Starting /dee2/code/volunteer_pipeline.sh ERR6133318 current disk space = 1548238368768 free memory = 1604048808 ERR6133318 SRAfilesize 369255fd50f243887d06f5ec0e01d76b ERR6133318.sra ERR6133318.sra file validated ERR6133318 is single end ERR6133318 is conventional basespace ERR6133318 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133318_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.14025 37.0 33.0 37.0 33.0 37.0 2 36.43825 37.0 37.0 37.0 37.0 37.0 3 36.045 37.0 37.0 37.0 33.0 37.0 4 35.5635 37.0 37.0 37.0 33.0 37.0 5 35.493 37.0 37.0 37.0 33.0 37.0 6 35.8875 37.0 37.0 37.0 33.0 37.0 7 37.644 40.0 37.0 40.0 33.0 40.0 8 37.699 40.0 37.0 40.0 33.0 40.0 9 37.7135 40.0 37.0 40.0 33.0 40.0 10-11 37.612375 40.0 37.0 40.0 33.0 40.0 12-13 37.558 40.0 37.0 40.0 33.0 40.0 14-15 37.590375 40.0 37.0 40.0 33.0 40.0 16-17 37.441125 40.0 37.0 40.0 33.0 40.0 18-19 37.436125000000004 38.5 37.0 40.0 33.0 40.0 20-21 37.255125 37.0 37.0 40.0 33.0 40.0 22-23 37.137 37.0 37.0 40.0 33.0 40.0 24-25 37.242875 37.0 37.0 40.0 33.0 40.0 26-27 37.17725 37.0 37.0 40.0 33.0 40.0 28-29 37.08475 37.0 37.0 40.0 33.0 40.0 30-31 37.036 37.0 37.0 40.0 33.0 40.0 32-33 37.020125 37.0 37.0 40.0 33.0 40.0 34-35 36.846875 37.0 37.0 40.0 33.0 40.0 36-37 36.690125 37.0 37.0 40.0 33.0 40.0 38-39 36.4895 37.0 37.0 40.0 33.0 40.0 40-41 36.345375000000004 37.0 37.0 40.0 33.0 40.0 42-43 36.03875 37.0 37.0 40.0 33.0 40.0 44-45 35.685249999999996 37.0 35.0 40.0 33.0 40.0 46-47 35.373625000000004 37.0 33.0 37.0 27.0 40.0 48-49 35.36475 37.0 33.0 37.0 30.0 40.0 50-51 35.08375 37.0 33.0 37.0 27.0 40.0 52-53 34.825 37.0 33.0 37.0 27.0 40.0 54-55 34.79175 37.0 33.0 37.0 27.0 40.0 56-57 34.500125 37.0 33.0 37.0 27.0 40.0 58-59 32.221875 33.0 30.0 37.0 24.5 37.0 60-61 33.818250000000006 37.0 33.0 37.0 27.0 37.0 62-63 33.987125 37.0 33.0 37.0 27.0 37.0 64-65 33.83225 37.0 33.0 37.0 27.0 37.0 66-67 33.7035 37.0 33.0 37.0 27.0 37.0 68-69 33.014375 35.0 33.0 37.0 27.0 37.0 70-71 33.067295483061486 35.0 33.0 37.0 27.0 37.0 72-73 33.42316871852954 37.0 33.0 37.0 27.0 37.0 74-75 33.428390562758125 37.0 33.0 37.0 27.0 37.0 76-77 33.45514212245301 37.0 33.0 37.0 27.0 37.0 78-79 33.54017133205291 37.0 33.0 37.0 27.0 37.0 80-81 33.51489292564601 37.0 33.0 37.0 27.0 37.0 82-83 33.219188616610424 35.0 33.0 37.0 27.0 37.0 84-85 32.98984280818035 33.0 33.0 37.0 27.0 37.0 86-87 32.92404227212681 33.0 33.0 37.0 27.0 37.0 88-89 33.09841479524439 37.0 33.0 37.0 27.0 37.0 90-91 32.917965653896964 33.0 33.0 37.0 27.0 37.0 92-93 32.8001321003963 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 14.0 21 15.0 22 19.0 23 25.0 24 29.0 25 41.0 26 49.0 27 54.0 28 51.0 29 76.0 30 85.0 31 117.0 32 176.0 33 191.0 34 257.0 35 479.0 36 755.0 37 965.0 38 582.0 39 20.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.625 3.4000000000000004 3.95 8.025 2 64.5 20.775 10.225 4.5 3 32.300000000000004 38.675 17.125 11.899999999999999 4 32.4 26.025 21.15 20.424999999999997 5 22.475 31.35 28.7 17.474999999999998 6 18.8 38.45 26.150000000000002 16.6 7 34.575 29.925 21.025 14.475 8 27.675 28.925 25.900000000000002 17.5 9 24.725 26.575 29.599999999999998 19.1 10-11 24.375 26.6 29.799999999999997 19.225 12-13 24.675 26.8375 28.7 19.787499999999998 14-15 20.5125 29.7375 30.2875 19.4625 16-17 23.825 30.9375 25.4375 19.8 18-19 23.2625 26.637499999999996 28.849999999999998 21.25 20-21 24.268567141785446 25.49387346836709 29.15728932233058 21.080270067516878 22-23 26.900000000000002 23.575 28.349999999999998 21.175 24-25 25.025 25.4375 29.049999999999997 20.4875 26-27 24.4 26.0375 31.9875 17.575 28-29 25.3125 27.275 27.8375 19.575 30-31 26.150000000000002 25.974999999999998 28.237499999999997 19.6375 32-33 23.1375 27.224999999999998 30.0375 19.6 34-35 23.252906613326665 27.390923865483185 28.103512939117394 21.25265658207276 36-37 24.184069025884707 25.4345379517319 28.660747780417655 21.720645241965737 38-39 26.63913913913914 24.11161161161161 30.91841841841842 18.33083083083083 40-41 25.6 24.75 28.9 20.75 42-43 23.69342335583896 28.619654913728432 27.894473618404604 19.79244811202801 44-45 21.970739027135174 26.08478179317244 30.861573089908717 21.082906089783666 46-47 23.643410852713178 25.743935983995996 29.21980495123781 21.392848212053014 48-49 24.55 25.4625 31.05 18.9375 50-51 23.66479049405879 26.303939962476548 29.606003752345217 20.425265791119447 52-53 24.186686686686688 27.427427427427425 27.627627627627625 20.75825825825826 54-55 23.400000000000002 27.0625 31.324999999999996 18.212500000000002 56-57 26.0375 26.25 28.812500000000004 18.9 58-59 24.3875 25.087500000000002 29.825000000000003 20.7 60-61 23.962500000000002 25.825 30.1875 20.025000000000002 62-63 21.375 28.175 32.5375 17.9125 64-65 22.112499999999997 29.099999999999998 29.849999999999998 18.9375 66-67 24.462500000000002 27.825 28.999999999999996 18.712500000000002 68-69 21.4125 27.025 30.049999999999997 21.512500000000003 70-71 24.671258609893552 26.41202254226675 29.542892924232937 19.373825923606763 72-73 24.70944921677615 25.821121778676098 28.612935826174834 20.856493178372915 74-75 23.554086691241896 26.642938858522946 30.34193466378543 19.461039786449728 76-77 22.263427109974423 27.250639386189256 29.130434782608695 21.355498721227622 78-79 23.447565060551405 25.72790517907756 30.572017521257404 20.252512239113628 80-81 22.14861002857885 29.410236425045465 30.52740971680956 17.91374382956612 82-83 23.235101506221348 26.182056319580877 31.329404060248855 19.25343811394892 84-85 23.368060134511406 23.89555584860873 32.66517209547673 20.07121192140314 86-87 20.898282694848085 26.974900924702773 31.770145310435932 20.35667107001321 88-89 21.42668428005284 30.17173051519155 29.93394980184941 18.46763540290621 90-91 24.9669749009247 27.278731836195508 29.28665785997358 18.46763540290621 92-93 21.20211360634082 30.990752972258917 29.207397622192865 18.599735799207398 >>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 0.5 13 0.5 14 0.0 15 0.5 16 1.0 17 10.5 18 12.0 19 2.5 20 1.0 21 4.0 22 6.5 23 8.0 24 7.0 25 7.0 26 11.5 27 16.5 28 24.0 29 29.5 30 36.0 31 47.5 32 57.5 33 72.5 34 90.0 35 107.0 36 138.0 37 191.5 38 210.5 39 206.0 40 211.0 41 198.0 42 211.5 43 231.5 44 212.0 45 186.0 46 197.0 47 179.0 48 145.0 49 164.5 50 164.5 51 145.0 52 131.5 53 115.5 54 107.5 55 85.5 56 63.5 57 61.0 58 49.0 59 33.5 60 21.5 61 18.5 62 21.5 63 20.0 64 20.0 65 16.0 66 13.5 67 10.5 68 6.5 69 5.5 70 5.5 71 6.0 72 8.5 73 6.5 74 1.5 75 2.0 76 2.5 77 2.5 78 2.0 79 0.5 80 0.5 81 0.5 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 0.025 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 0.0125 36-37 0.0375 38-39 0.1 40-41 0.0 42-43 0.025 44-45 0.0375 46-47 0.025 48-49 0.0 50-51 0.0625 52-53 0.1 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 15.0 71 18.0 72 18.0 73 11.0 74 9.0 75 15.0 76 8.0 77 17.0 78 16.0 79 17.0 80 14.0 81 16.0 82 17.0 83 11.0 84 13.0 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 3785.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.55 #Duplication Level Percentage of deduplicated Percentage of total 1 92.52068746021642 72.675 2 3.914704010184596 6.15 3 1.464035646085296 3.45 4 0.6365372374283895 2.0 5 0.2864417568427753 1.125 6 0.06365372374283895 0.3 7 0.1273074474856779 0.7000000000000001 8 0.06365372374283895 0.4 9 0.09548058561425843 0.675 >10 0.8274984086569064 12.525 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 40 1.0 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 39 0.975 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 39 0.975 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 35 0.8750000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 33 0.8250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 28 0.7000000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 20 0.5 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 20 0.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 20 0.5 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 20 0.5 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 19 0.475 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 15 0.375 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 15 0.375 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 11 0.27499999999999997 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 11 0.27499999999999997 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 11 0.27499999999999997 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 11 0.27499999999999997 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 10 0.25 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 9 0.22499999999999998 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 9 0.22499999999999998 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 9 0.22499999999999998 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 5 0.125 No Hit GTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTA 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 0.025 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167928 READS because READLEN < 1 Read 167928 spots for ERR6133318.sra Written 167928 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra Rejected 167924 READS because READLEN < 1 Read 167924 spots for ERR6133318.sra Written 167924 spots for ERR6133318.sra SRR ids: ['ERR6133318.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_nn1kpy5e ERR6133318.sra spots: 3358484 blocks: [[1, 167924], [167925, 335848], [335849, 503772], [503773, 671696], [671697, 839620], [839621, 1007544], [1007545, 1175468], [1175469, 1343392], [1343393, 1511316], [1511317, 1679240], [1679241, 1847164], [1847165, 2015088], [2015089, 2183012], [2183013, 2350936], [2350937, 2518860], [2518861, 2686784], [2686785, 2854708], [2854709, 3022632], [3022633, 3190556], [3190557, 3358484]] ERR6133318 file size 739955 ERR6133318 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 ERR6133318 ERR6133318_1.fastq Input file: ERR6133318_1.fastq trimmed: ERR6133318-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 00:32:44 2024 >> started Sat Dec 7 00:32:46 2024 >> done (1.760s) 3358484 reads processed; of these: 259 ( 0.01%) short reads filtered out after trimming by size control 36 ( 0.00%) empty reads filtered out after trimming by size control 3358189 (99.99%) reads available; of these: 49537 ( 1.48%) trimmed reads available after processing 3308652 (98.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 30 0.00% 19 77 0.00% 20 39 0.00% 21 45 0.00% 22 50 0.00% 23 13 0.00% 24 25 0.00% 25 16 0.00% 26 17 0.00% 27 19 0.00% 28 46 0.00% 29 45 0.00% 30 29 0.00% 31 60 0.00% 32 45 0.00% 33 27 0.00% 34 27 0.00% 35 201 0.01% 36 329 0.01% 37 34 0.00% 38 49 0.00% 39 184 0.01% 40 101 0.00% 41 65 0.00% 42 11 0.00% 43 13 0.00% 44 11 0.00% 45 12 0.00% 46 6 0.00% 47 14 0.00% 48 11 0.00% 49 16 0.00% 50 14 0.00% 51 41 0.00% 52 9 0.00% 53 12 0.00% 54 9 0.00% 55 14 0.00% 56 16 0.00% 57 18 0.00% 58 29 0.00% 59 13 0.00% 60 29 0.00% 61 17 0.00% 62 7 0.00% 63 2 0.00% 64 5 0.00% 65 7 0.00% 66 10 0.00% 67 14 0.00% 68 33 0.00% 69 99 0.00% 70 11725 0.35% 71 11471 0.34% 72 13376 0.40% 73 10897 0.32% 74 11420 0.34% 75 11925 0.36% 76 10184 0.30% 77 10240 0.30% 78 11801 0.35% 79 12816 0.38% 80 12060 0.36% 81 13542 0.40% 82 14943 0.44% 83 14969 0.45% 84 13359 0.40% 85 140 0.00% 86 278 0.01% 87 426 0.01% 88 809 0.02% 89 1417 0.04% 90 2781 0.08% 91 8395 0.25% 92 31351 0.93% 93 3125799 93.08% 3358189 reads passed initial QC criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.16 fanout-score-rank=30 prefix-density=0.55 prefix-fanout=2.1 sequence=AGTATTATGAAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=160.43 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=5.8 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 00:33:02 Started mapping on | Dec 07 00:33:02 Finished on | Dec 07 00:33:09 Mapping speed, Million of reads per hour | 1727.07 Number of input reads | 3358189 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2244940 Uniquely mapped reads % | 66.85% Average mapped length | 91.58 Number of splices: Total | 86139 Number of splices: Annotated (sjdb) | 70171 Number of splices: GT/AG | 82658 Number of splices: GC/AG | 1944 Number of splices: AT/AC | 46 Number of splices: Non-canonical | 1491 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.78 Insertion rate per base | 0.02% Insertion average length | 1.68 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 979353 % of reads mapped to multiple loci | 29.16% Number of reads mapped to too many loci | 77478 % of reads mapped to too many loci | 2.31% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.52% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 133896 133896 133896 N_multimapping 979353 979353 979353 N_noFeature 183699 205179 2149512 N_ambiguous 83958 9835 465 UnstrandedReadsAssigned:1977283 PositiveStrandReadsAssigned:2029926 NegativeStrandReadsAssigned:94963 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133318 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: ERR6133318-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,358,189 reads, 2,715,585 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,064 rounds 52973 ERR6133318.ke.tsv 35125 ERR6133318.se.tsv 88098 total ==> ERR6133318.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 71 25.5515 PNS24243 293 194 0 0 KQK14069 1603 1504 22 7.22249 KQK14071 474 375 0 0 ==> ERR6133318.se.tsv <== BRADI_1g14170v3 22 BRADI_1g53295v3 29 BRADI_1g59795v3 34 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 51 BRADI_1g74790v3 20 BRADI_1g09890v3 0 BRADI_1g77505v3 107 BRADI_1g48960v3 0 ERR6133318 completed mapping pipeline successfully