Starting /dee2/code/volunteer_pipeline.sh SRR13165377 current disk space = 1541769773056 free memory = 1602342096 SRR13165377 SRAfilesize 0429d994783b016c9df30f44aedf06ec SRR13165377.sra SRR13165377.sra file validated SRR13165377 is paired end SRR13165377 is conventional basespace SRR13165377 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165377_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6205 37.0 37.0 37.0 37.0 37.0 2 36.09775 37.0 37.0 37.0 37.0 37.0 3 36.4075 37.0 37.0 37.0 37.0 37.0 4 36.5735 37.0 37.0 37.0 37.0 37.0 5 36.541 37.0 37.0 37.0 37.0 37.0 6 36.4715 37.0 37.0 37.0 37.0 37.0 7 36.445 37.0 37.0 37.0 37.0 37.0 8 36.5065 37.0 37.0 37.0 37.0 37.0 9 36.5625 37.0 37.0 37.0 37.0 37.0 10-14 36.5406 37.0 37.0 37.0 37.0 37.0 15-19 36.513 37.0 37.0 37.0 37.0 37.0 20-24 36.491600000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.399800000000006 37.0 37.0 37.0 37.0 37.0 30-34 36.3921 37.0 37.0 37.0 37.0 37.0 35-39 36.3697 37.0 37.0 37.0 37.0 37.0 40-44 36.3845 37.0 37.0 37.0 37.0 37.0 45-49 36.323899999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.32170000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.2901 37.0 37.0 37.0 37.0 37.0 60-64 36.31269999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.1879 37.0 37.0 37.0 37.0 37.0 70-74 36.247499999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.218 37.0 37.0 37.0 37.0 37.0 80-84 36.1344 37.0 37.0 37.0 37.0 37.0 85-89 36.2033 37.0 37.0 37.0 37.0 37.0 90-94 36.1339 37.0 37.0 37.0 37.0 37.0 95-99 36.0887 37.0 37.0 37.0 37.0 37.0 100-104 36.134100000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.126400000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.0437 37.0 37.0 37.0 37.0 37.0 115-119 36.047 37.0 37.0 37.0 37.0 37.0 120-124 35.9396 37.0 37.0 37.0 37.0 37.0 125-129 35.969100000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.89 37.0 37.0 37.0 37.0 37.0 135-139 35.8318 37.0 37.0 37.0 37.0 37.0 140-144 35.7287 37.0 37.0 37.0 37.0 37.0 145-149 35.5669 37.0 37.0 37.0 37.0 37.0 150-151 35.38775 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 0.0 23 1.0 24 3.0 25 4.0 26 2.0 27 10.0 28 11.0 29 24.0 30 28.0 31 51.0 32 54.0 33 98.0 34 116.0 35 331.0 36 2847.0 37 417.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 51.025 10.549999999999999 5.175 33.25 2 23.93550012597632 12.446460065507685 31.695641219450742 31.922398589065253 3 20.424999999999997 15.625 25.174999999999997 38.775 4 28.425 21.65 20.549999999999997 29.375 5 27.825 28.975 21.3 21.9 6 26.025 29.675 20.200000000000003 24.099999999999998 7 18.75 26.224999999999998 35.925000000000004 19.1 8 21.325 24.55 27.875 26.25 9 20.849999999999998 21.325 32.625 25.2 10-14 23.04 26.474999999999998 26.085 24.4 15-19 23.635 24.645 24.959999999999997 26.76 20-24 22.830000000000002 25.569999999999997 25.52 26.08 25-29 23.185 25.900000000000002 25.47 25.445 30-34 23.97 25.025 25.555 25.45 35-39 23.465 24.92 25.6 26.015 40-44 23.9 24.93 25.605 25.564999999999998 45-49 24.04 25.569999999999997 24.495 25.895000000000003 50-54 23.695 25.71 24.29 26.305 55-59 23.93 25.035 25.624999999999996 25.41 60-64 24.099999999999998 25.180000000000003 24.85 25.869999999999997 65-69 23.95 25.395 24.79 25.865 70-74 23.54 25.795 25.005 25.66 75-79 24.665 25.485000000000003 24.42 25.430000000000003 80-84 23.96 25.53 24.805 25.705 85-89 25.105 25.635 24.05 25.21 90-94 24.97 25.119999999999997 24.23 25.679999999999996 95-99 24.88 25.615 23.955000000000002 25.55 100-104 24.77 25.275 24.365000000000002 25.590000000000003 105-109 24.62 25.924999999999997 24.14 25.314999999999998 110-114 24.165 25.979999999999997 23.65 26.205000000000002 115-119 24.02 26.05 24.645 25.285000000000004 120-124 24.990000000000002 25.005 23.435 26.57 125-129 23.945 25.095 24.490000000000002 26.47 130-134 24.745 25.4 23.705000000000002 26.150000000000002 135-139 23.79 26.150000000000002 24.07 25.990000000000002 140-144 24.375 25.435000000000002 24.435000000000002 25.755 145-149 24.51 25.330000000000002 24.26 25.900000000000002 150-151 24.9 24.5375 24.325 26.237500000000004 >>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 0.0 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 0.5 25 1.0 26 2.5 27 3.0 28 3.0 29 3.0 30 8.5 31 12.5 32 13.5 33 21.5 34 26.0 35 25.0 36 49.0 37 62.5 38 68.0 39 100.5 40 109.5 41 109.5 42 126.0 43 160.5 44 196.0 45 196.5 46 200.0 47 219.0 48 204.5 49 187.0 50 173.5 51 161.0 52 139.0 53 118.0 54 114.5 55 100.0 56 98.5 57 104.0 58 91.0 59 78.5 60 74.5 61 58.0 62 49.0 63 50.5 64 58.5 65 61.5 66 55.5 67 51.5 68 39.5 69 29.0 70 26.5 71 31.5 72 40.5 73 34.0 74 17.0 75 10.5 76 11.5 77 7.5 78 2.5 79 3.0 80 1.5 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 0.0 2 0.775 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 0.0 145-149 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 71.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 73.31245650661099 52.675000000000004 2 18.684759916492695 26.85 3 5.010438413361169 10.8 4 1.9485038274182327 5.6000000000000005 5 0.6610995128740431 2.375 6 0.3479471120389701 1.5 7 0.0 0.0 8 0.03479471120389701 0.2 9 0.0 0.0 >10 0.0 0.0 >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 GGATGCTAACTTTTCAATATGATGAAGTTCAATAGAGTCAAAACCCTTAA 8 0.2 No Hit GTCCTTTCGCATAGATGCTGCCACCTGCTCGCTGTGCCCCTGCGGGAAGT 6 0.15 No Hit TAGCACGAAGTAGAAGGTCTGAAGCACTAGCAAGAATTACCAATGCTTCA 6 0.15 No Hit GCCCACATCACCTCCCACAGACTTAGGGTCTGATCAAAGGTGAGCTCCCT 6 0.15 No Hit CTGAAGTCAAAGTTCTCCTTCACGATCTTCAGAATCTCCTTGTCAGGGAT 6 0.15 No Hit GGCCACTCTTGTTGACACCTTTTGGTCTCGCATTTCTGAGTATAGTGTTG 6 0.15 No Hit CCCCAGATAGCCAATAGCACCACAAAGTATCCCTAGCCCAAGACAGAACA 6 0.15 No Hit GGTGGCCCTCGACCTCGACGACGGTGTCGAAGGGTATGGATCCCCGCGCG 6 0.15 No Hit ACCAATTTCACGGATCCATTACACAAAGCAAACACCACAATTATCGAAAA 6 0.15 No Hit GTCGTCTCGGCGGCGAACGCGTCGGTGACCGCCTGGTGGATGGATGTCTC 6 0.15 No Hit GGTTAATTGGGCACTGGCTCCAGTTCCAAAATGTGTTCTGTTCCAGCTGT 6 0.15 No Hit CGGGACTGCGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCC 5 0.125 No Hit CCCCACAGCACAACATACAGGCCCAAGATGATTGTGATAGCACCTAACAC 5 0.125 No Hit CGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGC 5 0.125 No Hit GCTCGTCGAGCTTGAAGACACTCCTGACGTTCATGACGAAGAGGTAGAGC 5 0.125 No Hit GGGGAAACCTTTCACCCTCCACCTTGCAAACCTGAGACCTTAGCTAAGAA 5 0.125 No Hit GTGCGGACAACTTTGGCTTCCCATTAGCGATATCCTGCTGCTTCTCTTCA 5 0.125 No Hit GTTCAGCCAAGGCTCCACCTACGTGTACTTTCCAAGTATACAAGAGCGTA 5 0.125 No Hit GCCAACGAGATCAGCACCCACGTCAGCAGCCTTTGTGTAAATACCTCCAC 5 0.125 No Hit CGCCGAATATAATCTGGCTCTTCCATCATCAAGGATGCAACCCTCCTTTC 5 0.125 No Hit GGAGAAGGAGACCTCCGGGAACTTGTGGGCGAGCGCGGTGTCGGGATCGA 5 0.125 No Hit GGTGTTAGTTGTACAACGCTGCACAGAAGGTTCCAATGGGGAGATATAAA 5 0.125 No Hit TGGAGGGTGAGCTTCTTCCCTGGCTGGATGTCGCTCTCTAGGAAGAAGAG 5 0.125 No Hit GTCATAGAGTATCCGAAGGTTTCGCCTCTGGTATTTCCCATATGCACACA 5 0.125 No Hit GTCGGGATGGCAGCGGGGGCCGGAGCCACGAGTACTGGAGCGGCGGGAGG 5 0.125 No Hit CTCTCGGCTCTCGCGTCGCCTTCTTCAGTTTCTCTTTCTCGATCGGACGG 5 0.125 No Hit CAAACAAAACATGCACGGGCCAACCGACCAGACCCCTCTTACAAAGAAAA 5 0.125 No Hit AGTGTTTGGTTATGCATTGAAATAGTGCTGAAGCTATGCTAGACATGAGA 5 0.125 No Hit ATCGCGTTTCAAGCGTGCTTACAAATGAGCTGCTGTGTGGCCAATTCAGA 5 0.125 No Hit GAGTGTTTGAAAATTTGATGTATCATTCGGATGTTTAACTCCGAAGCACC 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 0.025 0.0 0.0 40-41 0.0 0.0 0.025 0.0 0.0 42-43 0.0 0.0 0.025 0.0 0.0 44-45 0.0 0.0 0.025 0.0 0.0 46-47 0.0 0.0 0.025 0.0 0.0 48-49 0.0 0.0 0.025 0.0 0.0 50-51 0.0 0.0 0.025 0.0 0.0 52-53 0.0 0.0 0.025 0.0 0.0 54-55 0.0 0.0 0.025 0.0 0.0 56-57 0.05 0.0 0.025 0.0 0.0 58-59 0.0625 0.0 0.025 0.0 0.0 60-61 0.0875 0.0 0.025 0.0 0.0 62-63 0.1 0.0 0.025 0.0 0.0 64-65 0.1 0.0 0.025 0.0 0.0 66-67 0.125 0.0 0.025 0.0 0.0 68-69 0.15 0.0 0.025 0.0 0.0 70-71 0.1875 0.0 0.025 0.0 0.0 72-73 0.2625 0.0 0.025 0.0 0.0 74-75 0.36250000000000004 0.0 0.025 0.0 0.0 76-77 0.425 0.0 0.025 0.0 0.0 78-79 0.525 0.0 0.025 0.0 0.0 80-81 0.625 0.0 0.025 0.0 0.0 82-83 0.7 0.0 0.025 0.0 0.0 84-85 0.8999999999999999 0.0 0.025 0.0 0.0 86-87 1.15 0.0 0.025 0.0 0.0 88-89 1.4500000000000002 0.0 0.025 0.0 0.0 90-91 1.6125 0.0 0.025 0.0 0.0 92-93 1.825 0.0 0.025 0.0 0.0 94-95 2.2875 0.0 0.025 0.0 0.0 96-97 2.875 0.0 0.025 0.0 0.0 98-99 3.325 0.0 0.025 0.0 0.0 100-101 3.775 0.0 0.025 0.0 0.0 102-103 4.2 0.0 0.025 0.0 0.0 104-105 5.074999999999999 0.0 0.025 0.0 0.0 106-107 5.725 0.0 0.025 0.0 0.0 108-109 6.262499999999999 0.0 0.025 0.0 0.0 110-111 6.800000000000001 0.0 0.025 0.0 0.0 112-113 7.3625 0.0 0.025 0.0 0.0 114-115 8.024999999999999 0.0 0.025 0.0 0.0 116-117 8.575 0.0 0.025 0.0 0.0 118-119 9.0625 0.0 0.025 0.0 0.0 120-121 9.7625 0.0 0.025 0.0 0.0 122-123 10.337499999999999 0.0 0.025 0.0 0.0 124-125 11.1125 0.0 0.025 0.0 0.0 126-127 11.8875 0.0 0.025 0.0 0.0 128-129 12.9 0.0 0.025 0.0 0.0 130-131 13.6 0.0 0.025 0.0 0.0 132-133 14.475 0.0 0.025 0.0 0.0 134-135 15.3125 0.0 0.025 0.0 0.0 136-137 16.1 0.0 0.025 0.0 0.0 138-139 16.625 0.0 0.025 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGGAGT 10 0.006830828 145.0 3 >>END_MODULE SRR13165377 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165377_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.88675 37.0 37.0 37.0 37.0 37.0 2 36.072 37.0 37.0 37.0 37.0 37.0 3 35.9505 37.0 37.0 37.0 37.0 37.0 4 36.129 37.0 37.0 37.0 37.0 37.0 5 36.27 37.0 37.0 37.0 37.0 37.0 6 36.15 37.0 37.0 37.0 37.0 37.0 7 36.0215 37.0 37.0 37.0 37.0 37.0 8 36.197 37.0 37.0 37.0 37.0 37.0 9 36.062 37.0 37.0 37.0 37.0 37.0 10-14 36.0938 37.0 37.0 37.0 37.0 37.0 15-19 36.0208 37.0 37.0 37.0 37.0 37.0 20-24 36.03225 37.0 37.0 37.0 37.0 37.0 25-29 35.90375 37.0 37.0 37.0 37.0 37.0 30-34 35.85685 37.0 37.0 37.0 37.0 37.0 35-39 35.87835 37.0 37.0 37.0 37.0 37.0 40-44 35.79105 37.0 37.0 37.0 37.0 37.0 45-49 35.763349999999996 37.0 37.0 37.0 37.0 37.0 50-54 35.72545000000001 37.0 37.0 37.0 37.0 37.0 55-59 35.72855 37.0 37.0 37.0 37.0 37.0 60-64 35.71655 37.0 37.0 37.0 37.0 37.0 65-69 35.701100000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.63345 37.0 37.0 37.0 37.0 37.0 75-79 35.64190000000001 37.0 37.0 37.0 37.0 37.0 80-84 35.67635 37.0 37.0 37.0 37.0 37.0 85-89 35.5774 37.0 37.0 37.0 37.0 37.0 90-94 35.604200000000006 37.0 37.0 37.0 37.0 37.0 95-99 35.612350000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.51025 37.0 37.0 37.0 37.0 37.0 105-109 35.54415 37.0 37.0 37.0 37.0 37.0 110-114 35.39315 37.0 37.0 37.0 37.0 37.0 115-119 35.307849999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.23105 37.0 37.0 37.0 37.0 37.0 125-129 35.19365 37.0 37.0 37.0 34.6 37.0 130-134 35.098349999999996 37.0 37.0 37.0 29.8 37.0 135-139 34.998000000000005 37.0 37.0 37.0 27.4 37.0 140-144 34.759249999999994 37.0 37.0 37.0 25.0 37.0 145-149 34.525600000000004 37.0 37.0 37.0 25.0 37.0 150-151 34.266000000000005 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 2.0 13 13.0 14 11.0 15 6.0 16 8.0 17 1.0 18 5.0 19 1.0 20 4.0 21 6.0 22 9.0 23 15.0 24 5.0 25 11.0 26 15.0 27 9.0 28 14.0 29 17.0 30 28.0 31 35.0 32 77.0 33 109.0 34 231.0 35 538.0 36 2607.0 37 222.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.118046816008054 19.254971054618675 8.18021646111251 25.446765668260763 2 31.85 22.825 24.175 21.15 3 23.0 26.450000000000003 28.075 22.475 4 28.9 28.825 20.5 21.775 5 28.875 33.5 18.675 18.95 6 24.175 34.9 18.925 22.0 7 22.675 20.8 33.725 22.8 8 23.974999999999998 24.099999999999998 24.0 27.925 9 23.925 22.35 24.575 29.15 10-14 26.38 25.96 22.884999999999998 24.775 15-19 26.185000000000002 24.54 24.325 24.95 20-24 25.53893862851998 25.418896613814834 24.133446706347222 24.908718051317962 25-29 26.274706029522143 24.878658994245683 23.937953465098825 24.90868151113335 30-34 26.009305117814797 25.228875881734954 24.27335034268848 24.488468657761768 35-39 26.12414345020757 25.25383884359526 24.428549992497377 24.193467713699796 40-44 26.304467457101406 25.924258342088148 22.832557906848766 24.93871629396168 45-49 26.096743534590566 24.8361762793257 24.89120104046821 24.17587914561553 50-54 27.63967388586005 24.913719801930675 24.23348171860151 23.213124593607763 55-59 27.015261446084565 24.73855391543658 23.852889667250437 24.39329497122842 60-64 26.66933426699345 24.65863052068224 25.05376881908668 23.618266393237633 65-69 25.785157031406282 25.40508101620324 24.78495699139828 24.0248049609922 70-74 26.199649737302977 25.1138353765324 24.163122341756317 24.523392544408306 75-79 27.076245747448468 25.05503301981189 24.004402641584953 23.864318591154692 80-84 26.116529132283073 24.93623405851463 24.381095273818453 24.566141535383846 85-89 27.2690883618533 24.69228459921945 24.251976383468428 23.78665065545882 90-94 26.285514205682276 24.98999599839936 25.10504201680672 23.619447779111642 95-99 26.79937978292402 25.46891411994198 23.903366178162358 23.82833991897164 100-104 27.9009256942707 25.459094320740554 23.457593194896173 23.18238679009257 105-109 27.20540405303978 25.27395546659995 23.307480610457844 24.213159869902427 110-114 27.824738658530485 25.959085679987997 23.443205121792626 22.77297053968889 115-119 28.41130848136102 25.53415061295972 23.887915936952712 22.166624968726545 120-124 27.675756817613212 25.514135601701277 23.462596947710786 23.34751063297473 125-129 29.294041126732377 25.92184920198129 22.80982638715165 21.97428328413469 130-134 29.51599179138095 25.601881976074882 23.039191150708245 21.842935081835925 135-139 29.79181263136823 24.932439195275748 23.941547392653387 21.334200780702634 140-144 30.540689241234432 25.41389486320212 22.998049317261042 21.047366578302405 145-149 30.727654889400462 24.677209488539688 23.501151035932338 21.093984586127515 150-151 30.683525287931896 26.176765147721582 22.245868803204807 20.893840761141714 >>END_MODULE >>Per sequence GC content fail #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 0.5 8 1.5 9 2.0 10 2.0 11 1.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 0.5 23 0.5 24 0.5 25 1.5 26 2.0 27 3.0 28 4.5 29 6.5 30 8.0 31 10.5 32 15.0 33 20.0 34 18.0 35 30.5 36 44.0 37 48.0 38 67.5 39 88.5 40 107.0 41 121.5 42 139.5 43 164.0 44 185.0 45 205.5 46 225.5 47 197.5 48 163.5 49 147.0 50 145.0 51 142.0 52 116.0 53 121.5 54 112.0 55 95.5 56 92.0 57 89.5 58 94.0 59 81.5 60 75.5 61 82.0 62 69.5 63 60.5 64 66.5 65 71.0 66 71.0 67 55.5 68 44.0 69 40.0 70 39.5 71 36.5 72 30.0 73 32.0 74 22.5 75 15.0 76 10.0 77 4.0 78 5.0 79 6.5 80 6.0 81 2.5 82 2.5 83 1.5 84 0.0 85 0.5 86 1.5 87 1.0 88 1.0 89 1.5 90 0.5 91 0.5 92 1.5 93 1.5 94 0.5 95 1.5 96 2.0 97 1.5 98 2.0 99 2.0 100 3.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.675 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 0.034999999999999996 25-29 0.075 30-34 0.055 35-39 0.034999999999999996 40-44 0.055 45-49 0.045 50-54 0.034999999999999996 55-59 0.075 60-64 0.034999999999999996 65-69 0.02 70-74 0.075 75-79 0.06 80-84 0.025 85-89 0.06999999999999999 90-94 0.04 95-99 0.034999999999999996 100-104 0.075 105-109 0.075 110-114 0.034999999999999996 115-119 0.075 120-124 0.075 125-129 0.065 130-134 0.105 135-139 0.09 140-144 0.034999999999999996 145-149 0.09 150-151 0.15 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.275 #Duplication Level Percentage of deduplicated Percentage of total 1 75.33265097236438 55.2 2 17.400204708290687 25.5 3 4.367110201296486 9.6 4 1.842374616171955 5.4 5 0.6482429205049471 2.375 6 0.3070624360286591 1.35 7 0.0341180484476288 0.17500000000000002 8 0.0682360968952576 0.4 9 0.0 0.0 >10 0.0 0.0 >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 GATTGTTCAAGAGCCTGGGTTTCACCCAAAATAAAGCTGATTCACAGGTG 8 0.2 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 8 0.2 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit CGTCAGGCCGCTTTGTCATCGGTGGCCCTCACGGTGATGCTGGTCTCACC 6 0.15 No Hit AGAAATCGGATATTGCCAGGGCATGAGTGACCTCCTCGCACCTTTGCTTG 6 0.15 No Hit AATGGAGTTGTGCCAAACCCACAAGGAAAAGTTTCGGGAGATGCATGCAC 6 0.15 No Hit CAAGTCGACCGAGTACTTCATCGGAGTGACGGCCATCAAGGTGAACGGCC 6 0.15 No Hit ACTGACCCGACATTCCTGTATTTCGCGCATGGGCTTAAGGAGGTCAAGTG 6 0.15 No Hit CAGGAACTATGCTTCTCTGTTGTCTCATTGCTCTGGCAGAAGCTTATTGC 6 0.15 No Hit GTGGTACGCCTGCGCGGGGCCGCTGGTGGCGCTGCCGCCGGCGGGGAGCC 6 0.15 No Hit CCACCTCAACGGCATACGCGTCGTCGAGGACGCGATCTACCTGCTCGAGG 6 0.15 No Hit CTTATTTCTTGTTGAACGCTGAGAACTACCATTGGCAATGGACATCGTTC 6 0.15 No Hit CGTCGCCCCTGAAGACGCTGCTGCTGCTGCTGCTGCGCCAGCACTACTGG 5 0.125 No Hit GTAATATTGCAATGGGTGTTGCTTCGATTTCGAGGATGGAACACAGTCGC 5 0.125 No Hit CAGGCAACCTTTGGAGATCTCCGTAGTTACATGATTGAAACAGCACTTCC 5 0.125 No Hit TGATCAAGTTTAACTCAAATATGAACACCTCACTATACAGGCCTGCAAGT 5 0.125 No Hit CGGAGATGCAACAACTGGAGCTCCGGCCGAGGAATACTGGAAGTCCGCTC 5 0.125 No Hit TGACAAGTTCCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCTCGAT 5 0.125 No Hit CAAGAGCAACCGCAACAGTCCCTCCTCCCAGAGTTGACGACGACACCGTC 5 0.125 No Hit GTAAGATCCAAGCTCGCCACCGCAGACCTTGTTAACGCGGGATTCAAGAA 5 0.125 No Hit GTATATAACTGATGATTTGATGCTTTTAGTTGGAGATAAAAACTCGTCAT 5 0.125 No Hit CGGTGACTCTCACGGCCGCCGAGTTCAAGTGCTCCGTCTGCGGCAGGTCC 5 0.125 No Hit ACCACGGCTCCCTCGCCGACCAGATCGTGCACCCGGCCGACCTCTGCTTC 5 0.125 No Hit AACAGTTTTTAAGCAATTCATCCTCTGAGCAATTTGCATGGACTTATTTC 5 0.125 No Hit GCTGAAATGACTGGTCCTGTTGATTTTGAGAAGACCCTTGAGTACTGGCA 5 0.125 No Hit CGAAAACTGATGCTGCTAGAACAAAGGCTGCTCAGGAAGCTTTCAGGGAA 5 0.125 No Hit CGTTAGAAACATTACTTTCCCAATGCTGTTCTTATTATGAACAGTGCGCA 5 0.125 No Hit CACGACAATACTATCTACGCTCTTCCTTCATGAAGAGCTCCATATTGGAA 5 0.125 No Hit GCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATT 5 0.125 No Hit AGCTGGGGTTGTCCGTAAGGGCCCGTGGACGGAGCAGGAGGACATGAAGC 5 0.125 No Hit GTGGTTCTTTACATTACCATCAACGTATTTAAGGTGTATTACGGTGATGA 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 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.037500000000000006 0.0 0.0 0.0 0.0 60-61 0.0625 0.0 0.0 0.0 0.0 62-63 0.075 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 0.1625 0.0 0.0 0.0 0.0 72-73 0.23750000000000002 0.0 0.0 0.0 0.0 74-75 0.3375 0.0 0.0 0.0 0.0 76-77 0.4 0.0 0.0 0.0 0.0 78-79 0.5 0.0 0.0 0.0 0.0 80-81 0.6 0.0 0.0 0.0 0.0 82-83 0.675 0.0 0.0 0.0 0.0 84-85 0.875 0.0 0.0 0.0 0.0 86-87 1.125 0.0 0.0 0.0 0.0 88-89 1.4249999999999998 0.0 0.0 0.0 0.0 90-91 1.5875 0.0 0.0 0.0 0.0 92-93 1.7875 0.0 0.0 0.0 0.0 94-95 2.2375 0.0 0.0 0.0 0.0 96-97 2.825 0.0 0.0 0.0 0.0 98-99 3.275 0.0 0.0 0.0 0.0 100-101 3.725 0.0 0.0 0.0 0.0 102-103 4.225 0.0 0.0 0.0 0.0 104-105 5.175000000000001 0.0 0.0 0.0 0.0 106-107 5.825 0.0 0.0 0.0 0.0 108-109 6.362500000000001 0.0 0.0 0.0 0.0 110-111 6.875 0.0 0.0 0.0 0.0 112-113 7.4 0.0 0.0 0.0 0.0 114-115 8.05 0.0 0.0 0.0 0.0 116-117 8.6375 0.0 0.0 0.0 0.0 118-119 9.1125 0.0 0.0 0.0 0.0 120-121 9.775 0.0 0.0 0.0 0.0 122-123 10.325 0.0 0.0 0.0 0.0 124-125 11.1125 0.0 0.0 0.0 0.0 126-127 11.8625 0.0 0.0 0.0 0.0 128-129 12.85 0.0 0.0 0.0 0.0 130-131 13.55 0.0 0.0 0.0 0.0 132-133 14.425 0.0 0.0 0.0 0.0 134-135 15.225 0.0 0.0 0.0 0.0 136-137 16.0 0.0 0.0 0.0 0.0 138-139 16.5125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTGAAC 10 0.006830828 145.0 145 >>END_MODULE Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra Read 1869926 spots for SRR13165377.sra Written 1869926 spots for SRR13165377.sra SRR ids: ['SRR13165377.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fj_xd9ir SRR13165377.sra spots: 37398520 blocks: [[1, 1869926], [1869927, 3739852], [3739853, 5609778], [5609779, 7479704], [7479705, 9349630], [9349631, 11219556], [11219557, 13089482], [13089483, 14959408], [14959409, 16829334], [16829335, 18699260], [18699261, 20569186], [20569187, 22439112], [22439113, 24309038], [24309039, 26178964], [26178965, 28048890], [28048891, 29918816], [29918817, 31788742], [31788743, 33658668], [33658669, 35528594], [35528595, 37398520]] SRR13165377 file size 12687952 SRR13165377 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 SRR13165377 SRR13165377_1.fastq SRR13165377_2.fastq Input file: SRR13165377_1.fastq Paired file: SRR13165377_2.fastq trimmed: SRR13165377-trimmed-pair1.fastq, SRR13165377-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 Sat Dec 7 16:48:59 2024 >> started Sat Dec 7 16:49:39 2024 >> done (40.449s) 37398520 read pairs processed; of these: 1063 ( 0.00%) short read pairs filtered out after trimming by size control 69233 ( 0.19%) empty read pairs filtered out after trimming by size control 37328224 (99.81%) read pairs available; of these: 8358911 (22.39%) trimmed read pairs available after processing 28969313 (77.61%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 45 0.00% 19 68 0.00% 20 68 0.00% 21 92 0.00% 22 112 0.00% 23 126 0.00% 24 151 0.00% 25 171 0.00% 26 199 0.00% 27 224 0.00% 28 226 0.00% 29 282 0.00% 30 286 0.00% 31 248 0.00% 32 305 0.00% 33 319 0.00% 34 345 0.00% 35 353 0.00% 36 318 0.00% 37 428 0.00% 38 400 0.00% 39 508 0.00% 40 531 0.00% 41 540 0.00% 42 556 0.00% 43 645 0.00% 44 617 0.00% 45 667 0.00% 46 698 0.00% 47 854 0.00% 48 1033 0.00% 49 1105 0.00% 50 1272 0.00% 51 1391 0.00% 52 1568 0.00% 53 1601 0.00% 54 1758 0.00% 55 1873 0.01% 56 1988 0.01% 57 2330 0.01% 58 2656 0.01% 59 3135 0.01% 60 3603 0.01% 61 3890 0.01% 62 4369 0.01% 63 5064 0.01% 64 5305 0.01% 65 5923 0.02% 66 6289 0.02% 67 6970 0.02% 68 7765 0.02% 69 9107 0.02% 70 9954 0.03% 71 11015 0.03% 72 12566 0.03% 73 14238 0.04% 74 15616 0.04% 75 17524 0.05% 76 18562 0.05% 77 20444 0.05% 78 22293 0.06% 79 24182 0.06% 80 26084 0.07% 81 29625 0.08% 82 32162 0.09% 83 35022 0.09% 84 39113 0.10% 85 41788 0.11% 86 44528 0.12% 87 46996 0.13% 88 49960 0.13% 89 52431 0.14% 90 56482 0.15% 91 58982 0.16% 92 63272 0.17% 93 67643 0.18% 94 71904 0.19% 95 74861 0.20% 96 78762 0.21% 97 82084 0.22% 98 83916 0.22% 99 87288 0.23% 100 89519 0.24% 101 91480 0.25% 102 95050 0.25% 103 99422 0.27% 104 102059 0.27% 105 106553 0.29% 106 108042 0.29% 107 110272 0.30% 108 113002 0.30% 109 115159 0.31% 110 117416 0.31% 111 119131 0.32% 112 121562 0.33% 113 122212 0.33% 114 126318 0.34% 115 128631 0.34% 116 130776 0.35% 117 133114 0.36% 118 133935 0.36% 119 134857 0.36% 120 135192 0.36% 121 137631 0.37% 122 136819 0.37% 123 140038 0.38% 124 142294 0.38% 125 142390 0.38% 126 144302 0.39% 127 146228 0.39% 128 146028 0.39% 129 146501 0.39% 130 147887 0.40% 131 148436 0.40% 132 150294 0.40% 133 150787 0.40% 134 151247 0.41% 135 152481 0.41% 136 153427 0.41% 137 153218 0.41% 138 154375 0.41% 139 154896 0.41% 140 154861 0.41% 141 156857 0.42% 142 156998 0.42% 143 157688 0.42% 144 159661 0.43% 145 160402 0.43% 146 158153 0.42% 147 160204 0.43% 148 160133 0.43% 149 160369 0.43% 150 160930 0.43% 151 28969313 77.61% 37328224 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=17.13 fanout-score-rank=7 prefix-density=0.18 prefix-fanout=17.1 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGCGAAGATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.09 sequence-density-rank=20 fanout-score=120.85 fanout-score-rank=1 prefix-density=0.68 prefix-fanout=16.3 sequence=CGGCGGCGGCGG criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=2.13 fanout-score-rank=33 prefix-density=0.27 prefix-fanout=2.1 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=32 fanout-score=268.57 fanout-score-rank=1 prefix-density=0.94 prefix-fanout=14.6 sequence=AAGAAGAAGGTGGAGTCCAAGAACGCCCTGGAGAACTACTCGTACAACATGCGCAACACCATCAAGGACGAGAAGATCGCCTCCAAGCTGCCGGCGGACGACAAGAAGAAGATCGAGGACGCCATTGATG SRR13165377 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 16:50:24 Started mapping on | Dec 07 16:50:24 Finished on | Dec 07 16:53:43 Mapping speed, Million of reads per hour | 675.28 Number of input reads | 37328224 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 35266492 Uniquely mapped reads % | 94.48% Average mapped length | 286.92 Number of splices: Total | 33049002 Number of splices: Annotated (sjdb) | 30739677 Number of splices: GT/AG | 32521363 Number of splices: GC/AG | 447244 Number of splices: AT/AC | 18394 Number of splices: Non-canonical | 62001 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.39 Insertion rate per base | 0.01% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 443739 % of reads mapped to multiple loci | 1.19% Number of reads mapped to too many loci | 39335 % of reads mapped to too many loci | 0.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.74% % of reads unmapped: other | 0.49% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1618416 1618416 1618416 N_multimapping 443739 443739 443739 N_noFeature 1551208 34263412 1921108 N_ambiguous 748257 4057 116011 UnstrandedReadsAssigned:32967027 PositiveStrandReadsAssigned:999023 NegativeStrandReadsAssigned:33229373 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=144 echo kmer=139 SRR13165377 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: SRR13165377-trimmed-pair1.fastq SRR13165377-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,328,224 reads, 33,936,284 reads pseudoaligned [quant] estimated average fragment length: 231.363 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,218 rounds 52973 SRR13165377.ke.tsv 35125 SRR13165377.se.tsv 88098 total ==> SRR13165377.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 706.152 0 0 PNS24247 1044 813.637 172.277 9.58386 PNS24249 1928 1697.64 289.491 7.7185 PNS24246 1044 813.637 172.277 9.58386 PNS24248 1044 813.637 172.277 9.58386 PNS24244 1471 1240.64 269.677 9.8388 PNS24243 293 115.296 0 0 KQK14069 1603 1372.64 57475.2 1895.25 KQK14071 474 262.108 829.82 143.3 ==> SRR13165377.se.tsv <== BRADI_1g14170v3 60980 BRADI_1g53295v3 731 BRADI_1g59795v3 1430 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 888 BRADI_1g74790v3 1031 BRADI_1g09890v3 0 BRADI_1g77505v3 576 BRADI_1g48960v3 0 SRR13165377 completed mapping pipeline successfully