28.537350910232266 21.268047708725675 74-75 23.712771327612316 27.54921756688541 29.164563351842503 19.573447753659767 76-77 22.781440162271803 26.407200811359026 30.096348884381342 20.71501014198783 78-79 24.688374459425084 24.777410328160773 30.361231238870516 20.17298397354363 80-81 24.34605078473906 28.288886053336736 30.21564374122751 17.149419420696695 82-83 25.012800819252433 24.679979518689198 29.697900665642603 20.60931899641577 84-85 25.083526085839114 23.02749935749165 31.341557440246724 20.547417116422515 86-87 22.209362139917697 25.295781893004115 34.10493827160494 18.38991769547325 88-89 21.617798353909464 28.768004115226336 30.709876543209873 18.904320987654323 90-91 26.99331275720165 26.761831275720166 28.677983539094647 17.56687242798354 92-93 24.292695473251026 28.549382716049383 28.343621399176953 18.814300411522634 >>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 0.0 16 0.0 17 3.0 18 4.0 19 1.5 20 1.0 21 0.5 22 1.5 23 3.0 24 3.5 25 5.0 26 7.5 27 10.0 28 19.0 29 25.5 30 24.0 31 28.5 32 39.5 33 48.5 34 55.0 35 69.5 36 91.5 37 123.5 38 160.5 39 166.0 40 168.5 41 183.0 42 201.5 43 218.0 44 203.5 45 202.0 46 283.0 47 278.0 48 195.0 49 194.0 50 196.0 51 184.0 52 173.0 53 166.5 54 136.5 55 92.5 56 73.5 57 69.5 58 57.5 59 38.5 60 26.5 61 22.0 62 17.5 63 16.0 64 14.0 65 9.0 66 6.0 67 3.0 68 5.5 69 7.0 70 3.5 71 1.0 72 2.0 73 2.0 74 0.5 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 0.0 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 0.0 36-37 0.0 38-39 0.0125 40-41 0.05 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0125 52-53 0.2625 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 8.0 71 5.0 72 9.0 73 12.0 74 8.0 75 11.0 76 6.0 77 8.0 78 4.0 79 7.0 80 7.0 81 4.0 82 10.0 83 7.0 84 6.0 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 3888.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.65 #Duplication Level Percentage of deduplicated Percentage of total 1 92.78091650973008 73.9 2 4.739485247959824 7.55 3 0.8788449466415568 2.1 4 0.34526051475204017 1.0999999999999999 5 0.34526051475204017 1.375 6 0.15693659761456372 0.75 7 0.06277463904582549 0.35000000000000003 8 0.09416195856873823 0.6 9 0.0 0.0 >10 0.5649717514124294 10.174999999999999 >50 0.031387319522912745 2.1 >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 GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 84 2.1 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 45 1.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 37 0.9249999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 36 0.8999999999999999 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 35 0.8750000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 28 0.7000000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 27 0.675 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 27 0.675 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 22 0.5499999999999999 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 21 0.525 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 17 0.42500000000000004 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 16 0.4 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 10 0.25 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 10 0.25 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 10 0.25 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 6 0.15 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 6 0.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit GGTCAAGAGGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGG 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGAGAGGGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTG 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 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 0.0125 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 15 9.0078975E-4 86.275 1 >>END_MODULE Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83209 READS because READLEN < 1 Read 83209 spots for ERR6133504.sra Written 83209 spots for ERR6133504.sra Rejected 83218 READS because READLEN < 1 Read 83218 spots for ERR6133504.sra Written 83218 spots for ERR6133504.sra SRR ids: ['ERR6133504.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mc03bzsz ERR6133504.sra spots: 1664189 blocks: [[1, 83209], [83210, 166418], [166419, 249627], [249628, 332836], [332837, 416045], [416046, 499254], [499255, 582463], [582464, 665672], [665673, 748881], [748882, 832090], [832091, 915299], [915300, 998508], [998509, 1081717], [1081718, 1164926], [1164927, 1248135], [1248136, 1331344], [1331345, 1414553], [1414554, 1497762], [1497763, 1580971], [1580972, 1664189]] ERR6133504 file size 367003 ERR6133504 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 ERR6133504 ERR6133504_1.fastq Input file: ERR6133504_1.fastq trimmed: ERR6133504-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 07:30:35 2024 >> started Sat Dec 7 07:30:37 2024 >> done (1.728s) 1664189 reads processed; of these: 285 ( 0.02%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 1663887 (99.98%) reads available; of these: 8442 ( 0.51%) trimmed reads available after processing 1655445 (99.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 28 0.00% 19 80 0.00% 20 30 0.00% 21 28 0.00% 22 25 0.00% 23 21 0.00% 24 11 0.00% 25 9 0.00% 26 13 0.00% 27 7 0.00% 28 35 0.00% 29 43 0.00% 30 16 0.00% 31 22 0.00% 32 33 0.00% 33 28 0.00% 34 23 0.00% 35 90 0.01% 36 328 0.02% 37 18 0.00% 38 23 0.00% 39 86 0.01% 40 85 0.01% 41 60 0.00% 42 14 0.00% 43 16 0.00% 44 34 0.00% 45 11 0.00% 46 16 0.00% 47 10 0.00% 48 4 0.00% 49 2 0.00% 50 8 0.00% 51 75 0.00% 52 13 0.00% 53 8 0.00% 54 4 0.00% 55 7 0.00% 56 9 0.00% 57 25 0.00% 58 14 0.00% 59 8 0.00% 60 4 0.00% 61 6 0.00% 62 1 0.00% 63 1 0.00% 64 0 0.00% 65 1 0.00% 66 5 0.00% 67 5 0.00% 68 4 0.00% 69 30 0.00% 70 3148 0.19% 71 3023 0.18% 72 2886 0.17% 73 2869 0.17% 74 2869 0.17% 75 2877 0.17% 76 2550 0.15% 77 2484 0.15% 78 2859 0.17% 79 2970 0.18% 80 2697 0.16% 81 2783 0.17% 82 3360 0.20% 83 3414 0.21% 84 2870 0.17% 85 17 0.00% 86 48 0.00% 87 71 0.00% 88 127 0.01% 89 237 0.01% 90 438 0.03% 91 1215 0.07% 92 4566 0.27% 93 1612032 96.88% 1663887 reads passed initial QC criterion=sequence-density sequence-density=0.70 sequence-density-rank=1 fanout-score=4.18 fanout-score-rank=21 prefix-density=0.89 prefix-fanout=3.3 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=84.14 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=6.0 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTG Started job on | Dec 07 07:30:54 Started mapping on | Dec 07 07:30:54 Finished on | Dec 07 07:31:00 Mapping speed, Million of reads per hour | 998.33 Number of input reads | 1663887 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1193213 Uniquely mapped reads % | 71.71% Average mapped length | 92.33 Number of splices: Total | 78165 Number of splices: Annotated (sjdb) | 65851 Number of splices: GT/AG | 76010 Number of splices: GC/AG | 1510 Number of splices: AT/AC | 22 Number of splices: Non-canonical | 623 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.04% Deletion average length | 1.79 Insertion rate per base | 0.02% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 409550 % of reads mapped to multiple loci | 24.61% Number of reads mapped to too many loci | 8002 % of reads mapped to too many loci | 0.48% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.16% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 61124 61124 61124 N_multimapping 409550 409550 409550 N_noFeature 71980 83026 1142288 N_ambiguous 45998 6080 158 UnstrandedReadsAssigned:1075235 PositiveStrandReadsAssigned:1104107 NegativeStrandReadsAssigned:50767 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133504 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: ERR6133504-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,663,887 reads, 1,416,839 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 943 rounds 52973 ERR6133504.ke.tsv 35125 ERR6133504.se.tsv 88098 total ==> ERR6133504.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 43 28.8331 PNS24243 293 194 0 0 KQK14069 1603 1504 16 9.78698 KQK14071 474 375 0 0 ==> ERR6133504.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 23 BRADI_1g59795v3 7 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 24 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 25 BRADI_1g48960v3 0 ERR6133504 completed mapping pipeline successfully