Starting /dee2/code/volunteer_pipeline.sh SRR22283138 current disk space = 1550682972160 free memory = 1598466924 SRR22283138 SRAfilesize bc9ffd6217c835c9ce7a4becbcc427c5 SRR22283138.sra SRR22283138.sra file validated SRR22283138 is single end SRR22283138 is conventional basespace SRR22283138 read1 length is 120 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR22283138_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 120 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3885 38.0 38.0 38.0 32.0 38.0 2 36.58675 38.0 38.0 38.0 32.0 38.0 3 36.80625 38.0 38.0 38.0 32.0 38.0 4 36.49825 38.0 38.0 38.0 32.0 38.0 5 36.8035 38.0 38.0 38.0 32.0 38.0 6 38.89 40.0 38.0 40.0 38.0 40.0 7 38.944 40.0 38.0 40.0 38.0 40.0 8 38.893 40.0 38.0 40.0 38.0 40.0 9 38.8385 40.0 38.0 40.0 38.0 40.0 10-11 38.780875 40.0 38.0 40.0 38.0 40.0 12-13 38.76575 40.0 38.0 40.0 38.0 40.0 14-15 38.6125 40.0 38.0 40.0 38.0 40.0 16-17 38.746375 40.0 38.0 40.0 38.0 40.0 18-19 38.754374999999996 40.0 38.0 40.0 38.0 40.0 20-21 38.766000000000005 40.0 38.0 40.0 38.0 40.0 22-23 38.757625 40.0 38.0 40.0 38.0 40.0 24-25 38.554375 40.0 38.0 40.0 38.0 40.0 26-27 38.620999999999995 40.0 38.0 40.0 38.0 40.0 28-29 38.694874999999996 40.0 38.0 40.0 38.0 40.0 30-31 38.663624999999996 40.0 38.0 40.0 38.0 40.0 32-33 38.62975 40.0 38.0 40.0 38.0 40.0 34-35 38.636625 40.0 38.0 40.0 38.0 40.0 36-37 38.557125 40.0 38.0 40.0 38.0 40.0 38-39 38.56675 40.0 38.0 40.0 38.0 40.0 40-41 38.58525 40.0 38.0 40.0 38.0 40.0 42-43 38.52675 40.0 38.0 40.0 38.0 40.0 44-45 38.467124999999996 40.0 38.0 40.0 38.0 40.0 46-47 38.434375 40.0 38.0 40.0 38.0 40.0 48-49 38.10125 40.0 38.0 40.0 38.0 40.0 50-51 38.129125 40.0 38.0 40.0 38.0 40.0 52-53 38.246375 40.0 38.0 40.0 38.0 40.0 54-55 38.127624999999995 40.0 38.0 40.0 38.0 40.0 56-57 38.224999999999994 40.0 38.0 40.0 38.0 40.0 58-59 38.189125000000004 40.0 38.0 40.0 38.0 40.0 60-61 37.355875 38.0 38.0 40.0 32.0 40.0 62-63 38.030625 40.0 38.0 40.0 38.0 40.0 64-65 38.114875 40.0 38.0 40.0 38.0 40.0 66-67 38.127125 40.0 38.0 40.0 38.0 40.0 68-69 38.162125 40.0 38.0 40.0 38.0 40.0 70-71 38.006125 40.0 38.0 40.0 38.0 40.0 72-73 37.853875 39.0 38.0 40.0 35.0 40.0 74-75 37.89375 40.0 38.0 40.0 38.0 40.0 76-77 37.043625000000006 38.0 38.0 40.0 35.0 40.0 78-79 37.379125 38.0 38.0 40.0 32.0 40.0 80-81 37.699124999999995 38.0 38.0 40.0 32.0 40.0 82-83 37.723124999999996 38.0 38.0 40.0 32.0 40.0 84-85 37.709875 38.0 38.0 40.0 35.0 40.0 86-87 37.548500000000004 38.0 38.0 40.0 32.0 40.0 88-89 37.5595 38.0 38.0 40.0 32.0 40.0 90-91 37.547625 38.0 38.0 40.0 32.0 40.0 92-93 37.571875000000006 38.0 38.0 40.0 32.0 40.0 94-95 37.425 38.0 38.0 40.0 32.0 40.0 96-97 37.2645 38.0 38.0 40.0 32.0 40.0 98-99 37.214 38.0 38.0 40.0 32.0 40.0 100-101 37.2295 38.0 38.0 40.0 32.0 40.0 102-103 35.590500000000006 38.0 35.0 38.0 29.5 38.0 104-105 37.306875 38.0 38.0 40.0 32.0 40.0 106-107 37.8535 38.0 38.0 40.0 38.0 40.0 108-109 37.95625 40.0 38.0 40.0 38.0 40.0 110-111 38.04025 40.0 38.0 40.0 38.0 40.0 112-113 37.883375 40.0 38.0 40.0 38.0 40.0 114-115 37.164375 38.0 38.0 40.0 32.0 40.0 116-117 37.545375 38.0 38.0 40.0 35.0 40.0 118-119 37.393125 38.0 38.0 40.0 35.0 40.0 120 33.976 38.0 32.0 38.0 27.0 40.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 1.0 10 0.0 11 0.0 12 2.0 13 0.0 14 0.0 15 1.0 16 1.0 17 0.0 18 2.0 19 0.0 20 0.0 21 0.0 22 2.0 23 3.0 24 4.0 25 9.0 26 5.0 27 16.0 28 18.0 29 41.0 30 34.0 31 53.0 32 55.0 33 83.0 34 89.0 35 146.0 36 224.0 37 317.0 38 814.0 39 2079.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.139369277721265 9.460834181078331 5.747711088504578 48.65208545269583 2 20.875 11.625 36.825 30.675 3 18.9 13.25 25.224999999999998 42.625 4 26.625 21.675 22.1 29.599999999999998 5 27.125 25.624999999999996 23.175 24.075 6 21.8 28.9 25.5 23.799999999999997 7 18.575 20.325 38.9 22.2 8 18.6 20.4 31.324999999999996 29.675 9 20.200000000000003 19.825 32.2 27.775 10-11 24.4375 25.15 22.85 27.5625 12-13 24.25 19.1875 26.875 29.6875 14-15 23.825 21.075 27.4125 27.6875 16-17 24.775 22.025 24.5375 28.6625 18-19 24.0625 22.3125 24.925 28.7 20-21 23.724999999999998 22.662499999999998 26.0625 27.55 22-23 24.474999999999998 22.3125 24.725 28.487499999999997 24-25 25.0 21.7875 25.5375 27.675 26-27 23.3375 22.2625 25.924999999999997 28.475 28-29 22.9625 22.6 25.575 28.8625 30-31 24.3875 20.599999999999998 25.575 29.4375 32-33 24.5375 22.037499999999998 25.4375 27.987499999999997 34-35 23.1625 21.95 26.275 28.6125 36-37 23.225 22.4625 25.412499999999998 28.9 38-39 23.6875 22.475 24.2375 29.599999999999998 40-41 24.9375 22.825 24.175 28.0625 42-43 24.212500000000002 23.0 25.0 27.787499999999998 44-45 23.9875 22.5125 26.174999999999997 27.325 46-47 23.5625 23.0375 25.0125 28.3875 48-49 22.8125 21.9 25.124999999999996 30.162499999999998 50-51 22.075 22.2125 25.8125 29.9 52-53 24.3 22.287499999999998 25.25 28.1625 54-55 24.4125 22.475 24.3875 28.725 56-57 23.375 21.6 26.375 28.65 58-59 23.3 22.275 25.275 29.15 60-61 24.0375 21.825 25.55 28.5875 62-63 23.974999999999998 21.025 26.400000000000002 28.599999999999998 64-65 24.0125 20.8125 26.7625 28.4125 66-67 23.225 22.45 25.224999999999998 29.099999999999998 68-69 24.8 22.375 24.925 27.900000000000002 70-71 24.712500000000002 22.5 24.5625 28.225 72-73 24.4375 21.325 24.95 29.2875 74-75 24.4875 21.25 25.7375 28.525 76-77 25.112499999999997 22.2 25.0375 27.650000000000002 78-79 23.9875 22.5125 24.65 28.849999999999998 80-81 24.175 22.5625 24.85 28.4125 82-83 25.337500000000002 22.25 23.875 28.537499999999998 84-85 23.4375 22.25 25.424999999999997 28.8875 86-87 25.8625 21.0625 24.1875 28.8875 88-89 24.975 22.075 24.962500000000002 27.987499999999997 90-91 25.0625 21.475 24.087500000000002 29.375 92-93 24.15 22.4875 24.55 28.812500000000004 94-95 25.087500000000002 21.987499999999997 24.762500000000003 28.1625 96-97 22.912499999999998 22.3375 25.7 29.049999999999997 98-99 25.074999999999996 22.1375 24.837500000000002 27.950000000000003 100-101 25.374999999999996 22.287499999999998 24.5375 27.800000000000004 102-103 24.775 22.075 25.2 27.950000000000003 104-105 24.775 22.0875 25.5625 27.575 106-107 24.4375 23.25 24.4875 27.825 108-109 24.3875 21.925 24.725 28.962500000000002 110-111 23.625 22.9875 25.2 28.1875 112-113 25.162499999999998 24.125 23.925 26.787499999999998 114-115 23.8375 22.4625 24.6625 29.037499999999998 116-117 25.0 22.8625 24.224999999999998 27.9125 118-119 24.75 22.7625 23.75 28.7375 120 25.8 22.3 24.5 27.400000000000002 >>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 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 0.5 27 0.5 28 0.5 29 0.5 30 2.0 31 3.5 32 2.0 33 3.5 34 9.0 35 14.0 36 23.0 37 27.5 38 31.5 39 44.5 40 56.5 41 76.0 42 85.0 43 91.0 44 99.5 45 108.5 46 128.5 47 129.0 48 127.5 49 153.0 50 167.0 51 163.0 52 153.0 53 175.5 54 234.0 55 270.5 56 285.5 57 240.0 58 189.5 59 148.5 60 124.0 61 113.0 62 75.5 63 68.0 64 69.0 65 57.5 66 39.5 67 39.5 68 42.0 69 30.0 70 20.0 71 20.0 72 19.5 73 12.5 74 8.5 75 7.5 76 6.5 77 2.5 78 0.5 79 0.0 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 1.7000000000000002 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 0.0 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 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 102-103 0.0 104-105 0.0 106-107 0.0 108-109 0.0 110-111 0.0 112-113 0.0 114-115 0.0 116-117 0.0 118-119 0.0 120 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 120 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.975 #Duplication Level Percentage of deduplicated Percentage of total 1 89.32038834951457 75.9 2 6.972639011473963 11.85 3 2.0888496616651957 5.325 4 0.9414533686378346 3.2 5 0.29420417769932333 1.25 6 0.14710208884966167 0.75 7 0.11768167107972932 0.7000000000000001 8 0.02942041776993233 0.2 9 0.02942041776993233 0.22499999999999998 >10 0.05884083553986466 0.6 >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 CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 14 0.35000000000000003 No Hit ATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTCAGGC 10 0.25 No Hit CTCCACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTCATTCTTGC 9 0.22499999999999998 No Hit CACTCATCTTGGGGTGGGCTTACTACTTATATGCTTTCAGCAGTTATCCT 8 0.2 No Hit GGTCGTTCGAGCTTTTCCTGGGAGTATGGCATCGGTTACATACTTCAGTG 7 0.17500000000000002 No Hit CTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCC 7 0.17500000000000002 No Hit CCCGAAGTTACGGGGCTATTTTGCCGAGTTCCTTAGAGAGAGTTGTCTCG 7 0.17500000000000002 No Hit ATCGTTTACGGCTAGGACTACTGGGGTCTCTAATCCCATTTGCTCCCCTA 7 0.17500000000000002 No Hit CTCCACCGGAAATTCCCTCTGCCCCTACCGTACTCCAGCTTGGTAGTTTC 6 0.15 No Hit GGCATGATGACTTGGCCTCATCCTCTCCTTCCTCCGGCTTAACACCGGCG 6 0.15 No Hit CTCATCTTGGGGTGGGCTTACTACTTATATGCTTTCAGCAGTTATCCTCT 6 0.15 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 6 0.15 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 6 0.15 No Hit GGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTG 5 0.125 No Hit CTGCAATCCGAACTGAGGACGGGTTTTTGGAGTTAGCTCACCCTCGCGAG 5 0.125 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 5 0.125 No Hit GCCTCCTCCGTCCCTCCGTACCAACAAGGGGTAGTACAGGAATATTGACC 5 0.125 No Hit ATCGACTACGCCTTTCGGCCTGATCTTAGGCCCTGACTCACCCTCCGTGG 5 0.125 No Hit GTCGGTTTCGGGTACAGGTACCCTTTTGTTGAAGGTCGTTCGAGCTTTTC 5 0.125 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 5 0.125 No Hit CCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACTCGGCACCGT 5 0.125 No Hit GCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCC 5 0.125 No Hit CCCGTTTTCACGGTTTAGGCTGCTCCCATTTCGCTCGCCGCTACTACGGG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0125 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 0.07500000000000001 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 0.15 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.2375 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.2875 0.0 0.0 0.0 0.0 84-85 0.3875 0.0 0.0 0.0 0.0 86-87 0.475 0.0 0.0 0.0 0.0 88-89 0.5375000000000001 0.0 0.0 0.0 0.0 90-91 0.7 0.0 0.0 0.0 0.0 92-93 0.8500000000000001 0.0 0.0 0.0 0.0 94-95 0.9874999999999999 0.0 0.0 0.0 0.0 96-97 1.1375 0.0 0.0 0.0 0.0 98-99 1.3375 0.0 0.0 0.0 0.0 100-101 1.7 0.0 0.0 0.0 0.0 102-103 2.0125 0.0 0.0 0.0 0.0 104-105 2.5 0.0 0.0 0.0 0.0 106-107 2.9625000000000004 0.0 0.0 0.0 0.0 108 3.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930106 READS because READLEN < 1 Read 930106 spots for SRR22283138.sra Written 930106 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra Rejected 930088 READS because READLEN < 1 Read 930088 spots for SRR22283138.sra Written 930088 spots for SRR22283138.sra SRR ids: ['SRR22283138.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hq2xszjr SRR22283138.sra spots: 18601778 blocks: [[1, 930088], [930089, 1860176], [1860177, 2790264], [2790265, 3720352], [3720353, 4650440], [4650441, 5580528], [5580529, 6510616], [6510617, 7440704], [7440705, 8370792], [8370793, 9300880], [9300881, 10230968], [10230969, 11161056], [11161057, 12091144], [12091145, 13021232], [13021233, 13951320], [13951321, 14881408], [14881409, 15811496], [15811497, 16741584], [16741585, 17671672], [17671673, 18601778]] SRR22283138 file size 5173718 SRR22283138 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 SRR22283138 SRR22283138_1.fastq Input file: SRR22283138_1.fastq trimmed: SRR22283138-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 Fri Dec 6 14:04:45 2024 >> started Fri Dec 6 14:04:54 2024 >> done (9.675s) 18601778 reads processed; of these: 1076 ( 0.01%) short reads filtered out after trimming by size control 836 ( 0.00%) empty reads filtered out after trimming by size control 18599866 (99.99%) reads available; of these: 2020703 (10.86%) trimmed reads available after processing 16579163 (89.14%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 134 0.00% 19 166 0.00% 20 203 0.00% 21 240 0.00% 22 292 0.00% 23 380 0.00% 24 459 0.00% 25 559 0.00% 26 781 0.00% 27 551 0.00% 28 419 0.00% 29 505 0.00% 30 449 0.00% 31 522 0.00% 32 560 0.00% 33 519 0.00% 34 549 0.00% 35 605 0.00% 36 651 0.00% 37 842 0.00% 38 699 0.00% 39 694 0.00% 40 651 0.00% 41 732 0.00% 42 677 0.00% 43 716 0.00% 44 650 0.00% 45 630 0.00% 46 728 0.00% 47 677 0.00% 48 702 0.00% 49 846 0.00% 50 809 0.00% 51 802 0.00% 52 825 0.00% 53 950 0.01% 54 929 0.00% 55 1060 0.01% 56 1015 0.01% 57 1000 0.01% 58 1021 0.01% 59 1175 0.01% 60 1245 0.01% 61 1387 0.01% 62 1489 0.01% 63 1557 0.01% 64 1781 0.01% 65 1761 0.01% 66 1876 0.01% 67 2029 0.01% 68 2189 0.01% 69 2313 0.01% 70 2570 0.01% 71 2789 0.01% 72 3175 0.02% 73 3407 0.02% 74 3720 0.02% 75 3869 0.02% 76 4358 0.02% 77 4636 0.02% 78 5076 0.03% 79 5744 0.03% 80 6251 0.03% 81 6729 0.04% 82 7476 0.04% 83 8153 0.04% 84 8628 0.05% 85 10092 0.05% 86 10931 0.06% 87 11625 0.06% 88 12405 0.07% 89 2286 0.01% 90 2434 0.01% 91 2544 0.01% 92 2809 0.02% 93 2932 0.02% 94 2985 0.02% 95 3018 0.02% 96 3276 0.02% 97 3317 0.02% 98 3601 0.02% 99 3921 0.02% 100 4470 0.02% 101 5092 0.03% 102 1852 0.01% 103 2990 0.02% 104 3825 0.02% 105 5037 0.03% 106 6214 0.03% 107 8044 0.04% 108 9750 0.05% 109 11517 0.06% 110 13774 0.07% 111 17920 0.10% 112 22000 0.12% 113 28034 0.15% 114 37511 0.20% 115 51300 0.28% 116 75052 0.40% 117 113450 0.61% 118 250539 1.35% 119 1152574 6.20% 120 16579163 89.14% 18599866 reads passed initial QC criterion=sequence-density sequence-density=2.76 sequence-density-rank=1 fanout-score=57.12 fanout-score-rank=2 prefix-density=3.67 prefix-fanout=43.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=119.49 fanout-score-rank=1 prefix-density=1.13 prefix-fanout=1.0 sequence=CTCGCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAACGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCCAAGCAGCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGGAACCATGCATAGCACTGAATAGGGAACCGCCGAAAACACCAGCTACACCTAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGT -o SRR22283138 - Input file: STDIN trimmed: SRR22283138-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGT -- 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 Fri Dec 6 14:05:34 2024 >> started Fri Dec 6 14:05:43 2024 >> done (9.047s) 6199955 reads processed; of these: 6 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 6199949 (100.00%) reads available; of these: 508846 ( 8.21%) trimmed reads available after processing 5691103 (91.79%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 46 0.00% 19 43 0.00% 20 77 0.00% 21 85 0.00% 22 100 0.00% 23 138 0.00% 24 156 0.00% 25 195 0.00% 26 305 0.00% 27 193 0.00% 28 138 0.00% 29 180 0.00% 30 147 0.00% 31 181 0.00% 32 172 0.00% 33 160 0.00% 34 205 0.00% 35 224 0.00% 36 199 0.00% 37 272 0.00% 38 221 0.00% 39 210 0.00% 40 234 0.00% 41 224 0.00% 42 237 0.00% 43 216 0.00% 44 222 0.00% 45 220 0.00% 46 224 0.00% 47 227 0.00% 48 231 0.00% 49 289 0.00% 50 263 0.00% 51 274 0.00% 52 249 0.00% 53 322 0.01% 54 300 0.00% 55 340 0.01% 56 328 0.01% 57 316 0.01% 58 339 0.01% 59 396 0.01% 60 414 0.01% 61 479 0.01% 62 497 0.01% 63 561 0.01% 64 576 0.01% 65 596 0.01% 66 595 0.01% 67 706 0.01% 68 750 0.01% 69 818 0.01% 70 896 0.01% 71 952 0.02% 72 1070 0.02% 73 1198 0.02% 74 1212 0.02% 75 1269 0.02% 76 1438 0.02% 77 1498 0.02% 78 1732 0.03% 79 1877 0.03% 80 2080 0.03% 81 2338 0.04% 82 2515 0.04% 83 2746 0.04% 84 2927 0.05% 85 3342 0.05% 86 3607 0.06% 87 3868 0.06% 88 4260 0.07% 89 4597 0.07% 90 4942 0.08% 91 5433 0.09% 92 6244 0.10% 93 6869 0.11% 94 7325 0.12% 95 8124 0.13% 96 8927 0.14% 97 9695 0.16% 98 10423 0.17% 99 11261 0.18% 100 12394 0.20% 101 13255 0.21% 102 13117 0.21% 103 13953 0.23% 104 15359 0.25% 105 16315 0.26% 106 17725 0.29% 107 19425 0.31% 108 20905 0.34% 109 23357 0.38% 110 24702 0.40% 111 26927 0.43% 112 29797 0.48% 113 32029 0.52% 114 39796 0.64% 115 52119 0.84% 116 70485 1.14% 117 123944 2.00% 118 77535 1.25% 119 352897 5.69% 120 5064158 81.68% criterion=sequence-density sequence-density=2.04 sequence-density-rank=1 fanout-score=1.92 fanout-score-rank=36 prefix-density=2.03 prefix-fanout=1.9 sequence=GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGTGCCCCATGCTACTCGGGTCAGAGCGTAAGCTAGTGATGCTTTCGGCTACTGGACTTTAGCCATCTAGGGTGCGGCACTCAACCGCTTCGCCTAGCAGCACAACGCTTGTATTGCTCTCCCACAACCCCGTTTTCACGGTTTAGGCTGCTCCCATTTCGCTCGCCGCTACTACGGGAATCGCTTTTGCTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCTTGCCTGCTCATGGATTCAGCAGGCAGTTTAAAAGGTTGACCTATTTGGGAATCTCCGGATCTATGCTTATTTTCAACTCCCCGAAGCATTTCGTCGCTTGCTACGCCCTTCCTCGTCTCTGGGTGCCTAGGTATCCACCGCAAGCCTTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=127.33 fanout-score-rank=1 prefix-density=1.13 prefix-fanout=1.0 sequence=CTCGCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAACGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCCAAGCAGCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGGAACCATGCATAGCACTGAATAGGGAACCGCCGAAAACACCAGCTACACCTAA Started job on | Dec 06 14:06:07 Started mapping on | Dec 06 14:06:07 Finished on | Dec 06 14:06:52 Mapping speed, Million of reads per hour | 1487.99 Number of input reads | 18599860 Average input read length | 119 UNIQUE READS: Uniquely mapped reads number | 9459768 Uniquely mapped reads % | 50.86% Average mapped length | 118.25 Number of splices: Total | 3531206 Number of splices: Annotated (sjdb) | 3347341 Number of splices: GT/AG | 3472909 Number of splices: GC/AG | 44819 Number of splices: AT/AC | 1455 Number of splices: Non-canonical | 12023 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.02% Deletion average length | 2.71 Insertion rate per base | 0.02% Insertion average length | 2.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5491445 % of reads mapped to multiple loci | 29.52% Number of reads mapped to too many loci | 3249227 % of reads mapped to too many loci | 17.47% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.62% % of reads unmapped: other | 1.53% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3648647 3648647 3648647 N_multimapping 5491445 5491445 5491445 N_noFeature 1075790 9248669 1127464 N_ambiguous 185600 567 26553 UnstrandedReadsAssigned:8198378 PositiveStrandReadsAssigned:210532 NegativeStrandReadsAssigned:8305751 Dataset is classified negative stranded MeadianReadLen=120 20thPercentileLength=120 echo kmer=115 SRR22283138 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: SRR22283138-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,599,860 reads, 8,975,357 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,101 rounds 52973 SRR22283138.ke.tsv 35125 SRR22283138.se.tsv 88098 total ==> SRR22283138.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 27.6623 4.97995 PNS24247 1044 945 22.1829 3.5371 PNS24249 1928 1829 43.436 3.57848 PNS24246 1044 945 22.1829 3.5371 PNS24248 1044 945 22.1829 3.5371 PNS24244 1471 1372 30.3531 3.33357 PNS24243 293 194 0 0 KQK14069 1603 1504 3134.16 314.003 KQK14071 474 375 342.604 137.665 ==> SRR22283138.se.tsv <== BRADI_1g14170v3 3944 BRADI_1g53295v3 93 BRADI_1g59795v3 15 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 117 BRADI_1g74790v3 75 BRADI_1g09890v3 0 BRADI_1g77505v3 192 BRADI_1g48960v3 0 SRR22283138 completed mapping pipeline successfully