Starting /dee2/code/volunteer_pipeline.sh SRR6793143 current disk space = 3089415364608 free memory = 1476763732 SRR6793143 SRAfilesize 856c83b67170d55775e252563c15a8dd SRR6793143.sra SRR6793143.sra file validated SRR6793143 is single end SRR6793143 is conventional basespace SRR6793143 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793143_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.95075 32.0 32.0 32.0 32.0 32.0 2 30.366 32.0 32.0 32.0 21.0 32.0 3 30.66025 32.0 32.0 32.0 32.0 32.0 4 30.93025 32.0 32.0 32.0 32.0 32.0 5 31.03275 32.0 32.0 32.0 32.0 32.0 6 34.24775 36.0 36.0 36.0 32.0 36.0 7 34.56375 36.0 36.0 36.0 32.0 36.0 8 34.48175 36.0 36.0 36.0 32.0 36.0 9 34.24225 36.0 36.0 36.0 32.0 36.0 10-14 34.40075 36.0 36.0 36.0 32.0 36.0 15-19 34.495850000000004 36.0 36.0 36.0 32.0 36.0 20-24 34.368849999999995 36.0 36.0 36.0 32.0 36.0 25-29 34.245999999999995 36.0 36.0 36.0 32.0 36.0 30-34 34.167100000000005 36.0 36.0 36.0 32.0 36.0 35-39 34.141650000000006 36.0 36.0 36.0 32.0 36.0 40-44 34.033699999999996 36.0 36.0 36.0 31.0 36.0 45-49 33.78765 36.0 36.0 36.0 29.0 36.0 50-54 33.67765 36.0 36.0 36.0 28.0 36.0 55-59 33.56905 36.0 36.0 36.0 27.0 36.0 60-64 33.388999999999996 36.0 36.0 36.0 27.0 36.0 65-69 33.3073 36.0 36.0 36.0 25.8 36.0 70-74 33.23625 36.0 34.4 36.0 25.8 36.0 75-79 33.227199999999996 36.0 35.2 36.0 25.8 36.0 80-84 33.06185 36.0 35.2 36.0 23.4 36.0 85-89 32.98785 36.0 33.6 36.0 21.0 36.0 90-94 32.86015 36.0 32.0 36.0 18.2 36.0 95-99 32.728649999999995 36.0 32.0 36.0 18.2 36.0 100-104 32.613800000000005 36.0 32.0 36.0 16.8 36.0 105-109 32.517999999999994 36.0 32.0 36.0 15.4 36.0 110-114 32.39655 36.0 32.0 36.0 14.0 36.0 115-119 32.0279 36.0 32.0 36.0 14.0 36.0 120-124 31.8053 36.0 32.0 36.0 14.0 36.0 125-129 30.4995 32.0 27.0 36.0 14.0 36.0 130-134 30.624149999999997 32.0 27.0 36.0 14.0 36.0 135-139 30.212 32.0 27.0 36.0 14.0 36.0 140-144 29.781799999999997 32.0 27.0 36.0 14.0 36.0 145-149 28.981050000000003 32.0 27.0 33.6 14.0 36.0 150-151 25.7315 26.5 20.5 32.0 14.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 1.0 20 2.0 21 5.0 22 10.0 23 15.0 24 40.0 25 57.0 26 71.0 27 109.0 28 168.0 29 189.0 30 246.0 31 327.0 32 395.0 33 622.0 34 1151.0 35 591.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 15.325 16.75 12.1 55.825 2 22.475 21.85 33.225 22.45 3 22.375 27.375 22.925 27.325 4 26.674999999999997 30.875000000000004 18.275 24.175 5 27.0 34.525 19.125 19.35 6 22.1 35.3 21.0 21.6 7 20.925 16.375 39.925 22.775000000000002 8 20.825 19.025 29.299999999999997 30.85 9 21.8 20.175 32.925 25.1 10-14 23.567356735673567 26.782678267826782 24.76247624762476 24.887488748874887 15-19 24.465 25.215 26.405 23.915 20-24 24.775 25.685000000000002 25.585 23.955000000000002 25-29 23.990000000000002 26.284999999999997 25.264999999999997 24.46 30-34 23.265 25.77 25.72 25.245 35-39 23.207405554165625 26.825118839129345 25.589191893920436 24.378283712784587 40-44 24.175 26.21 26.090000000000003 23.525 45-49 23.848577286592988 26.408961344201632 26.078911836775514 23.663549532429865 50-54 23.674999999999997 26.805 25.69 23.830000000000002 55-59 24.055 26.345000000000002 25.765 23.835 60-64 23.97 25.014999999999997 26.490000000000002 24.525 65-69 24.2706300355302 26.102186858830006 25.066306360406344 24.560876745233447 70-74 24.167083541770886 26.133066533266636 25.49774887443722 24.20210105052526 75-79 24.349999999999998 26.200000000000003 25.724999999999998 23.724999999999998 80-84 24.14 25.71 25.395 24.755 85-89 23.52 26.61 26.165 23.705000000000002 90-94 24.265 26.5 25.705 23.53 95-99 23.919999999999998 25.990000000000002 26.08 24.01 100-104 24.3 27.08 25.355 23.265 105-109 24.55 26.265 25.929999999999996 23.255 110-114 25.585 26.995 23.849999999999998 23.57 115-119 25.430000000000003 26.575 24.01 23.985 120-124 25.715 27.215 22.89 24.18 125-129 25.540000000000003 27.400000000000002 22.21 24.85 130-134 25.465 26.935 22.245 25.355 135-139 25.11 27.944999999999997 21.485000000000003 25.46 140-144 24.779999999999998 26.275 21.57 27.375 145-149 24.355 26.105 21.535 28.005000000000003 150-151 25.025 25.15 21.475 28.349999999999998 >>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 1.0 15 1.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 3.0 28 6.5 29 7.0 30 6.0 31 7.5 32 12.0 33 18.5 34 35.5 35 54.5 36 78.0 37 100.5 38 93.0 39 90.5 40 106.0 41 111.5 42 124.0 43 144.0 44 167.5 45 182.0 46 206.0 47 218.5 48 203.5 49 184.0 50 164.5 51 159.5 52 165.0 53 177.5 54 195.0 55 189.5 56 164.5 57 147.5 58 110.5 59 73.5 60 60.5 61 50.5 62 44.0 63 36.0 64 19.0 65 12.5 66 11.0 67 9.0 68 10.5 69 10.5 70 6.5 71 3.5 72 4.5 73 4.0 74 2.0 75 0.5 76 0.5 77 2.5 78 2.0 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 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 10-14 0.01 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.075 40-44 0.0 45-49 0.015 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.08499999999999999 70-74 0.05 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.975 #Duplication Level Percentage of deduplicated Percentage of total 1 91.48008141901715 78.64999999999999 2 5.0305321314335565 8.649999999999999 3 1.8028496656004651 4.65 4 0.7269555103227682 2.5 5 0.40709508578075027 1.7500000000000002 6 0.20354754289037513 1.05 7 0.11631288165164291 0.7000000000000001 8 0.05815644082582146 0.4 9 0.05815644082582146 0.44999999999999996 >10 0.11631288165164291 1.2 >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 CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 14 0.35000000000000003 No Hit CCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTA 13 0.325 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 11 0.27499999999999997 No Hit CTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCG 10 0.25 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 9 0.22499999999999998 No Hit CCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 9 0.22499999999999998 No Hit CGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACG 8 0.2 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 8 0.2 No Hit CAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATG 7 0.17500000000000002 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 7 0.17500000000000002 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 7 0.17500000000000002 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 7 0.17500000000000002 No Hit CTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGAC 6 0.15 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 6 0.15 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 6 0.15 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 6 0.15 No Hit CTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATC 6 0.15 No Hit CAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTCGA 6 0.15 No Hit CCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTAT 6 0.15 No Hit CTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAAC 5 0.125 No Hit GGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAA 5 0.125 No Hit AGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGAG 5 0.125 No Hit CAGGGATTGGCGGATGTTGCTTTTAGGACTCCGCCAGCACCTTATGAGAA 5 0.125 No Hit CTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTAT 5 0.125 No Hit CCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAAT 5 0.125 No Hit AAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGA 5 0.125 No Hit CAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCAC 5 0.125 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 5 0.125 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCC 5 0.125 No Hit CGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATT 5 0.125 No Hit CGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCA 5 0.125 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 5 0.125 No Hit CAACGAGTCTATAGCCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.025 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 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.0875 0.0 0.0 0.0 0.0 70-71 0.1125 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.2125 0.0 0.0 0.0 0.0 76-77 0.2625 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.3375 0.0 0.0 0.0 0.0 82-83 0.35 0.0 0.0 0.0 0.0 84-85 0.48750000000000004 0.0 0.0 0.0 0.0 86-87 0.6625 0.0 0.0 0.0 0.0 88-89 0.8500000000000001 0.0 0.0 0.0 0.0 90-91 1.0125 0.0 0.0 0.0 0.0 92-93 1.325 0.0 0.0 0.0 0.0 94-95 1.6875 0.0 0.0 0.0 0.0 96-97 2.225 0.0 0.0 0.0 0.0 98-99 2.9 0.0 0.0 0.0 0.0 100-101 3.6 0.0 0.0 0.0 0.0 102-103 4.3125 0.0 0.0 0.0 0.0 104-105 5.324999999999999 0.0 0.0 0.0 0.0 106-107 6.2875 0.0 0.0 0.0 0.0 108-109 7.3625 0.0 0.0 0.0 0.0 110-111 8.5125 0.0 0.0 0.0 0.0 112-113 9.8375 0.0 0.0 0.0 0.0 114-115 11.4625 0.0 0.0 0.0 0.0 116-117 13.100000000000001 0.0 0.0 0.0 0.0 118-119 14.575 0.0 0.0 0.0 0.0 120-121 16.3125 0.0 0.0 0.0 0.0 122-123 18.2375 0.0 0.0 0.0 0.0 124-125 20.175 0.0 0.0 0.0 0.0 126-127 21.924999999999997 0.0 0.0 0.0 0.0 128-129 24.2375 0.0 0.0 0.0 0.0 130-131 26.5125 0.0 0.0 0.0 0.0 132-133 28.275 0.0 0.0 0.0 0.0 134-135 30.025 0.0 0.0 0.0 0.0 136-137 32.125 0.0 0.0 0.0 0.0 138-139 33.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574666 READS because READLEN < 1 Read 3574666 spots for SRR6793143.sra Written 3574666 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra Rejected 3574664 READS because READLEN < 1 Read 3574664 spots for SRR6793143.sra Written 3574664 spots for SRR6793143.sra SRR ids: ['SRR6793143.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a5076fvc SRR6793143.sra spots: 71493282 blocks: [[1, 3574664], [3574665, 7149328], [7149329, 10723992], [10723993, 14298656], [14298657, 17873320], [17873321, 21447984], [21447985, 25022648], [25022649, 28597312], [28597313, 32171976], [32171977, 35746640], [35746641, 39321304], [39321305, 42895968], [42895969, 46470632], [46470633, 50045296], [50045297, 53619960], [53619961, 57194624], [57194625, 60769288], [60769289, 64343952], [64343953, 67918616], [67918617, 71493282]] SRR6793143 file size 24205027 SRR6793143 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 SRR6793143 SRR6793143_1.fastq Input file: SRR6793143_1.fastq trimmed: SRR6793143-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 Thu Feb 13 14:53:04 2025 >> started Thu Feb 13 14:54:04 2025 >> done (59.794s) 71493282 reads processed; of these: 3909 ( 0.01%) short reads filtered out after trimming by size control 4022 ( 0.01%) empty reads filtered out after trimming by size control 71485351 (99.99%) reads available; of these: 12135218 (16.98%) trimmed reads available after processing 59350133 (83.02%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 174 0.00% 19 189 0.00% 20 196 0.00% 21 200 0.00% 22 226 0.00% 23 229 0.00% 24 267 0.00% 25 306 0.00% 26 357 0.00% 27 377 0.00% 28 431 0.00% 29 425 0.00% 30 482 0.00% 31 524 0.00% 32 610 0.00% 33 563 0.00% 34 611 0.00% 35 687 0.00% 36 795 0.00% 37 780 0.00% 38 861 0.00% 39 839 0.00% 40 971 0.00% 41 1136 0.00% 42 1102 0.00% 43 1160 0.00% 44 1242 0.00% 45 1201 0.00% 46 1316 0.00% 47 1404 0.00% 48 1484 0.00% 49 1549 0.00% 50 1634 0.00% 51 1888 0.00% 52 1834 0.00% 53 2031 0.00% 54 1977 0.00% 55 2160 0.00% 56 2263 0.00% 57 2677 0.00% 58 2793 0.00% 59 3315 0.00% 60 3875 0.01% 61 4188 0.01% 62 4327 0.01% 63 4645 0.01% 64 4523 0.01% 65 4655 0.01% 66 5377 0.01% 67 6113 0.01% 68 6743 0.01% 69 7573 0.01% 70 8759 0.01% 71 11213 0.02% 72 11986 0.02% 73 13567 0.02% 74 13921 0.02% 75 15662 0.02% 76 17115 0.02% 77 19320 0.03% 78 22876 0.03% 79 24865 0.03% 80 29280 0.04% 81 34125 0.05% 82 39418 0.06% 83 44575 0.06% 84 49310 0.07% 85 56085 0.08% 86 63233 0.09% 87 67403 0.09% 88 74575 0.10% 89 83845 0.12% 90 96655 0.14% 91 109106 0.15% 92 128175 0.18% 93 142488 0.20% 94 153548 0.21% 95 168415 0.24% 96 183057 0.26% 97 206729 0.29% 98 220685 0.31% 99 242271 0.34% 100 251816 0.35% 101 279437 0.39% 102 313015 0.44% 103 330858 0.46% 104 359054 0.50% 105 371167 0.52% 106 390669 0.55% 107 427160 0.60% 108 449550 0.63% 109 480593 0.67% 110 500588 0.70% 111 562993 0.79% 112 578450 0.81% 113 584538 0.82% 114 604020 0.84% 115 631928 0.88% 116 657010 0.92% 117 638075 0.89% 118 646218 0.90% 119 628220 0.88% 120 0 0.00% 121 0 0.00% 122 11 0.00% 123 0 0.00% 124 0 0.00% 125 0 0.00% 126 0 0.00% 127 4 0.00% 128 0 0.00% 129 3 0.00% 130 0 0.00% 131 0 0.00% 132 21 0.00% 133 16 0.00% 134 3 0.00% 135 11 0.00% 136 0 0.00% 137 4 0.00% 138 1 0.00% 139 0 0.00% 140 13 0.00% 141 0 0.00% 142 0 0.00% 143 2 0.00% 144 5 0.00% 145 0 0.00% 146 12 0.00% 147 4 0.00% 148 0 0.00% 149 78 0.00% 150 124 0.00% 151 59350133 83.02% 71485351 reads passed initial QC criterion=sequence-density sequence-density=18.00 sequence-density-rank=1 fanout-score=44.88 fanout-score-rank=1 prefix-density=21.12 prefix-fanout=38.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCC criterion=fanout-score sequence-density=18.00 sequence-density-rank=1 fanout-score=44.88 fanout-score-rank=1 prefix-density=21.12 prefix-fanout=38.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCC Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCC -o SRR6793143 - Input file: STDIN trimmed: SRR6793143-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Thu Feb 13 14:56:46 2025 >> started Thu Feb 13 14:57:53 2025 >> done (67.418s) 63542534 reads processed; of these: 50 ( 0.00%) short reads filtered out after trimming by size control 87 ( 0.00%) empty reads filtered out after trimming by size control 63542397 (100.00%) reads available; of these: 18968035 (29.85%) trimmed reads available after processing 44574362 (70.15%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 158 0.00% 19 162 0.00% 20 185 0.00% 21 180 0.00% 22 204 0.00% 23 205 0.00% 24 247 0.00% 25 272 0.00% 26 320 0.00% 27 348 0.00% 28 401 0.00% 29 371 0.00% 30 418 0.00% 31 471 0.00% 32 569 0.00% 33 528 0.00% 34 540 0.00% 35 611 0.00% 36 724 0.00% 37 713 0.00% 38 773 0.00% 39 770 0.00% 40 874 0.00% 41 996 0.00% 42 993 0.00% 43 1044 0.00% 44 1134 0.00% 45 1081 0.00% 46 1197 0.00% 47 1263 0.00% 48 1338 0.00% 49 1394 0.00% 50 1462 0.00% 51 1706 0.00% 52 1673 0.00% 53 1788 0.00% 54 1770 0.00% 55 1927 0.00% 56 2051 0.00% 57 2426 0.00% 58 2562 0.00% 59 3000 0.00% 60 3487 0.01% 61 3728 0.01% 62 3833 0.01% 63 4191 0.01% 64 4064 0.01% 65 4165 0.01% 66 4888 0.01% 67 5525 0.01% 68 6125 0.01% 69 6839 0.01% 70 7871 0.01% 71 10016 0.02% 72 10578 0.02% 73 12139 0.02% 74 12594 0.02% 75 14185 0.02% 76 15350 0.02% 77 17428 0.03% 78 20421 0.03% 79 22517 0.04% 80 26470 0.04% 81 30625 0.05% 82 35248 0.06% 83 39717 0.06% 84 44310 0.07% 85 50166 0.08% 86 56635 0.09% 87 60309 0.09% 88 66877 0.11% 89 75812 0.12% 90 87411 0.14% 91 98076 0.15% 92 114280 0.18% 93 126904 0.20% 94 137556 0.22% 95 150574 0.24% 96 163524 0.26% 97 184870 0.29% 98 197269 0.31% 99 217899 0.34% 100 225258 0.35% 101 249980 0.39% 102 278666 0.44% 103 295323 0.46% 104 321759 0.51% 105 332445 0.52% 106 349045 0.55% 107 382124 0.60% 108 401190 0.63% 109 428985 0.68% 110 445280 0.70% 111 501781 0.79% 112 516993 0.81% 113 520814 0.82% 114 538242 0.85% 115 559979 0.88% 116 582343 0.92% 117 560869 0.88% 118 571187 0.90% 119 594875 0.94% 120 627268 0.99% 121 638412 1.00% 122 639830 1.01% 123 663551 1.04% 124 637893 1.00% 125 652098 1.03% 126 679444 1.07% 127 664541 1.05% 128 696930 1.10% 129 655800 1.03% 130 660488 1.04% 131 638105 1.00% 132 646882 1.02% 133 671917 1.06% 134 678074 1.07% 135 662399 1.04% 136 626593 0.99% 137 617823 0.97% 138 605544 0.95% 139 588590 0.93% 140 589801 0.93% 141 594281 0.94% 142 610897 0.96% 143 621975 0.98% 144 577208 0.91% 145 558301 0.88% 146 514337 0.81% 147 658373 1.04% 148 1082123 1.70% 149 65 0.00% 150 68 0.00% 151 33930323 53.40% criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=2.64 fanout-score-rank=28 prefix-density=0.43 prefix-fanout=2.6 sequence=GTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAGCAACATCCGCCAATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGACCCGGCCAGTTAAGGCCAGGAGCGCATCGCCGGTAGAAGGGACGAGGC criterion=fanout-score sequence-density=0.05 sequence-density-rank=34 fanout-score=39.11 fanout-score-rank=1 prefix-density=1.55 prefix-fanout=1.3 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCT Started job on | Feb 13 14:58:44 Started mapping on | Feb 13 14:58:44 Finished on | Feb 13 15:04:41 Mapping speed, Million of reads per hour | 720.86 Number of input reads | 71485214 Average input read length | 139 UNIQUE READS: Uniquely mapped reads number | 35200474 Uniquely mapped reads % | 49.24% Average mapped length | 137.27 Number of splices: Total | 10910016 Number of splices: Annotated (sjdb) | 10623596 Number of splices: GT/AG | 10680307 Number of splices: GC/AG | 163578 Number of splices: AT/AC | 13639 Number of splices: Non-canonical | 52492 Mismatch rate per base, % | 0.95% Deletion rate per base | 0.03% Deletion average length | 2.36 Insertion rate per base | 0.04% Insertion average length | 2.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5402668 % of reads mapped to multiple loci | 7.56% Number of reads mapped to too many loci | 27963525 % of reads mapped to too many loci | 39.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.44% % of reads unmapped: other | 1.64% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 30882072 30882072 30882072 N_multimapping 5402668 5402668 5402668 N_noFeature 6984174 20597843 20742029 N_ambiguous 999319 78229 77037 UnstrandedReadsAssigned:27216981 PositiveStrandReadsAssigned:14524402 NegativeStrandReadsAssigned:14381408 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=122 echo kmer=117 SRR6793143 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in single-end mode [quant] will process file 1: SRR6793143-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 71,485,214 reads, 52,493,488 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,382 rounds 52401 SRR6793143.ke.tsv 34699 SRR6793143.se.tsv 87100 total ==> SRR6793143.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 6915.89 68.6379 Potri.005G024800.1.v4.1 1035 936 556.071 11.3148 Potri.004G059700.1.v4.1 961 862 9 0.19885 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2027.08 13.5748 Potri.016G087400.1.v4.1 270 171 785.383 87.4735 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 153 1.74071 Potri.012G127500.1.v4.1 977 878 213 4.62037 ==> SRR6793143.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 329 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 243 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 5 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 4 SRR6793143 completed mapping pipeline successfully