Starting /dee2/code/volunteer_pipeline.sh ERR6133436 current disk space = 1546062176256 free memory = 1442386076 ERR6133436 SRAfilesize 51436fb5ac2099be546d04f81582e43d ERR6133436.sra ERR6133436.sra file validated ERR6133436 is single end ERR6133436 is conventional basespace ERR6133436 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133436_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 35.0775 37.0 33.0 37.0 33.0 37.0 2 36.30625 37.0 37.0 37.0 33.0 37.0 3 35.59825 37.0 37.0 37.0 33.0 37.0 4 35.397 37.0 37.0 37.0 33.0 37.0 5 35.32975 37.0 37.0 37.0 33.0 37.0 6 35.531 37.0 37.0 37.0 33.0 37.0 7 37.24825 37.0 37.0 40.0 33.0 40.0 8 37.26275 37.0 37.0 40.0 33.0 40.0 9 37.32175 37.0 37.0 40.0 33.0 40.0 10-11 37.238125 37.0 37.0 40.0 33.0 40.0 12-13 37.126999999999995 37.0 37.0 40.0 33.0 40.0 14-15 37.135125 37.0 37.0 40.0 33.0 40.0 16-17 36.96675 37.0 37.0 40.0 33.0 40.0 18-19 37.124 37.0 37.0 40.0 33.0 40.0 20-21 37.337374999999994 37.0 37.0 40.0 33.0 40.0 22-23 37.15125 37.0 37.0 40.0 33.0 40.0 24-25 37.194500000000005 37.0 37.0 40.0 33.0 40.0 26-27 37.1365 37.0 37.0 40.0 33.0 40.0 28-29 37.23524999999999 37.0 37.0 40.0 33.0 40.0 30-31 37.172875000000005 37.0 37.0 40.0 33.0 40.0 32-33 37.037 37.0 37.0 40.0 33.0 40.0 34-35 36.891000000000005 37.0 37.0 40.0 33.0 40.0 36-37 36.87975 37.0 37.0 40.0 33.0 40.0 38-39 36.67125 37.0 37.0 40.0 33.0 40.0 40-41 36.553124999999994 37.0 37.0 40.0 33.0 40.0 42-43 36.4195 37.0 37.0 40.0 33.0 40.0 44-45 36.12125 37.0 35.0 40.0 33.0 40.0 46-47 36.006874999999994 37.0 35.0 37.0 33.0 40.0 48-49 35.80525 37.0 35.0 37.0 33.0 40.0 50-51 35.774 37.0 35.0 37.0 33.0 40.0 52-53 35.643375 37.0 33.0 37.0 33.0 40.0 54-55 35.439625 37.0 33.0 37.0 33.0 40.0 56-57 35.28125 37.0 33.0 37.0 33.0 37.0 58-59 34.79 37.0 33.0 37.0 30.0 37.0 60-61 34.702875 37.0 33.0 37.0 33.0 37.0 62-63 34.806375 37.0 33.0 37.0 33.0 37.0 64-65 34.36275 37.0 33.0 37.0 30.0 37.0 66-67 34.322874999999996 37.0 33.0 37.0 27.0 37.0 68-69 32.945875 35.0 33.0 35.0 30.0 37.0 70-71 33.23068382352941 33.0 33.0 37.0 27.0 37.0 72-73 33.90968862088833 37.0 33.0 37.0 27.0 37.0 74-75 34.150711614763225 37.0 33.0 37.0 33.0 37.0 76-77 34.07577512081843 37.0 33.0 37.0 30.0 37.0 78-79 34.05756054545248 37.0 33.0 37.0 27.0 37.0 80-81 34.108524367712704 37.0 33.0 37.0 30.0 37.0 82-83 34.002325461645825 37.0 33.0 37.0 27.0 37.0 84-85 34.00045541318035 37.0 33.0 37.0 30.0 37.0 86-87 33.73063063063063 37.0 33.0 37.0 27.0 37.0 88-89 33.864736164736165 37.0 33.0 37.0 27.0 37.0 90-91 33.702960102960105 33.0 33.0 37.0 27.0 37.0 92-93 33.343758043758044 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 15.0 22 16.0 23 15.0 24 22.0 25 19.0 26 25.0 27 31.0 28 39.0 29 55.0 30 74.0 31 109.0 32 149.0 33 180.0 34 271.0 35 497.0 36 944.0 37 1095.0 38 434.0 39 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.75 2.6 3.375 7.2749999999999995 2 70.97420485850238 17.129977460555974 7.488104182319058 4.40771349862259 3 36.95 37.85 13.100000000000001 12.1 4 34.425 27.175 17.4 21.0 5 27.125 29.475 25.724999999999998 17.675 6 18.675 40.775 24.075 16.475 7 37.625 28.125 19.175 15.075 8 29.275000000000002 29.575000000000003 23.474999999999998 17.675 9 26.05 29.725 26.825 17.4 10-11 23.8625 28.6875 28.575 18.875 12-13 25.85 27.6 26.400000000000002 20.150000000000002 14-15 22.8375 32.237500000000004 26.224999999999998 18.7 16-17 25.112499999999997 30.3 24.962500000000002 19.625 18-19 24.7 26.2125 28.487499999999997 20.599999999999998 20-21 25.662499999999998 25.025 29.175 20.1375 22-23 27.962500000000002 23.0875 27.450000000000003 21.5 24-25 24.775 25.0 28.675 21.55 26-27 24.587500000000002 24.4 31.2125 19.8 28-29 24.025 27.3125 28.999999999999996 19.662499999999998 30-31 27.6125 25.7625 27.5875 19.037499999999998 32-33 25.5375 25.174999999999997 28.075 21.212500000000002 34-35 24.325 30.0875 26.0125 19.575 36-37 26.2875 25.3125 25.900000000000002 22.5 38-39 27.987499999999997 23.400000000000002 30.612499999999997 18.0 40-41 26.4125 24.8125 28.812500000000004 19.9625 42-43 26.650000000000002 28.549999999999997 26.775 18.025 44-45 24.887500000000003 25.687500000000004 29.549999999999997 19.875 46-47 24.425 24.349999999999998 27.0125 24.212500000000002 48-49 23.7625 23.674999999999997 30.862499999999997 21.7 50-51 22.2 27.987499999999997 29.7125 20.1 52-53 24.9 27.275 25.6 22.225 54-55 23.5125 26.8375 29.5375 20.1125 56-57 26.924999999999997 25.4375 27.762500000000003 19.875 58-59 24.3 24.575 30.8125 20.3125 60-61 26.4625 25.662499999999998 29.15 18.725 62-63 20.349999999999998 27.775 32.8375 19.037499999999998 64-65 21.4875 30.7625 27.725 20.025000000000002 66-67 24.15 29.4 28.125 18.325 68-69 21.462500000000002 26.1125 28.65 23.775 70-71 23.677298311444652 26.70419011882427 28.455284552845526 21.163227016885553 72-73 26.837220968146475 24.078254326561325 28.856282919488336 20.228241785803863 74-75 24.984258909457246 28.396927339126055 27.313940309784662 19.304873441632036 76-77 22.776160951537392 24.53498671390611 28.62204226243199 24.066810072124508 78-79 23.851814260340014 25.412331895458006 30.575995940116723 20.159857904085257 80-81 21.70424149789836 30.633040377022034 30.034390523500193 17.628327601579414 82-83 22.69349051768324 24.654023577652488 30.240902101486416 22.411583803177855 84-85 22.3623262995368 24.343798250128668 33.06742151312403 20.226453937210497 86-87 22.702702702702705 27.773487773487776 29.25353925353925 20.27027027027027 88-89 20.347490347490346 29.099099099099103 30.656370656370658 19.897039897039896 90-91 26.795366795366792 25.90733590733591 28.751608751608753 18.545688545688545 92-93 21.634491634491635 29.549549549549546 29.845559845559844 18.97039897039897 >>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 4.0 18 5.5 19 1.5 20 0.5 21 4.0 22 3.5 23 3.5 24 7.0 25 7.0 26 8.0 27 9.5 28 11.5 29 12.0 30 24.0 31 38.5 32 48.5 33 58.0 34 61.5 35 74.5 36 112.0 37 169.0 38 205.0 39 197.0 40 196.5 41 190.0 42 200.0 43 231.0 44 195.0 45 173.5 46 189.5 47 174.5 48 152.0 49 151.5 50 160.5 51 145.5 52 135.5 53 171.5 54 212.5 55 157.5 56 74.5 57 58.0 58 59.0 59 54.5 60 38.0 61 24.5 62 19.0 63 19.0 64 20.0 65 18.0 66 11.5 67 6.0 68 5.5 69 5.5 70 5.5 71 5.0 72 3.5 73 1.5 74 0.5 75 0.5 76 1.5 77 1.0 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 0.17500000000000002 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 0.03858520900321543 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 5.0 71 4.0 72 8.0 73 8.0 74 9.0 75 11.0 76 7.0 77 4.0 78 6.0 79 8.0 80 9.0 81 14.0 82 10.0 83 7.0 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 3885.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.97500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 92.22710375126732 68.22500000000001 2 3.852652923284894 5.7 3 1.4193984454207502 3.15 4 0.7434944237918215 2.1999999999999997 5 0.43933761405880367 1.625 6 0.3041568097330179 1.35 7 0.1013856032443393 0.525 8 0.16897600540723218 1.0 9 0.1013856032443393 0.675 >10 0.5407232173031429 9.3 >50 0.06759040216289286 2.775 >100 0.03379520108144643 3.4750000000000005 >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 139 3.4750000000000005 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 58 1.4500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 53 1.325 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 42 1.05 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 36 0.8999999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 34 0.8500000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 33 0.8250000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 29 0.7250000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 29 0.7250000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 23 0.575 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 21 0.525 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 20 0.5 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 19 0.475 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 18 0.44999999999999996 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 9 0.22499999999999998 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 8 0.2 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 6 0.15 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCA 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 5 0.125 No Hit GGAGTAAACTAGCATAAATAATTTGTTTGATGCCAGTCATCAAGGTTGAG 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGAGAGAGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTG 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 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 0.025 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 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142318 READS because READLEN < 1 Read 142318 spots for ERR6133436.sra Written 142318 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra Rejected 142303 READS because READLEN < 1 Read 142303 spots for ERR6133436.sra Written 142303 spots for ERR6133436.sra SRR ids: ['ERR6133436.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kf2ya2sg ERR6133436.sra spots: 2846075 blocks: [[1, 142303], [142304, 284606], [284607, 426909], [426910, 569212], [569213, 711515], [711516, 853818], [853819, 996121], [996122, 1138424], [1138425, 1280727], [1280728, 1423030], [1423031, 1565333], [1565334, 1707636], [1707637, 1849939], [1849940, 1992242], [1992243, 2134545], [2134546, 2276848], [2276849, 2419151], [2419152, 2561454], [2561455, 2703757], [2703758, 2846075]] ERR6133436 file size 628738 ERR6133436 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 ERR6133436 ERR6133436_1.fastq Input file: ERR6133436_1.fastq trimmed: ERR6133436-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 05:33:45 2024 >> started Sat Dec 7 05:33:47 2024 >> done (1.925s) 2846075 reads processed; of these: 814 ( 0.03%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 2845241 (99.97%) reads available; of these: 35661 ( 1.25%) trimmed reads available after processing 2809580 (98.75%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 42 0.00% 20 38 0.00% 21 18 0.00% 22 18 0.00% 23 9 0.00% 24 3 0.00% 25 10 0.00% 26 7 0.00% 27 5 0.00% 28 6 0.00% 29 16 0.00% 30 2 0.00% 31 10 0.00% 32 7 0.00% 33 7 0.00% 34 3 0.00% 35 4 0.00% 36 4 0.00% 37 7 0.00% 38 16 0.00% 39 19 0.00% 40 36 0.00% 41 13 0.00% 42 11 0.00% 43 21 0.00% 44 13 0.00% 45 12 0.00% 46 8 0.00% 47 5 0.00% 48 9 0.00% 49 13 0.00% 50 7 0.00% 51 33 0.00% 52 16 0.00% 53 11 0.00% 54 10 0.00% 55 12 0.00% 56 11 0.00% 57 13 0.00% 58 16 0.00% 59 8 0.00% 60 11 0.00% 61 7 0.00% 62 2 0.00% 63 1 0.00% 64 1 0.00% 65 1 0.00% 66 3 0.00% 67 13 0.00% 68 24 0.00% 69 67 0.00% 70 5585 0.20% 71 5462 0.19% 72 6009 0.21% 73 5533 0.19% 74 5359 0.19% 75 5328 0.19% 76 5001 0.18% 77 5138 0.18% 78 5717 0.20% 79 6155 0.22% 80 6148 0.22% 81 7496 0.26% 82 8079 0.28% 83 7250 0.25% 84 7328 0.26% 85 50 0.00% 86 124 0.00% 87 220 0.01% 88 417 0.01% 89 818 0.03% 90 1967 0.07% 91 5829 0.20% 92 24380 0.86% 93 2719158 95.57% 2845241 reads passed initial QC criterion=sequence-density sequence-density=0.89 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=31 prefix-density=0.89 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=23 fanout-score=241.97 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=6.9 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGA Started job on | Dec 07 05:34:17 Started mapping on | Dec 07 05:34:17 Finished on | Dec 07 05:34:24 Mapping speed, Million of reads per hour | 1463.27 Number of input reads | 2845241 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1801010 Uniquely mapped reads % | 63.30% Average mapped length | 92.05 Number of splices: Total | 63786 Number of splices: Annotated (sjdb) | 49468 Number of splices: GT/AG | 60184 Number of splices: GC/AG | 1996 Number of splices: AT/AC | 39 Number of splices: Non-canonical | 1567 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.86 Insertion rate per base | 0.02% Insertion average length | 1.56 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 960782 % of reads mapped to multiple loci | 33.77% Number of reads mapped to too many loci | 32261 % of reads mapped to too many loci | 1.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.73% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 83449 83449 83449 N_multimapping 960782 960782 960782 N_noFeature 133891 149802 1723555 N_ambiguous 69150 7547 263 UnstrandedReadsAssigned:1597969 PositiveStrandReadsAssigned:1643661 NegativeStrandReadsAssigned:77192 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133436 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: ERR6133436-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,845,241 reads, 2,246,682 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52973 ERR6133436.ke.tsv 35125 ERR6133436.se.tsv 88098 total ==> ERR6133436.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 74 31.8012 PNS24243 293 194 0 0 KQK14069 1603 1504 90 35.2826 KQK14071 474 375 0 0 ==> ERR6133436.se.tsv <== BRADI_1g14170v3 90 BRADI_1g53295v3 21 BRADI_1g59795v3 22 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 24 BRADI_1g74790v3 28 BRADI_1g09890v3 0 BRADI_1g77505v3 53 BRADI_1g48960v3 0 ERR6133436 completed mapping pipeline successfully