Starting /dee2/code/volunteer_pipeline.sh SRR24040054 current disk space = 1548898185216 free memory = 1595616760 SRR24040054 SRAfilesize 293e801d0211727038c6b427c538c73a SRR24040054.sra SRR24040054.sra file validated SRR24040054 is paired end SRR24040054 is conventional basespace SRR24040054 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040054_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 54 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.76275 37.0 37.0 37.0 37.0 37.0 2 36.4225 37.0 37.0 37.0 37.0 37.0 3 36.364 37.0 37.0 37.0 37.0 37.0 4 36.5325 37.0 37.0 37.0 37.0 37.0 5 36.6185 37.0 37.0 37.0 37.0 37.0 6 34.8965 37.0 37.0 37.0 25.0 37.0 7 36.515 37.0 37.0 37.0 37.0 37.0 8 36.5645 37.0 37.0 37.0 37.0 37.0 9 33.1875 37.0 37.0 37.0 11.0 37.0 10-14 36.5185 37.0 37.0 37.0 37.0 37.0 15-19 36.3779 37.0 37.0 37.0 37.0 37.0 20-24 36.397400000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.356 37.0 37.0 37.0 37.0 37.0 30-34 36.0343 37.0 37.0 37.0 34.6 37.0 35-39 36.437200000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.27380000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.257000000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.3114 37.0 37.0 37.0 37.0 37.0 55-59 36.1113 37.0 37.0 37.0 37.0 37.0 60-64 36.1289 37.0 37.0 37.0 37.0 37.0 65-69 36.3087 37.0 37.0 37.0 37.0 37.0 70-74 36.3048 37.0 37.0 37.0 37.0 37.0 75-79 36.3894 37.0 37.0 37.0 37.0 37.0 80-84 35.9995 37.0 37.0 37.0 37.0 37.0 85-89 36.204899999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.26465 37.0 37.0 37.0 37.0 37.0 95-99 36.2414 37.0 37.0 37.0 37.0 37.0 100-104 36.1322 37.0 37.0 37.0 37.0 37.0 105-109 36.211850000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.0522 37.0 37.0 37.0 37.0 37.0 115-119 35.74444999999999 37.0 37.0 37.0 37.0 37.0 120-124 35.6537 37.0 37.0 37.0 34.6 37.0 125-129 35.8292 37.0 37.0 37.0 37.0 37.0 130-134 35.348699999999994 37.0 37.0 37.0 34.6 37.0 135-139 35.412549999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.08855 37.0 37.0 37.0 27.4 37.0 145-149 34.78895 37.0 37.0 37.0 27.4 37.0 150 32.017 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 2.0 24 5.0 25 4.0 26 10.0 27 19.0 28 17.0 29 24.0 30 25.0 31 41.0 32 63.0 33 114.0 34 188.0 35 470.0 36 2666.0 37 351.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.30788485607009 11.48936170212766 4.755944931163955 37.4468085106383 2 25.525 12.8 32.125 29.549999999999997 3 23.25 15.049999999999999 23.7 38.0 4 29.549999999999997 22.725 18.925 28.799999999999997 5 26.85 26.974999999999998 22.75 23.425 6 25.2 29.4 21.675 23.724999999999998 7 19.175 20.825 38.875 21.125 8 22.075 20.5 28.95 28.475 9 20.424999999999997 21.375 30.575000000000003 27.625 10-14 25.590000000000003 23.455000000000002 23.605 27.35 15-19 25.205 22.155 23.935000000000002 28.705000000000002 20-24 25.81 23.369999999999997 23.355 27.465 25-29 24.975 22.3 23.605 29.12 30-34 25.290000000000003 22.075 23.47 29.165000000000003 35-39 25.569999999999997 22.040000000000003 23.674999999999997 28.715000000000003 40-44 26.0 22.17 23.355 28.475 45-49 25.405 21.44 24.495 28.660000000000004 50-54 25.09 22.06 24.36 28.49 55-59 25.380000000000003 22.17 24.04 28.410000000000004 60-64 25.365 21.755 23.845 29.035 65-69 25.290000000000003 22.235 24.415 28.060000000000002 70-74 25.650000000000002 22.564999999999998 23.244999999999997 28.54 75-79 26.145000000000003 22.115000000000002 23.76 27.98 80-84 26.305 22.535 22.965 28.194999999999997 85-89 26.135 22.225 23.32 28.32 90-94 26.75133756687834 21.986099304965247 23.14615730786539 28.116405820291014 95-99 25.759999999999998 22.770000000000003 23.225 28.244999999999997 100-104 26.22 22.475 22.975 28.33 105-109 26.116305815290765 23.566178308915443 22.601130056502825 27.716385819290963 110-114 26.825 23.46 22.05 27.665 115-119 26.561328066403323 23.941197059852993 21.951097554877744 27.546377318865943 120-124 26.772677267726774 23.612361236123615 22.247224722472247 27.367736773677372 125-129 26.095000000000002 23.51 21.73 28.665000000000003 130-134 27.089999999999996 23.51 21.65 27.750000000000004 135-139 26.471323566178306 23.52617630881544 21.75608780439022 28.24641232061603 140-144 26.246312315615782 24.056202810140505 21.626081304065202 28.07140357017851 145-149 26.991349567478373 23.35116755837792 22.296114805740284 27.36136806840342 150 27.200000000000003 24.825 21.5 26.474999999999998 >>END_MODULE >>Per sequence GC content fail #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 0.5 16 0.5 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 0.5 26 0.5 27 0.0 28 1.0 29 2.0 30 1.0 31 1.0 32 4.0 33 6.5 34 7.5 35 12.5 36 18.5 37 26.0 38 35.5 39 41.5 40 48.0 41 65.5 42 80.0 43 94.5 44 108.5 45 107.0 46 126.0 47 164.0 48 173.0 49 160.0 50 174.5 51 177.0 52 170.5 53 170.5 54 156.5 55 154.5 56 146.0 57 134.0 58 122.5 59 115.0 60 116.5 61 95.5 62 79.5 63 83.5 64 87.0 65 90.0 66 86.0 67 90.5 68 87.5 69 71.5 70 70.0 71 66.0 72 51.5 73 35.5 74 22.5 75 20.5 76 18.5 77 12.0 78 7.0 79 2.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.125 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 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.005 95-99 0.0 100-104 0.0 105-109 0.005 110-114 0.0 115-119 0.005 120-124 0.01 125-129 0.0 130-134 0.0 135-139 0.005 140-144 0.005 145-149 0.005 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.95 #Duplication Level Percentage of deduplicated Percentage of total 1 89.87783595113437 77.25 2 6.835369400814427 11.75 3 1.7452006980802792 4.5 4 0.9016870273414777 3.1 5 0.4072134962187318 1.7500000000000002 6 0.029086678301337987 0.15 7 0.08726003490401396 0.525 8 0.029086678301337987 0.2 9 0.058173356602675974 0.44999999999999996 >10 0.029086678301337987 0.325 >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 CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 13 0.325 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 9 0.22499999999999998 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 9 0.22499999999999998 No Hit GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 8 0.2 No Hit GTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTC 7 0.17500000000000002 No Hit GTCGTCTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAG 7 0.17500000000000002 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 7 0.17500000000000002 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 6 0.15 No Hit ATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTCAGGC 5 0.125 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 5 0.125 No Hit GGTAGCTTCGCGCCACTGGCTTTTCAACCAAGCGCGATGACCAATTGTGT 5 0.125 No Hit CTCCTACTCATCGGGGCATGGCGCTCGCCCAGATGGCCGGGTGTGGGTCG 5 0.125 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 5 0.125 No Hit CTTGTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCCCC 5 0.125 No Hit GGTAAAACTAACCTGTCTCACGACGGTCTAATCCCAGCTCACGTTCCCTA 5 0.125 No Hit GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 5 0.125 No Hit AGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGC 5 0.125 No Hit GGCAGAAATCACATTGCGTCAGCATCCGCGAGGACCATCGCAATGCTTTG 5 0.125 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 5 0.125 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 5 0.125 No Hit GTCCCGACAGGCGTGCTCCAACTCGAACCCTTCACAGAAGATCAGGGTCG 5 0.125 No Hit GTTCAGTCATAATCCGGCACACGGTAGCTTCGCGCCACTGGCTTTTCAAC 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 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.05 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 0.0625 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.0875 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.21250000000000002 0.0 0.0 0.0 0.0 52-53 0.2375 0.0 0.0 0.0 0.0 54-55 0.3 0.0 0.0 0.0 0.0 56-57 0.325 0.0 0.0 0.0 0.0 58-59 0.35 0.0 0.0 0.0 0.0 60-61 0.4 0.0 0.0 0.0 0.0 62-63 0.44999999999999996 0.0 0.0 0.0 0.0 64-65 0.6375 0.0 0.0 0.0 0.0 66-67 0.7375 0.0 0.0 0.0 0.0 68-69 0.8125 0.0 0.0 0.0 0.0 70-71 1.0 0.0 0.0 0.0 0.0 72-73 1.25 0.0 0.0 0.0 0.0 74-75 1.6375 0.0 0.0 0.0 0.0 76-77 1.9 0.0 0.0 0.0 0.0 78-79 2.3125 0.0 0.0 0.0 0.0 80-81 2.575 0.0 0.0 0.0 0.0 82-83 2.8125 0.0 0.0 0.0 0.0 84-85 3.275 0.0 0.0 0.0 0.0 86-87 3.7875 0.0 0.0 0.0 0.0 88-89 4.387499999999999 0.0 0.0 0.0 0.0 90-91 4.9875 0.0 0.0 0.0 0.0 92-93 5.475 0.0 0.0 0.0 0.0 94-95 6.0375 0.0 0.0 0.0 0.0 96-97 6.75 0.0 0.0 0.0 0.0 98-99 7.387499999999999 0.0 0.0 0.0 0.0 100-101 8.075 0.0 0.0 0.0 0.0 102-103 9.05 0.0 0.0 0.0 0.0 104-105 9.95 0.0 0.0 0.0 0.0 106-107 10.8875 0.0 0.0 0.0 0.0 108-109 12.05 0.0 0.0 0.0 0.0 110-111 13.2625 0.0 0.0 0.0 0.0 112-113 14.2875 0.0 0.0 0.0 0.0 114-115 15.3875 0.0 0.0 0.0 0.0 116-117 16.674999999999997 0.0 0.0 0.0 0.0 118-119 17.5 0.0 0.0 0.0 0.0 120-121 18.4375 0.0 0.0 0.0 0.0 122-123 19.5 0.0 0.0 0.0 0.0 124-125 20.7625 0.0 0.0 0.0 0.0 126-127 22.0 0.0 0.0 0.0 0.0 128-129 23.2125 0.0 0.0 0.0 0.0 130-131 24.55 0.0 0.0 0.0 0.0 132-133 25.875 0.0 0.0 0.0 0.0 134-135 27.1375 0.0 0.0 0.0 0.0 136-137 28.425 0.0 0.0 0.0 0.0 138 29.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 210 0.006203352 6.8571424 125-129 >>END_MODULE SRR24040054 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040054_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.367 37.0 37.0 37.0 37.0 37.0 2 36.063 37.0 37.0 37.0 37.0 37.0 3 33.1835 37.0 37.0 37.0 11.0 37.0 4 35.7995 37.0 37.0 37.0 37.0 37.0 5 36.4215 37.0 37.0 37.0 37.0 37.0 6 36.353 37.0 37.0 37.0 37.0 37.0 7 36.349 37.0 37.0 37.0 37.0 37.0 8 35.8975 37.0 37.0 37.0 37.0 37.0 9 35.242 37.0 37.0 37.0 37.0 37.0 10-14 35.938 37.0 37.0 37.0 37.0 37.0 15-19 35.6547 37.0 37.0 37.0 34.6 37.0 20-24 35.804199999999994 37.0 37.0 37.0 34.6 37.0 25-29 35.9268 37.0 37.0 37.0 37.0 37.0 30-34 34.8612 37.0 37.0 37.0 29.4 37.0 35-39 36.1129 37.0 37.0 37.0 37.0 37.0 40-44 36.0935 37.0 37.0 37.0 37.0 37.0 45-49 36.12179999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.116400000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.1135 37.0 37.0 37.0 37.0 37.0 60-64 36.0753 37.0 37.0 37.0 37.0 37.0 65-69 35.8361 37.0 37.0 37.0 37.0 37.0 70-74 35.6825 37.0 37.0 37.0 34.6 37.0 75-79 35.2551 37.0 37.0 37.0 31.8 37.0 80-84 35.7992 37.0 37.0 37.0 34.6 37.0 85-89 35.555099999999996 37.0 37.0 37.0 32.2 37.0 90-94 35.1045 37.0 37.0 37.0 32.2 37.0 95-99 35.8164 37.0 37.0 37.0 37.0 37.0 100-104 35.3786 37.0 37.0 37.0 34.6 37.0 105-109 35.632000000000005 37.0 37.0 37.0 37.0 37.0 110-114 34.91539999999999 37.0 37.0 37.0 32.2 37.0 115-119 35.222 37.0 37.0 37.0 34.6 37.0 120-124 34.6807 37.0 37.0 37.0 25.0 37.0 125-129 34.752599999999994 37.0 37.0 37.0 25.0 37.0 130-134 34.373999999999995 37.0 37.0 37.0 25.0 37.0 135-139 34.221900000000005 37.0 37.0 37.0 25.0 37.0 140-144 33.83105 37.0 37.0 37.0 25.0 37.0 145-149 33.4185 37.0 37.0 37.0 13.8 37.0 150 33.452 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 6.0 14 10.0 15 6.0 16 3.0 17 1.0 18 1.0 19 2.0 20 6.0 21 7.0 22 9.0 23 13.0 24 8.0 25 11.0 26 7.0 27 11.0 28 22.0 29 15.0 30 31.0 31 73.0 32 124.0 33 164.0 34 348.0 35 745.0 36 2178.0 37 198.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.9 21.099999999999998 6.800000000000001 31.2 2 32.7 22.225 25.825 19.25 3 24.0 23.724999999999998 24.325 27.950000000000003 4 28.4 31.525 18.05 22.025 5 30.599999999999998 31.624999999999996 17.150000000000002 20.625 6 28.875 30.85 17.0 23.275000000000002 7 25.4 19.375 30.7 24.525 8 26.575 20.95 22.15 30.325000000000003 9 26.275 20.849999999999998 25.2 27.675 10-14 28.09 24.255 20.01 27.644999999999996 15-19 28.975 23.445 21.41 26.169999999999998 20-24 27.965 23.674999999999997 21.634999999999998 26.724999999999998 25-29 28.455000000000002 24.615000000000002 21.42 25.509999999999998 30-34 28.349999999999998 24.77 20.979999999999997 25.900000000000002 35-39 28.54 24.265 21.11 26.085 40-44 28.395 23.695 21.415 26.495 45-49 28.12 24.535 21.51 25.835 50-54 28.485 24.404999999999998 21.18 25.929999999999996 55-59 28.044999999999998 24.12 21.654999999999998 26.179999999999996 60-64 28.970000000000002 23.315 21.685 26.029999999999998 65-69 28.854999999999997 23.799999999999997 21.36 25.985000000000003 70-74 28.999999999999996 23.595 21.51 25.895000000000003 75-79 29.580000000000002 23.425 21.535 25.46 80-84 28.83 24.060000000000002 21.404999999999998 25.705 85-89 29.515 22.99 20.990000000000002 26.505000000000003 90-94 28.854999999999997 24.69 21.15 25.305 95-99 29.304999999999996 24.740000000000002 20.885 25.069999999999997 100-104 30.395 24.03 21.555 24.02 105-109 30.81 23.990000000000002 21.735 23.465 110-114 31.6 24.97 20.215 23.215 115-119 32.72 24.310000000000002 20.46 22.509999999999998 120-124 32.745000000000005 24.560000000000002 19.86 22.835 125-129 34.339999999999996 23.915 19.875 21.87 130-134 35.93 23.995 19.27 20.805 135-139 37.21 23.415 18.845 20.53 140-144 38.17690884544227 23.53617680884044 18.740937046852345 19.545977298864944 145-149 40.1 22.585 18.060000000000002 19.255 150 41.625 22.400000000000002 19.05 16.925 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 1.0 11 1.0 12 1.0 13 1.0 14 0.5 15 0.5 16 0.5 17 0.5 18 1.0 19 0.5 20 0.0 21 0.5 22 2.0 23 1.5 24 0.0 25 1.0 26 1.5 27 1.5 28 1.5 29 0.5 30 0.0 31 0.5 32 2.0 33 3.0 34 5.0 35 13.5 36 18.0 37 21.0 38 31.5 39 46.0 40 52.5 41 53.5 42 72.5 43 93.5 44 96.0 45 119.0 46 147.5 47 151.0 48 148.5 49 145.5 50 154.0 51 166.5 52 169.5 53 177.5 54 160.0 55 146.5 56 134.5 57 109.0 58 119.0 59 127.0 60 114.5 61 101.0 62 91.0 63 89.5 64 90.5 65 84.5 66 87.0 67 103.5 68 106.0 69 86.5 70 66.0 71 52.5 72 48.0 73 34.0 74 26.5 75 31.0 76 29.0 77 18.0 78 9.5 79 6.0 80 2.0 81 2.0 82 1.5 83 1.0 84 0.5 85 0.5 86 0.5 87 0.0 88 0.5 89 0.5 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 95 0.0 96 1.0 97 1.5 98 1.5 99 2.5 100 3.5 >>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 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 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 0.005 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.35 #Duplication Level Percentage of deduplicated Percentage of total 1 91.39784946236558 80.75 2 6.168647425014148 10.9 3 1.697792869269949 4.5 4 0.2829654782116582 1.0 5 0.1697792869269949 0.75 6 0.08488964346349745 0.44999999999999996 7 0.028296547821165818 0.17500000000000002 8 0.056593095642331635 0.4 9 0.056593095642331635 0.44999999999999996 >10 0.056593095642331635 0.625 >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 GGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAA 14 0.35000000000000003 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 11 0.27499999999999997 No Hit GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 9 0.22499999999999998 No Hit GGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCA 9 0.22499999999999998 No Hit AGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAG 8 0.2 No Hit GTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGT 8 0.2 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit ACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 6 0.15 No Hit AGCGAAACCACAGCCAAGGGAACGGGCTTGGCGGAATCAGCGGGGAAAGA 6 0.15 No Hit GTCCAGTGGCCGGAAGAGCACCGCACGTCGCGCGGTGTCCGGTGCGCCCC 6 0.15 No Hit CTCAAAAGCAAGCAAGCTAGCTAGCGAGCATCAATGGCGATGACCATGAG 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit GTCAGGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGA 5 0.125 No Hit AGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAA 5 0.125 No Hit AGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGC 5 0.125 No Hit AAGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCG 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 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.037500000000000006 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.0625 0.0 0.0 0.0 0.0 48-49 0.1375 0.0 0.0 0.0 0.0 50-51 0.21250000000000002 0.0 0.0 0.0 0.0 52-53 0.2375 0.0 0.0 0.0 0.0 54-55 0.3 0.0 0.0 0.0 0.0 56-57 0.325 0.0 0.0 0.0 0.0 58-59 0.35 0.0 0.0 0.0 0.0 60-61 0.4 0.0 0.0 0.0 0.0 62-63 0.44999999999999996 0.0 0.0 0.0 0.0 64-65 0.6375 0.0 0.0 0.0 0.0 66-67 0.7375 0.0 0.0 0.0 0.0 68-69 0.8125 0.0 0.0 0.0 0.0 70-71 1.0 0.0 0.0 0.0 0.0 72-73 1.2625000000000002 0.0 0.0 0.0 0.0 74-75 1.6 0.0 0.0 0.0 0.0 76-77 1.8 0.0 0.0 0.0 0.0 78-79 2.2125 0.0 0.0 0.0 0.0 80-81 2.4749999999999996 0.0 0.0 0.0 0.0 82-83 2.7125 0.0 0.0 0.0 0.0 84-85 3.15 0.0 0.0 0.0 0.0 86-87 3.65 0.0 0.0 0.0 0.0 88-89 4.225 0.0 0.0 0.0 0.0 90-91 4.8125 0.0 0.0 0.0 0.0 92-93 5.324999999999999 0.0 0.0 0.0 0.0 94-95 5.9125 0.0 0.0 0.0 0.0 96-97 6.625 0.0 0.0 0.0 0.0 98-99 7.2875 0.0 0.0 0.0 0.0 100-101 7.9875 0.0 0.0 0.0 0.0 102-103 8.95 0.0 0.0 0.0 0.0 104-105 9.825 0.0 0.0 0.0 0.0 106-107 10.75 0.0 0.0 0.0 0.0 108-109 11.8875 0.0 0.0 0.0 0.0 110-111 13.1125 0.0 0.0 0.0 0.0 112-113 14.1375 0.0 0.0 0.0 0.0 114-115 15.2375 0.0 0.0 0.0 0.0 116-117 16.475 0.0 0.0 0.0 0.0 118-119 17.299999999999997 0.0 0.0 0.0 0.0 120-121 18.2625 0.0 0.0 0.0 0.0 122-123 19.275 0.0 0.0 0.0 0.0 124-125 20.512500000000003 0.0 0.0 0.0 0.0 126-127 21.762500000000003 0.0 0.0 0.0 0.0 128-129 23.0125 0.0 0.0 0.0 0.0 130-131 24.387500000000003 0.0 0.0 0.0 0.0 132-133 25.7125 0.0 0.0 0.0 0.0 134-135 26.9625 0.0 0.0 0.0 0.0 136-137 28.275 0.0 0.0 0.0 0.0 138 29.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGTAGTC 10 0.006973645 144.0 7 CCAGTAG 10 0.006973645 144.0 5 CAGTAGT 10 0.006973645 144.0 6 GTAGTCA 10 0.006973645 144.0 8 CCGCTGG 20 0.006139246 28.8 85-89 ACCCGAA 20 0.006139246 28.8 140-144 GATCTTC 30 0.0015031899 23.999998 100-104 >>END_MODULE Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989252 spots for SRR24040054.sra Written 4989252 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra Read 4989239 spots for SRR24040054.sra Written 4989239 spots for SRR24040054.sra SRR ids: ['SRR24040054.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5qi0n2x_ SRR24040054.sra spots: 99784793 blocks: [[1, 4989239], [4989240, 9978478], [9978479, 14967717], [14967718, 19956956], [19956957, 24946195], [24946196, 29935434], [29935435, 34924673], [34924674, 39913912], [39913913, 44903151], [44903152, 49892390], [49892391, 54881629], [54881630, 59870868], [59870869, 64860107], [64860108, 69849346], [69849347, 74838585], [74838586, 79827824], [79827825, 84817063], [84817064, 89806302], [89806303, 94795541], [94795542, 99784793]] SRR24040054 file size 33694645 SRR24040054 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 SRR24040054 SRR24040054_1.fastq SRR24040054_2.fastq Input file: SRR24040054_1.fastq Paired file: SRR24040054_2.fastq trimmed: SRR24040054-trimmed-pair1.fastq, SRR24040054-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Fri Dec 6 22:06:04 2024 >> started Fri Dec 6 22:07:57 2024 >> done (112.970s) 99784793 read pairs processed; of these: 22038 ( 0.02%) short read pairs filtered out after trimming by size control 212206 ( 0.21%) empty read pairs filtered out after trimming by size control 99550549 (99.77%) read pairs available; of these: 36405713 (36.57%) trimmed read pairs available after processing 63144836 (63.43%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 929 0.00% 19 681 0.00% 20 559 0.00% 21 638 0.00% 22 730 0.00% 23 617 0.00% 24 671 0.00% 25 687 0.00% 26 904 0.00% 27 955 0.00% 28 1187 0.00% 29 1508 0.00% 30 2395 0.00% 31 1899 0.00% 32 2037 0.00% 33 2189 0.00% 34 2556 0.00% 35 2883 0.00% 36 3341 0.00% 37 3749 0.00% 38 4655 0.00% 39 5418 0.01% 40 6265 0.01% 41 7193 0.01% 42 7381 0.01% 43 7883 0.01% 44 8543 0.01% 45 9379 0.01% 46 10567 0.01% 47 12572 0.01% 48 15063 0.02% 49 17399 0.02% 50 19818 0.02% 51 21972 0.02% 52 24652 0.02% 53 25982 0.03% 54 26839 0.03% 55 28278 0.03% 56 31238 0.03% 57 34167 0.03% 58 40808 0.04% 59 45187 0.05% 60 50456 0.05% 61 56545 0.06% 62 60379 0.06% 63 65013 0.07% 64 66569 0.07% 65 69471 0.07% 66 73058 0.07% 67 79647 0.08% 68 86415 0.09% 69 92888 0.09% 70 99515 0.10% 71 108341 0.11% 72 120116 0.12% 73 132640 0.13% 74 137156 0.14% 75 140855 0.14% 76 147652 0.15% 77 153396 0.15% 78 164421 0.17% 79 178755 0.18% 80 193508 0.19% 81 204684 0.21% 82 219708 0.22% 83 226316 0.23% 84 241299 0.24% 85 258933 0.26% 86 276685 0.28% 87 283722 0.29% 88 289840 0.29% 89 294952 0.30% 90 305980 0.31% 91 316907 0.32% 92 340676 0.34% 93 363155 0.36% 94 368012 0.37% 95 396893 0.40% 96 403588 0.41% 97 409266 0.41% 98 430338 0.43% 99 430580 0.43% 100 449627 0.45% 101 447536 0.45% 102 454439 0.46% 103 477309 0.48% 104 477088 0.48% 105 472321 0.47% 106 486936 0.49% 107 500343 0.50% 108 484268 0.49% 109 502573 0.50% 110 497037 0.50% 111 522254 0.52% 112 534875 0.54% 113 521622 0.52% 114 540047 0.54% 115 550605 0.55% 116 563568 0.57% 117 548983 0.55% 118 543133 0.55% 119 559881 0.56% 120 574907 0.58% 121 568943 0.57% 122 583388 0.59% 123 593756 0.60% 124 602231 0.60% 125 595796 0.60% 126 602323 0.61% 127 594977 0.60% 128 582650 0.59% 129 599022 0.60% 130 570820 0.57% 131 580275 0.58% 132 574925 0.58% 133 587977 0.59% 134 586418 0.59% 135 585726 0.59% 136 590814 0.59% 137 591682 0.59% 138 584904 0.59% 139 582610 0.59% 140 569309 0.57% 141 573755 0.58% 142 590958 0.59% 143 574387 0.58% 144 597551 0.60% 145 575907 0.58% 146 577232 0.58% 147 577554 0.58% 148 562231 0.56% 149 557536 0.56% 150 63144836 63.43% 99550549 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=4.67 fanout-score-rank=22 prefix-density=1.32 prefix-fanout=1.8 sequence=CGACGGTCTAAACCCAGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAACTCCGAAGATCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGGTCAGACCGGGCCTTGGAGCCAAAAGGAGGGGACTTGCCCCGCTTCCGACCCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTAT criterion=fanout-score sequence-density=0.10 sequence-density-rank=23 fanout-score=34.54 fanout-score-rank=1 prefix-density=1.71 prefix-fanout=2.0 sequence=CCTGTTATTTTGGGGTCATATCTAGTATTCAGAGTTTGCCTCGATTTGGTACCGCTCGCGCAGCCCGCACCGAAACAGTGCTTTACCCCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCTCTGGGTTCGAGTGGCATTTCACCCCTAACCACAACTCATCCGCTGATTCTTCAACATCAGTCGGTTCGGACCTCTGCTTAGTTTCATCCAAGCTTCATCCTGGTCATGGATAGATCACCCAGGTTCGGGTCCATAAGCAGTGACAATCGCCCTATGAAGACTCGCTTTCGCTACGGCTCCGGTGGGTTCCGTTCCCTTAACCAAGCCACTGCCTATGAGTCGCCGGCTCATTCTTCAACAGGCACGCGGTCAGAGATCACTTTCCCCTCCCACTGCTTGGGAGCTCAGCACGGTTTCACGTTCTATTTCACTACCCACTGGGGGTTCTTTTCACCTTTCCCTCACGGTACTACTTCGCTATCGG criterion=sequence-density sequence-density=0.68 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=29 prefix-density=0.69 prefix-fanout=2.1 sequence=CATCATCTGTGCTCCACCTGTCCCTGGCCGTGCTGGCCCTGGTGGCCGCATTGTCGGAGGCCGGGTTCTACGACCAGTTCGACGTGGGCGGCTCCGGCCAGCACGTCCGCGTGATCGAGGACGGCAAGACCCAGCAGGTGGCCCTCACGATGGACCAACGCTCCGGCGGTGCAGGGTTCACCTCCAAGGCCATGTACCTCTACGGCGAGTTCAGCGTCCAGATGAAGCTCGTCAGCGGCAACTCCGCTGGCACTGTCACCTCCTTCTACTTGAAGTCCGGGGAAGGCGAGGGCCATGACGAGATCGACATCGAGTTCATGGGCAACCTGAGCGGCAACCCCTACGTGATGAACACCAACGTCTGGGCCAACGGCGACGGCAAGAAGGAGCACCAGTTCTACCTCTGGTTCGACCCCTCCGCCGACTTCCACACCTACAAGATCGTCTGGAACCCCACGAACATCATATTCCAGGTGGACGACGTGCCGGTGAGGACGTTCAGGAAGTACGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=245.42 fanout-score-rank=1 prefix-density=0.42 prefix-fanout=8.1 sequence=GCAGCAGCAAGAACAGGGGCAGCAAGGTCAGATCCCTTCGCGCCGGTTCGGGGCCCAGTCACAGGAGTGCGGACAACAGGGTATCTTCTCGCCCCAGCTGCTAGCTCAGATACTACCGGCGATGTGCAATGTGTACCTCCCACCGTACTGCCGCGCCACCGCCGCTGATCAGCCATTCGGACCCGGTGGCTACTGATAAGACAAAGGGCTCTTGTAGTAGATAGATAGGGATCACCGCT SRR24040054 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:08:46 Started mapping on | Dec 06 22:08:46 Finished on | Dec 06 22:19:54 Mapping speed, Million of reads per hour | 536.50 Number of input reads | 99550549 Average input read length | 274 UNIQUE READS: Uniquely mapped reads number | 54675820 Uniquely mapped reads % | 54.92% Average mapped length | 274.76 Number of splices: Total | 42703314 Number of splices: Annotated (sjdb) | 39940717 Number of splices: GT/AG | 41915674 Number of splices: GC/AG | 499755 Number of splices: AT/AC | 25098 Number of splices: Non-canonical | 262787 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.49 Insertion rate per base | 0.01% Insertion average length | 2.54 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 8525067 % of reads mapped to multiple loci | 8.56% Number of reads mapped to too many loci | 5689276 % of reads mapped to too many loci | 5.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.15% % of reads unmapped: other | 27.65% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 36349662 36349662 36349662 N_multimapping 8525067 8525067 8525067 N_noFeature 2090510 53280482 2492645 N_ambiguous 1241650 3704 343426 UnstrandedReadsAssigned:51343660 PositiveStrandReadsAssigned:1391634 NegativeStrandReadsAssigned:51839749 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=120 echo kmer=115 SRR24040054 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: SRR24040054-trimmed-pair1.fastq SRR24040054-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 99,550,549 reads, 59,311,900 reads pseudoaligned [quant] estimated average fragment length: 186.82 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,216 rounds 52973 SRR24040054.ke.tsv 35125 SRR24040054.se.tsv 88098 total ==> SRR24040054.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 750.385 270.319 7.27267 PNS24247 1044 858.18 65.5497 1.54204 PNS24249 1928 1742.18 666.391 7.72215 PNS24246 1044 858.18 65.5497 1.54204 PNS24248 1044 858.18 65.5497 1.54204 PNS24244 1471 1285.18 153.64 2.41348 PNS24243 293 130.332 0 0 KQK14069 1603 1417.18 12815 182.556 KQK14071 474 292.32 202.423 13.9799 ==> SRR24040054.se.tsv <== BRADI_1g14170v3 12897 BRADI_1g53295v3 112 BRADI_1g59795v3 118 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 2499 BRADI_1g74790v3 103 BRADI_1g09890v3 44 BRADI_1g77505v3 753 BRADI_1g48960v3 33 SRR24040054 completed mapping pipeline successfully