Starting /dee2/code/volunteer_pipeline.sh SRR6793144 current disk space = 3089355956224 free memory = 1495355668 SRR6793144 SRAfilesize e9dfe8219c920d7c3ccab9cfd5f451af SRR6793144.sra SRR6793144.sra file validated SRR6793144 is single end SRR6793144 is conventional basespace SRR6793144 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793144_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.973 32.0 32.0 32.0 32.0 32.0 2 30.29675 32.0 32.0 32.0 21.0 32.0 3 30.68625 32.0 32.0 32.0 32.0 32.0 4 30.962 32.0 32.0 32.0 32.0 32.0 5 30.98975 32.0 32.0 32.0 32.0 32.0 6 34.31525 36.0 36.0 36.0 32.0 36.0 7 34.29425 36.0 36.0 36.0 32.0 36.0 8 34.38375 36.0 36.0 36.0 32.0 36.0 9 34.47925 36.0 36.0 36.0 32.0 36.0 10-14 34.36555 36.0 36.0 36.0 32.0 36.0 15-19 34.4473 36.0 36.0 36.0 32.0 36.0 20-24 34.3187 36.0 36.0 36.0 32.0 36.0 25-29 34.114000000000004 36.0 36.0 36.0 32.0 36.0 30-34 34.14025 36.0 36.0 36.0 32.0 36.0 35-39 33.9647 36.0 36.0 36.0 32.0 36.0 40-44 33.93905 36.0 36.0 36.0 31.0 36.0 45-49 33.77095 36.0 36.0 36.0 29.0 36.0 50-54 33.7014 36.0 36.0 36.0 28.0 36.0 55-59 33.52720000000001 36.0 36.0 36.0 27.0 36.0 60-64 33.2398 36.0 35.2 36.0 25.8 36.0 65-69 33.178250000000006 36.0 33.6 36.0 25.8 36.0 70-74 33.07295 36.0 33.6 36.0 23.4 36.0 75-79 33.095749999999995 36.0 34.4 36.0 23.4 36.0 80-84 32.9856 36.0 32.8 36.0 22.2 36.0 85-89 32.938399999999994 36.0 32.0 36.0 20.8 36.0 90-94 32.8515 36.0 32.0 36.0 19.6 36.0 95-99 32.623149999999995 36.0 32.0 36.0 16.8 36.0 100-104 32.508950000000006 36.0 32.0 36.0 14.0 36.0 105-109 32.322050000000004 36.0 32.0 36.0 14.0 36.0 110-114 32.268499999999996 36.0 32.0 36.0 14.0 36.0 115-119 31.880399999999998 36.0 32.0 36.0 14.0 36.0 120-124 31.5476 36.0 29.0 36.0 14.0 36.0 125-129 30.354200000000002 32.0 27.0 36.0 14.0 36.0 130-134 30.396500000000003 32.0 27.0 36.0 14.0 36.0 135-139 30.1181 32.0 27.0 36.0 14.0 36.0 140-144 29.738099999999996 32.0 27.0 36.0 14.0 36.0 145-149 28.87055 32.0 27.0 33.6 14.0 36.0 150-151 25.786625 29.5 20.5 32.0 14.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 1.0 19 0.0 20 3.0 21 6.0 22 13.0 23 18.0 24 37.0 25 73.0 26 80.0 27 124.0 28 164.0 29 184.0 30 269.0 31 304.0 32 396.0 33 643.0 34 1079.0 35 605.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 16.150000000000002 17.925 12.425 53.5 2 20.849999999999998 22.35 34.425 22.375 3 20.575 26.174999999999997 25.25 28.000000000000004 4 26.375 31.175000000000004 17.75 24.7 5 26.875 32.425 21.475 19.225 6 20.4 35.175 23.225 21.2 7 18.475 17.474999999999998 41.075 22.975 8 20.849999999999998 19.25 30.2 29.7 9 22.0 21.525 31.25 25.224999999999998 10-14 22.09831474721208 28.649297394609192 25.463819572935943 23.788568285242786 15-19 24.7 25.509999999999998 27.11 22.68 20-24 24.529999999999998 26.295 25.590000000000003 23.585 25-29 23.61 26.450000000000003 25.575 24.365000000000002 30-34 23.105 25.505 26.505000000000003 24.884999999999998 35-39 22.975272800080088 26.754429872860147 25.848433276604265 24.421864050455504 40-44 23.455000000000002 26.284999999999997 26.685 23.575 45-49 22.988448267240084 26.393959093864076 26.769015352302844 23.848577286592988 50-54 23.585 26.68 25.95 23.785 55-59 23.435 26.135 26.865 23.565 60-64 23.674999999999997 26.245 25.545 24.535 65-69 23.867220748009814 26.02513393080659 26.100235317678866 24.00741000350473 70-74 23.852660027025674 26.590260747710325 25.834542815674894 23.72253640958911 75-79 24.22 26.169999999999998 25.345000000000002 24.265 80-84 23.71 25.345000000000002 26.815 24.13 85-89 23.16 26.52 27.22 23.1 90-94 23.53 26.465 26.400000000000002 23.605 95-99 23.34 25.979999999999997 27.07 23.61 100-104 24.21 26.240000000000002 26.345000000000002 23.205000000000002 105-109 24.154999999999998 26.474999999999998 26.52 22.85 110-114 25.115 26.58 25.124999999999996 23.18 115-119 24.275 27.284999999999997 25.124999999999996 23.315 120-124 25.11 27.825 23.599999999999998 23.465 125-129 24.45 27.82 22.98 24.75 130-134 24.905 27.62 23.285 24.19 135-139 24.93 28.705000000000002 22.66 23.705000000000002 140-144 25.09 28.025 22.625 24.26 145-149 25.295 28.28 21.755 24.67 150-151 24.3875 28.050000000000004 22.9625 24.6 >>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 0.5 8 0.5 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 1.0 21 1.0 22 0.0 23 0.0 24 0.0 25 1.5 26 2.5 27 3.0 28 4.0 29 3.5 30 4.0 31 10.5 32 16.0 33 18.5 34 33.0 35 71.0 36 94.0 37 102.0 38 113.0 39 120.0 40 129.5 41 133.0 42 137.0 43 143.0 44 182.5 45 208.5 46 194.5 47 199.5 48 219.5 49 210.5 50 174.0 51 163.5 52 165.5 53 166.5 54 151.0 55 129.5 56 133.5 57 124.0 58 90.5 59 73.0 60 62.5 61 40.5 62 27.5 63 20.5 64 15.5 65 13.0 66 10.0 67 13.0 68 16.0 69 15.0 70 10.0 71 6.5 72 7.0 73 4.0 74 1.0 75 1.0 76 1.0 77 0.0 78 1.0 79 2.0 80 1.0 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 0.5 90 0.5 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 0.015 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.11 40-44 0.0 45-49 0.015 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.135 70-74 0.095 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 82.25 #Duplication Level Percentage of deduplicated Percentage of total 1 89.0273556231003 73.225 2 6.4741641337386024 10.65 3 2.127659574468085 5.25 4 1.094224924012158 3.5999999999999996 5 0.5775075987841946 2.375 6 0.2735562310030395 1.35 7 0.060790273556231005 0.35000000000000003 8 0.060790273556231005 0.4 9 0.0911854103343465 0.675 >10 0.2127659574468085 2.125 >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 17 0.42500000000000004 No Hit CCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTAT 13 0.325 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 12 0.3 No Hit CCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 12 0.3 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 11 0.27499999999999997 No Hit CCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTA 10 0.25 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCT 10 0.25 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 9 0.22499999999999998 No Hit CTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGT 9 0.22499999999999998 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 9 0.22499999999999998 No Hit CTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGAC 8 0.2 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 8 0.2 No Hit CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGAGGCCTACCATGG 7 0.17500000000000002 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 7 0.17500000000000002 No Hit CTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGCACGT 6 0.15 No Hit CGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCA 6 0.15 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATC 6 0.15 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 6 0.15 No Hit CTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTG 6 0.15 No Hit CTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTC 6 0.15 No Hit CACGTATTAGCTCTAGAATTACTACGGTTATCCGAGTAGCAAATACCATC 6 0.15 No Hit ATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCT 6 0.15 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 6 0.15 No Hit CCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTC 5 0.125 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit ATTTCTTCAAAGTAACAGCACCGGAGGCACGACCCGGCCAGTTAAGGCCA 5 0.125 No Hit CTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAGT 5 0.125 No Hit GGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAA 5 0.125 No Hit TAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGC 5 0.125 No Hit AGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGAG 5 0.125 No Hit CATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGAGGCCT 5 0.125 No Hit CAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAA 5 0.125 No Hit ACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACC 5 0.125 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 5 0.125 No Hit CAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGACTGTGAAA 5 0.125 No Hit TAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTG 5 0.125 No Hit CTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATC 5 0.125 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 5 0.125 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 5 0.125 No Hit CTAATGTATCCAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAA 5 0.125 No Hit CAGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGA 5 0.125 No Hit CCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 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 0.0 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 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0125 0.0 0.0 0.0 0.0 54-55 0.037500000000000006 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 0.075 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 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 0.2 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.3875 0.0 0.0 0.0 0.0 86-87 0.4125 0.0 0.0 0.0 0.0 88-89 0.5125 0.0 0.0 0.0 0.0 90-91 0.625 0.0 0.0 0.0 0.0 92-93 0.7125 0.0 0.0 0.0 0.0 94-95 0.8875 0.0 0.0 0.0 0.0 96-97 1.0125 0.0 0.0 0.0 0.0 98-99 1.35 0.0 0.0 0.0 0.0 100-101 1.6375 0.0 0.0 0.0 0.0 102-103 2.0 0.0 0.0 0.0 0.0 104-105 2.35 0.0 0.0 0.0 0.0 106-107 2.9 0.0 0.0 0.0 0.0 108-109 3.425 0.0 0.0 0.0 0.0 110-111 4.4 0.0 0.0 0.0 0.0 112-113 5.4 0.0 0.0 0.0 0.0 114-115 6.300000000000001 0.0 0.0 0.0 0.0 116-117 7.3875 0.0 0.0 0.0 0.0 118-119 8.3625 0.0 0.0 0.0 0.0 120-121 9.412500000000001 0.0 0.0 0.0 0.0 122-123 10.3 0.0 0.0 0.0 0.0 124-125 11.575 0.0 0.0 0.0 0.0 126-127 13.15 0.0 0.0 0.0 0.0 128-129 14.725000000000001 0.0 0.0 0.0 0.0 130-131 16.1375 0.0 0.0 0.0 0.0 132-133 17.7125 0.0 0.0 0.0 0.0 134-135 19.6625 0.0 0.0 0.0 0.0 136-137 21.325 0.0 0.0 0.0 0.0 138-139 23.112499999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAAAAT 10 0.006830828 145.0 1 >>END_MODULE Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275958 READS because READLEN < 1 Read 5275958 spots for SRR6793144.sra Written 5275958 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra Rejected 5275951 READS because READLEN < 1 Read 5275951 spots for SRR6793144.sra Written 5275951 spots for SRR6793144.sra SRR ids: ['SRR6793144.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ykf1_x0l SRR6793144.sra spots: 105519027 blocks: [[1, 5275951], [5275952, 10551902], [10551903, 15827853], [15827854, 21103804], [21103805, 26379755], [26379756, 31655706], [31655707, 36931657], [36931658, 42207608], [42207609, 47483559], [47483560, 52759510], [52759511, 58035461], [58035462, 63311412], [63311413, 68587363], [68587364, 73863314], [73863315, 79139265], [79139266, 84415216], [84415217, 89691167], [89691168, 94967118], [94967119, 100243069], [100243070, 105519027]] SRR6793144 file size 35746014 SRR6793144 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 SRR6793144 SRR6793144_1.fastq Input file: SRR6793144_1.fastq trimmed: SRR6793144-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 14:59:39 2025 >> started Thu Feb 13 15:00:45 2025 >> done (65.664s) 105519027 reads processed; of these: 7429 ( 0.01%) short reads filtered out after trimming by size control 1786 ( 0.00%) empty reads filtered out after trimming by size control 105509812 (99.99%) reads available; of these: 10081514 ( 9.56%) trimmed reads available after processing 95428298 (90.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 571 0.00% 19 527 0.00% 20 527 0.00% 21 549 0.00% 22 666 0.00% 23 651 0.00% 24 721 0.00% 25 759 0.00% 26 961 0.00% 27 944 0.00% 28 1042 0.00% 29 1082 0.00% 30 1202 0.00% 31 1252 0.00% 32 1453 0.00% 33 1368 0.00% 34 1533 0.00% 35 1782 0.00% 36 1752 0.00% 37 1856 0.00% 38 1985 0.00% 39 2009 0.00% 40 2281 0.00% 41 2480 0.00% 42 2535 0.00% 43 2557 0.00% 44 2759 0.00% 45 2886 0.00% 46 2858 0.00% 47 3112 0.00% 48 3266 0.00% 49 3370 0.00% 50 3260 0.00% 51 3551 0.00% 52 3655 0.00% 53 4032 0.00% 54 3797 0.00% 55 4237 0.00% 56 4276 0.00% 57 4970 0.00% 58 4852 0.00% 59 5567 0.01% 60 5859 0.01% 61 6198 0.01% 62 6357 0.01% 63 6622 0.01% 64 6060 0.01% 65 6032 0.01% 66 6724 0.01% 67 7622 0.01% 68 7547 0.01% 69 7526 0.01% 70 8722 0.01% 71 10765 0.01% 72 10436 0.01% 73 10879 0.01% 74 11221 0.01% 75 12567 0.01% 76 13281 0.01% 77 14053 0.01% 78 16814 0.02% 79 16871 0.02% 80 19107 0.02% 81 23007 0.02% 82 25339 0.02% 83 28185 0.03% 84 31234 0.03% 85 34800 0.03% 86 39256 0.04% 87 41126 0.04% 88 45672 0.04% 89 51853 0.05% 90 60003 0.06% 91 68004 0.06% 92 82965 0.08% 93 92716 0.09% 94 99994 0.09% 95 111346 0.11% 96 123457 0.12% 97 142049 0.13% 98 151727 0.14% 99 168717 0.16% 100 179688 0.17% 101 201101 0.19% 102 226916 0.22% 103 245864 0.23% 104 269436 0.26% 105 283819 0.27% 106 304741 0.29% 107 343200 0.33% 108 366960 0.35% 109 396788 0.38% 110 419782 0.40% 111 489584 0.46% 112 511174 0.48% 113 526081 0.50% 114 551652 0.52% 115 580563 0.55% 116 609173 0.58% 117 601657 0.57% 118 622122 0.59% 119 622464 0.59% 120 0 0.00% 121 0 0.00% 122 17 0.00% 123 0 0.00% 124 4 0.00% 125 0 0.00% 126 0 0.00% 127 13 0.00% 128 0 0.00% 129 12 0.00% 130 4 0.00% 131 0 0.00% 132 34 0.00% 133 38 0.00% 134 3 0.00% 135 16 0.00% 136 0 0.00% 137 20 0.00% 138 4 0.00% 139 0 0.00% 140 19 0.00% 141 0 0.00% 142 0 0.00% 143 0 0.00% 144 14 0.00% 145 0 0.00% 146 19 0.00% 147 3 0.00% 148 0 0.00% 149 123 0.00% 150 200 0.00% 151 95428298 90.44% 105509812 reads passed initial QC criterion=sequence-density sequence-density=14.22 sequence-density-rank=1 fanout-score=48.70 fanout-score-rank=1 prefix-density=16.94 prefix-fanout=40.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATC criterion=fanout-score sequence-density=14.22 sequence-density-rank=1 fanout-score=48.70 fanout-score-rank=1 prefix-density=16.94 prefix-fanout=40.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATC 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATC -o SRR6793144 - Input file: STDIN trimmed: SRR6793144-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATC -- 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 15:05:20 2025 >> started Thu Feb 13 15:07:05 2025 >> done (105.107s) 91441837 reads processed; of these: 140 ( 0.00%) short reads filtered out after trimming by size control 83 ( 0.00%) empty reads filtered out after trimming by size control 91441614 (100.00%) reads available; of these: 23314670 (25.50%) trimmed reads available after processing 68126944 (74.50%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 493 0.00% 19 463 0.00% 20 446 0.00% 21 476 0.00% 22 583 0.00% 23 563 0.00% 24 609 0.00% 25 665 0.00% 26 819 0.00% 27 822 0.00% 28 901 0.00% 29 933 0.00% 30 1009 0.00% 31 1099 0.00% 32 1280 0.00% 33 1234 0.00% 34 1342 0.00% 35 1543 0.00% 36 1521 0.00% 37 1606 0.00% 38 1694 0.00% 39 1750 0.00% 40 1949 0.00% 41 2178 0.00% 42 2203 0.00% 43 2254 0.00% 44 2381 0.00% 45 2519 0.00% 46 2482 0.00% 47 2717 0.00% 48 2767 0.00% 49 2908 0.00% 50 2841 0.00% 51 3103 0.00% 52 3230 0.00% 53 3510 0.00% 54 3336 0.00% 55 3664 0.00% 56 3697 0.00% 57 4300 0.00% 58 4252 0.00% 59 4948 0.01% 60 5104 0.01% 61 5375 0.01% 62 5502 0.01% 63 5916 0.01% 64 5298 0.01% 65 5187 0.01% 66 5802 0.01% 67 6640 0.01% 68 6558 0.01% 69 6574 0.01% 70 7702 0.01% 71 9340 0.01% 72 8994 0.01% 73 9539 0.01% 74 9888 0.01% 75 10956 0.01% 76 11550 0.01% 77 12255 0.01% 78 14706 0.02% 79 14821 0.02% 80 16884 0.02% 81 20165 0.02% 82 22000 0.02% 83 24508 0.03% 84 27322 0.03% 85 30363 0.03% 86 34173 0.04% 87 35957 0.04% 88 40114 0.04% 89 45887 0.05% 90 53166 0.06% 91 59762 0.07% 92 71730 0.08% 93 80457 0.09% 94 87777 0.10% 95 96978 0.11% 96 107585 0.12% 97 123267 0.13% 98 132141 0.14% 99 148376 0.16% 100 156408 0.17% 101 174843 0.19% 102 196564 0.21% 103 213573 0.23% 104 236592 0.26% 105 248077 0.27% 106 265628 0.29% 107 299792 0.33% 108 318685 0.35% 109 346213 0.38% 110 363644 0.40% 111 426271 0.47% 112 446410 0.49% 113 457483 0.50% 114 480022 0.52% 115 502336 0.55% 116 527062 0.58% 117 514832 0.56% 118 535520 0.59% 119 570775 0.62% 120 609752 0.67% 121 628097 0.69% 122 645835 0.71% 123 681251 0.75% 124 666906 0.73% 125 699442 0.76% 126 736059 0.80% 127 742155 0.81% 128 761361 0.83% 129 739526 0.81% 130 750970 0.82% 131 739463 0.81% 132 762362 0.83% 133 814865 0.89% 134 854612 0.93% 135 823967 0.90% 136 793443 0.87% 137 791058 0.87% 138 773203 0.85% 139 763533 0.83% 140 784211 0.86% 141 800423 0.88% 142 840594 0.92% 143 861736 0.94% 144 813174 0.89% 145 794001 0.87% 146 729644 0.80% 147 1000887 1.09% 148 1739671 1.90% 149 95 0.00% 150 137 0.00% 151 59509042 65.08% criterion=sequence-density sequence-density=0.76 sequence-density-rank=1 fanout-score=2.60 fanout-score-rank=13 prefix-density=0.77 prefix-fanout=2.6 sequence=GTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAGCAACATCCGCCAATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGACCCGGCCAGTTAAGGCCAGGAGCGCATCGCCGGTAGAAGGGACGAGGC criterion=fanout-score sequence-density=0.22 sequence-density-rank=9 fanout-score=14.75 fanout-score-rank=1 prefix-density=1.96 prefix-fanout=1.7 sequence=CTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCT Started job on | Feb 13 15:08:12 Started mapping on | Feb 13 15:08:13 Finished on | Feb 13 15:17:38 Mapping speed, Million of reads per hour | 672.27 Number of input reads | 105509589 Average input read length | 143 UNIQUE READS: Uniquely mapped reads number | 43359535 Uniquely mapped reads % | 41.10% Average mapped length | 141.92 Number of splices: Total | 16882359 Number of splices: Annotated (sjdb) | 16468163 Number of splices: GT/AG | 16559210 Number of splices: GC/AG | 240840 Number of splices: AT/AC | 17305 Number of splices: Non-canonical | 65004 Mismatch rate per base, % | 0.79% Deletion rate per base | 0.04% Deletion average length | 2.70 Insertion rate per base | 0.03% Insertion average length | 2.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6092023 % of reads mapped to multiple loci | 5.77% Number of reads mapped to too many loci | 51465820 % of reads mapped to too many loci | 48.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.26% % of reads unmapped: other | 2.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 56058031 56058031 56058031 N_multimapping 6092023 6092023 6092023 N_noFeature 4898436 23707179 23778244 N_ambiguous 942652 85709 85475 UnstrandedReadsAssigned:37518447 PositiveStrandReadsAssigned:19566647 NegativeStrandReadsAssigned:19495816 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=133 echo kmer=129 SRR6793144 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: SRR6793144-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 105,509,589 reads, 81,444,040 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,151 rounds 52401 SRR6793144.ke.tsv 34699 SRR6793144.se.tsv 87100 total ==> SRR6793144.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3438 27.452 Potri.005G024800.1.v4.1 1035 936 1436 23.5083 Potri.004G059700.1.v4.1 961 862 3 0.0533282 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3290.92 17.7309 Potri.016G087400.1.v4.1 270 171 1833.25 164.274 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 2561.9 23.4503 Potri.012G127500.1.v4.1 977 878 549 9.58122 ==> SRR6793144.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 102 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 800 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 36 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 18 SRR6793144 completed mapping pipeline successfully