Starting /dee2/code/volunteer_pipeline.sh SRR12951305 current disk space = 1543218630656 free memory = 1601475488 SRR12951305 SRAfilesize eba074587aaa1b7621b09e38110197bc SRR12951305.sra SRR12951305.sra file validated SRR12951305 is paired end SRR12951305 is conventional basespace SRR12951305 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951305_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5395 37.0 37.0 37.0 37.0 37.0 2 36.23775 37.0 37.0 37.0 37.0 37.0 3 36.5595 37.0 37.0 37.0 37.0 37.0 4 36.634 37.0 37.0 37.0 37.0 37.0 5 36.7045 37.0 37.0 37.0 37.0 37.0 6 36.6335 37.0 37.0 37.0 37.0 37.0 7 36.6135 37.0 37.0 37.0 37.0 37.0 8 36.6365 37.0 37.0 37.0 37.0 37.0 9 36.5635 37.0 37.0 37.0 37.0 37.0 10-14 36.586600000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.5435 37.0 37.0 37.0 37.0 37.0 20-24 36.5142 37.0 37.0 37.0 37.0 37.0 25-29 36.535000000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5056 37.0 37.0 37.0 37.0 37.0 35-39 36.4744 37.0 37.0 37.0 37.0 37.0 40-44 36.4692 37.0 37.0 37.0 37.0 37.0 45-49 36.3865 37.0 37.0 37.0 37.0 37.0 50-54 36.42620000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.326299999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.294599999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.227199999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.3019 37.0 37.0 37.0 37.0 37.0 75-79 36.3051 37.0 37.0 37.0 37.0 37.0 80-84 36.3166 37.0 37.0 37.0 37.0 37.0 85-89 36.2414 37.0 37.0 37.0 37.0 37.0 90-94 36.2755 37.0 37.0 37.0 37.0 37.0 95-99 36.2587 37.0 37.0 37.0 37.0 37.0 100-104 36.2902 37.0 37.0 37.0 37.0 37.0 105-109 36.3104 37.0 37.0 37.0 37.0 37.0 110-114 36.248 37.0 37.0 37.0 37.0 37.0 115-119 36.176100000000005 37.0 37.0 37.0 37.0 37.0 120-124 36.131800000000005 37.0 37.0 37.0 37.0 37.0 125-129 36.0685 37.0 37.0 37.0 37.0 37.0 130-134 36.0659 37.0 37.0 37.0 37.0 37.0 135-139 36.0674 37.0 37.0 37.0 37.0 37.0 140-144 35.892 37.0 37.0 37.0 37.0 37.0 145-149 35.8505 37.0 37.0 37.0 37.0 37.0 150-151 35.77825 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 2.0 24 1.0 25 2.0 26 7.0 27 8.0 28 7.0 29 17.0 30 18.0 31 45.0 32 40.0 33 73.0 34 127.0 35 274.0 36 2832.0 37 547.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.8 10.975 5.975 34.25 2 21.243392902089102 11.678832116788321 32.54467656682608 34.533098414296504 3 21.224999999999998 16.625 25.575 36.575 4 25.624999999999996 21.425 22.75 30.2 5 26.0 28.225 22.35 23.425 6 25.724999999999998 30.325000000000003 21.925 22.025 7 17.974999999999998 24.875 36.85 20.3 8 21.45 23.9 28.925 25.724999999999998 9 21.175 21.3 32.2 25.324999999999996 10-14 23.44 25.81 25.05 25.7 15-19 23.64 24.92 24.72 26.72 20-24 23.82 25.22 25.155 25.805 25-29 23.735 25.055 24.834999999999997 26.375 30-34 23.244999999999997 24.62 26.064999999999998 26.07 35-39 24.125 24.48 25.174999999999997 26.22 40-44 24.095 24.335 24.91 26.66 45-49 23.755000000000003 25.575 24.65 26.02 50-54 24.645 24.595 24.87 25.89 55-59 24.43 24.41 25.124999999999996 26.035000000000004 60-64 23.74 24.654999999999998 25.455 26.150000000000002 65-69 24.4 24.65 24.245 26.705000000000002 70-74 25.035 24.465 24.26 26.240000000000002 75-79 24.785 24.995 24.07 26.150000000000002 80-84 24.925 24.54 24.235 26.3 85-89 25.074999999999996 23.47 24.759999999999998 26.695 90-94 24.69 24.91 24.515 25.885 95-99 25.385 23.715 24.65 26.25 100-104 25.35 24.605 23.595 26.450000000000003 105-109 25.165 24.33 24.12 26.384999999999998 110-114 25.330000000000002 24.645 24.03 25.995 115-119 25.0 24.98 23.875 26.145000000000003 120-124 25.2 24.72 24.23 25.85 125-129 25.185000000000002 24.39 24.075 26.35 130-134 25.490000000000002 24.905 23.06 26.545 135-139 25.3 24.44 23.34 26.919999999999998 140-144 25.14 24.349999999999998 24.01 26.5 145-149 25.605 23.919999999999998 23.625 26.85 150-151 25.7125 24.6875 23.150000000000002 26.450000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 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 0.5 24 1.0 25 1.0 26 1.0 27 1.5 28 4.0 29 4.5 30 5.5 31 11.5 32 15.0 33 19.0 34 24.0 35 30.0 36 41.5 37 59.0 38 68.5 39 80.0 40 123.0 41 138.5 42 140.5 43 169.0 44 180.5 45 190.5 46 187.5 47 175.0 48 178.5 49 178.0 50 172.0 51 147.0 52 131.5 53 128.0 54 113.5 55 99.0 56 88.0 57 84.5 58 69.0 59 63.5 60 65.5 61 61.5 62 65.5 63 63.0 64 60.0 65 66.0 66 62.0 67 55.0 68 59.0 69 52.0 70 48.0 71 44.0 72 32.5 73 30.5 74 27.0 75 17.5 76 17.5 77 21.0 78 13.0 79 4.5 80 1.5 81 2.5 82 2.5 83 1.5 84 0.5 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 0.675 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 79.75 #Duplication Level Percentage of deduplicated Percentage of total 1 81.31661442006269 64.85 2 14.420062695924765 23.0 3 2.978056426332288 7.124999999999999 4 0.8150470219435737 2.6 5 0.3448275862068966 1.375 6 0.09404388714733543 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.031347962382445145 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTCAGTTATCTCGTAT 24 0.6 TruSeq Adapter, Index 23 (97% over 37bp) CGGGAAAATGACAGTAAAACACTATCTTGGATGATGCCTTTAGTTTAAGT 6 0.15 No Hit GTGGCCAACTATCCTGGATAAGTAGCATTTTTTGGGGGGTAGGGGGGTTT 6 0.15 No Hit TGAGGAGGTGGATGATCTCCATGGTGTGCTTGATGATGCGGACGGCCATG 6 0.15 No Hit CGGCGCGGGGGCGTAGCGGGCGGCGTAGGAGGCGCTGTGGGAGCGGAGGT 5 0.125 No Hit GCAGCATTTAATCTGATGTTTTTGTTCAAATCTAGAAAACTACAATGAGC 5 0.125 No Hit GTTGTCCATGGAGACACCGATGGGGGTGCCCTGGAAGTTACCACCGTGGA 5 0.125 No Hit GTTATGAAGTATGATGCAAGCTTGCATGATTTTTCCTAGAGTTGCTTGCT 5 0.125 No Hit CGTAATTTGGCTCTTCATCAAACTTCATATTAGAGACCATCTCAAAAAAA 5 0.125 No Hit ATTGGCCAGAGGCTGTTCACCTTGGAGACCTGATGCGGTTATGAGTACGA 5 0.125 No Hit CCCCTCTCTCCGGCCGCTCGCCCAAATCAACCAACCACCGGACCAAATCA 5 0.125 No Hit CAGTTCTCGGCGAGGTGGAAGAGGTGAGCGTGGTCGAGGGAGAGGCCGCT 5 0.125 No Hit GGCCGCCCTCCCTGCTCTGCTCGGCACCGTGAGCAACGCCGTTCTCCTTT 5 0.125 No Hit GGGTTGCTGATCTTTCAGTCTGACATAGGTACTATGTAAAATGAACACAG 5 0.125 No Hit GTGGGGAATTCCTTGGATCTTCTTGCCGGTGACCGGGCATTTCGGCCCAC 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 0.0125 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 0.025 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 0.0625 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.16249999999999998 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.44999999999999996 0.0 0.0 0.0 0.0 78-79 0.5375000000000001 0.0 0.0 0.0 0.0 80-81 0.6625 0.0 0.0 0.0 0.0 82-83 0.85 0.0 0.0 0.0 0.0 84-85 0.9625 0.0 0.0 0.0 0.0 86-87 1.125 0.0 0.0 0.0 0.0 88-89 1.2625 0.0 0.0 0.0 0.0 90-91 1.475 0.0 0.0 0.0 0.0 92-93 1.675 0.0 0.0 0.0 0.0 94-95 1.8625 0.0 0.0 0.0 0.0 96-97 2.0625 0.0 0.0 0.0 0.0 98-99 2.4 0.0 0.0 0.0 0.0 100-101 2.7 0.0 0.0 0.0 0.0 102-103 3.15 0.0 0.0 0.0 0.0 104-105 3.4000000000000004 0.0 0.0 0.0 0.0 106-107 3.5999999999999996 0.0 0.0 0.0 0.0 108-109 3.9375 0.0 0.0 0.0 0.0 110-111 4.35 0.0 0.0 0.0 0.0 112-113 5.0125 0.0 0.0 0.0 0.0 114-115 5.4625 0.0 0.0 0.0 0.0 116-117 6.025 0.0 0.0 0.0 0.0 118-119 6.6 0.0 0.0 0.0 0.0 120-121 7.175000000000001 0.0 0.0 0.0 0.0 122-123 7.487500000000001 0.0 0.0 0.0 0.0 124-125 8.1875 0.0 0.0 0.0 0.0 126-127 8.725 0.0 0.0 0.0 0.0 128-129 9.5625 0.0 0.0 0.0 0.0 130-131 10.3875 0.0 0.0 0.0 0.0 132-133 10.8875 0.0 0.0 0.0 0.0 134-135 11.4875 0.0 0.0 0.0 0.0 136-137 12.399999999999999 0.0 0.0 0.0 0.0 138-139 12.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGAAT 10 0.006830828 145.0 1 AATTAGT 10 0.006830828 145.0 9 AGAATCA 10 0.006830828 145.0 3 CTGAACA 10 0.006830828 145.0 7 ATCAATT 10 0.006830828 145.0 6 TAGAATC 10 0.006830828 145.0 2 TCCAGTC 45 0.008957279 48.333332 145 >>END_MODULE SRR12951305 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951305_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2165 37.0 37.0 37.0 37.0 37.0 2 35.9775 37.0 37.0 37.0 37.0 37.0 3 35.813 37.0 37.0 37.0 37.0 37.0 4 35.8685 37.0 37.0 37.0 37.0 37.0 5 36.103 37.0 37.0 37.0 37.0 37.0 6 36.0495 37.0 37.0 37.0 37.0 37.0 7 36.002 37.0 37.0 37.0 37.0 37.0 8 36.016 37.0 37.0 37.0 37.0 37.0 9 35.951 37.0 37.0 37.0 37.0 37.0 10-14 36.0092 37.0 37.0 37.0 37.0 37.0 15-19 35.9738 37.0 37.0 37.0 37.0 37.0 20-24 35.9163 37.0 37.0 37.0 37.0 37.0 25-29 35.817 37.0 37.0 37.0 37.0 37.0 30-34 35.76649999999999 37.0 37.0 37.0 37.0 37.0 35-39 35.7039 37.0 37.0 37.0 37.0 37.0 40-44 35.7429 37.0 37.0 37.0 37.0 37.0 45-49 35.7008 37.0 37.0 37.0 37.0 37.0 50-54 35.6553 37.0 37.0 37.0 37.0 37.0 55-59 35.669799999999995 37.0 37.0 37.0 37.0 37.0 60-64 35.65089999999999 37.0 37.0 37.0 37.0 37.0 65-69 35.593399999999995 37.0 37.0 37.0 37.0 37.0 70-74 35.5788 37.0 37.0 37.0 37.0 37.0 75-79 35.5869 37.0 37.0 37.0 37.0 37.0 80-84 35.5382 37.0 37.0 37.0 37.0 37.0 85-89 35.5827 37.0 37.0 37.0 37.0 37.0 90-94 35.576800000000006 37.0 37.0 37.0 37.0 37.0 95-99 35.6152 37.0 37.0 37.0 37.0 37.0 100-104 35.4957 37.0 37.0 37.0 37.0 37.0 105-109 35.5044 37.0 37.0 37.0 37.0 37.0 110-114 35.4336 37.0 37.0 37.0 37.0 37.0 115-119 35.5058 37.0 37.0 37.0 37.0 37.0 120-124 35.4195 37.0 37.0 37.0 34.6 37.0 125-129 35.3692 37.0 37.0 37.0 37.0 37.0 130-134 35.262299999999996 37.0 37.0 37.0 34.6 37.0 135-139 35.1495 37.0 37.0 37.0 29.8 37.0 140-144 35.0724 37.0 37.0 37.0 27.4 37.0 145-149 34.8784 37.0 37.0 37.0 25.0 37.0 150-151 34.6165 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 7.0 14 10.0 15 6.0 16 4.0 17 3.0 18 6.0 19 5.0 20 9.0 21 13.0 22 6.0 23 16.0 24 13.0 25 6.0 26 13.0 27 17.0 28 22.0 29 20.0 30 33.0 31 25.0 32 52.0 33 103.0 34 211.0 35 532.0 36 2561.0 37 305.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.875 20.175 8.05 25.900000000000002 2 31.15 21.975 24.525 22.35 3 25.624999999999996 24.85 27.474999999999998 22.05 4 28.075 29.425 19.925 22.575 5 29.675 31.8 18.375 20.150000000000002 6 25.474999999999998 33.675 19.1 21.75 7 24.0 19.725 32.675 23.599999999999998 8 24.875 21.975 25.624999999999996 27.525 9 24.625 21.3 26.724999999999998 27.35 10-14 27.62 24.91 22.235 25.235000000000003 15-19 27.525 24.55 22.785 25.14 20-24 27.060000000000002 24.45 23.25 25.240000000000002 25-29 26.950000000000003 25.369999999999997 22.835 24.845 30-34 27.029999999999998 25.03 23.175 24.765 35-39 25.915 25.095 23.555 25.435000000000002 40-44 26.369999999999997 25.005 23.82 24.805 45-49 27.425 24.205 23.535 24.834999999999997 50-54 27.16 24.79 23.825 24.224999999999998 55-59 27.66 24.349999999999998 23.74 24.25 60-64 27.54 24.255 24.415 23.79 65-69 27.66 24.68 23.79 23.87 70-74 27.625 24.73 23.485 24.16 75-79 27.250000000000004 25.635 23.205000000000002 23.91 80-84 27.555000000000003 24.545 23.69 24.21 85-89 27.55 25.014999999999997 22.695 24.740000000000002 90-94 28.249999999999996 24.75 22.855 24.145 95-99 27.67 25.290000000000003 22.62 24.42 100-104 27.87 24.805 23.285 24.04 105-109 27.950000000000003 25.135 22.634999999999998 24.279999999999998 110-114 28.084999999999997 25.235000000000003 23.1 23.580000000000002 115-119 28.46 25.11 22.67 23.76 120-124 27.905 25.46 22.845 23.79 125-129 29.01 25.629999999999995 22.11 23.25 130-134 28.785 24.865000000000002 22.939999999999998 23.41 135-139 29.220000000000002 25.290000000000003 22.225 23.265 140-144 29.799999999999997 25.080000000000002 22.345000000000002 22.775000000000002 145-149 30.464999999999996 24.445 22.765 22.325 150-151 31.0125 23.9125 22.875 22.2 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.5 8 1.0 9 1.5 10 1.0 11 0.5 12 1.0 13 0.5 14 0.0 15 2.0 16 2.0 17 0.0 18 1.0 19 1.5 20 0.5 21 0.5 22 1.5 23 1.0 24 0.5 25 1.0 26 2.0 27 2.0 28 4.0 29 5.5 30 5.5 31 6.0 32 9.0 33 15.0 34 18.5 35 24.5 36 35.5 37 50.0 38 74.0 39 83.0 40 99.5 41 136.5 42 154.5 43 164.0 44 175.5 45 184.0 46 174.0 47 164.0 48 173.5 49 150.5 50 122.5 51 125.5 52 121.5 53 111.0 54 106.0 55 103.0 56 91.0 57 80.5 58 90.5 59 91.0 60 76.0 61 74.5 62 68.0 63 67.5 64 65.5 65 58.0 66 66.5 67 68.5 68 60.0 69 57.0 70 55.5 71 55.0 72 43.0 73 35.5 74 38.5 75 27.0 76 19.0 77 17.0 78 11.5 79 6.0 80 2.5 81 1.0 82 2.0 83 3.5 84 3.0 85 1.0 86 0.5 87 1.5 88 1.0 89 1.5 90 2.0 91 0.5 92 0.5 93 1.0 94 1.0 95 3.0 96 3.5 97 2.5 98 4.5 99 5.0 100 9.0 >>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 0.0 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 80.85 #Duplication Level Percentage of deduplicated Percentage of total 1 82.6530612244898 66.825 2 13.172541743970315 21.3 3 2.937538651824366 7.124999999999999 4 0.7421150278293136 2.4 5 0.3401360544217687 1.375 6 0.12368583797155226 0.6 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.030921459492888066 0.375 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 15 0.375 No Hit CGAGCGACAGCGGCGCAGGTCTCTGCCGCCCCTCTTCCTCTTTCTCTCTT 6 0.15 No Hit GGTGGGTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGT 6 0.15 No Hit GTTTCTCTTCTCTCCGCCGCCGGCGCCGCGTCTTCCCGCGCGAACCATCG 6 0.15 No Hit GGAAGAGATGCGCAGGAAAGCCCAAGCTGCTGCTCAGGAGGCGTACGACG 6 0.15 No Hit CCCAAAACCAGTACGAAGCCCTTCTTCCTCTGAATCTTGAACCCCCGAAT 5 0.125 No Hit GGAAGGAAGCTCCTACATGAAGGAGGCAAAGAAGCAAGGCGAGCTCGACC 5 0.125 No Hit CCTCATCAAGGACAAATACGTAGCCCTACCCAACATTCTCGGGTTCGCCT 5 0.125 No Hit GGAGACTGCTGGGGCATACAAAGTCGCGGTCCTCAACAGGAAGAGGCCAT 5 0.125 No Hit TGAAAGGTCAAGGTCCTCATGTGCAATTCTCCGTCAACAGGACCCAATAC 5 0.125 No Hit GCAAAGCGAAAAAGCGCCGCCCGACGGAAACGGGGTGCGGCGGCGATGTT 5 0.125 No Hit GGTTGGACCGTATGCTGTACGTAGGACTTACAGAAGATCATGAAGAATCT 5 0.125 No Hit GCCGATCCTAAGGGACGGGGTAACCCCGGCAGATAGCGCGATCACGCGTA 5 0.125 No Hit AGAAGCTTTTCCTCATTGATCTTGGTTTAGCATCCAAGTGGAAAAAAGCA 5 0.125 No Hit CCCTGCTGCTACCAAGAAGGATGCTACTGAGACATTGCAGGATGGTGATG 5 0.125 No Hit CAACAAACACGTCGGCATACCACACAGAGCAGAGACAGAGAGAGCGAGCC 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 0.0125 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 0.025 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 0.0625 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.16249999999999998 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.44999999999999996 0.0 0.0 0.0 0.0 78-79 0.55 0.0 0.0 0.0 0.0 80-81 0.6875 0.0 0.0 0.0 0.0 82-83 0.875 0.0 0.0 0.0 0.0 84-85 0.975 0.0 0.0 0.0 0.0 86-87 1.1375000000000002 0.0 0.0 0.0 0.0 88-89 1.2875 0.0 0.0 0.0 0.0 90-91 1.5 0.0 0.0 0.0 0.0 92-93 1.7 0.0 0.0 0.0 0.0 94-95 1.8875 0.0 0.0 0.0 0.0 96-97 2.0875 0.0 0.0 0.0 0.0 98-99 2.425 0.0 0.0 0.0 0.0 100-101 2.7249999999999996 0.0 0.0 0.0 0.0 102-103 3.2 0.0 0.0 0.0 0.0 104-105 3.45 0.0 0.0 0.0 0.0 106-107 3.6500000000000004 0.0 0.0 0.0 0.0 108-109 3.9875 0.0 0.0 0.0 0.0 110-111 4.4 0.0 0.0 0.0 0.0 112-113 5.075 0.0 0.0 0.0 0.0 114-115 5.5375 0.0 0.0 0.0 0.0 116-117 6.1 0.0 0.0 0.0 0.0 118-119 6.675 0.0 0.0 0.0 0.0 120-121 7.275 0.0 0.0 0.0 0.0 122-123 7.612500000000001 0.0 0.0 0.0 0.0 124-125 8.3125 0.0 0.0 0.0 0.0 126-127 8.85 0.0 0.0 0.0 0.0 128-129 9.7125 0.0 0.0 0.0 0.0 130-131 10.5625 0.0 0.0 0.0 0.0 132-133 11.075 0.0 0.0 0.0 0.0 134-135 11.725000000000001 0.0 0.0 0.0 0.0 136-137 12.6875 0.0 0.0 0.0 0.0 138-139 13.2125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATTGCC 10 0.006830828 145.0 7 >>END_MODULE Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569447 spots for SRR12951305.sra Written 1569447 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra Read 1569446 spots for SRR12951305.sra Written 1569446 spots for SRR12951305.sra SRR ids: ['SRR12951305.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_siog09jc SRR12951305.sra spots: 31388921 blocks: [[1, 1569446], [1569447, 3138892], [3138893, 4708338], [4708339, 6277784], [6277785, 7847230], [7847231, 9416676], [9416677, 10986122], [10986123, 12555568], [12555569, 14125014], [14125015, 15694460], [15694461, 17263906], [17263907, 18833352], [18833353, 20402798], [20402799, 21972244], [21972245, 23541690], [23541691, 25111136], [25111137, 26680582], [26680583, 28250028], [28250029, 29819474], [29819475, 31388921]] SRR12951305 file size 10645628 SRR12951305 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 SRR12951305 SRR12951305_1.fastq SRR12951305_2.fastq Input file: SRR12951305_1.fastq Paired file: SRR12951305_2.fastq trimmed: SRR12951305-trimmed-pair1.fastq, SRR12951305-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 11:14:59 2024 >> started Sat Dec 7 11:15:48 2024 >> done (48.844s) 31388921 read pairs processed; of these: 222 ( 0.00%) short read pairs filtered out after trimming by size control 104520 ( 0.33%) empty read pairs filtered out after trimming by size control 31284179 (99.67%) read pairs available; of these: 5188258 (16.58%) trimmed read pairs available after processing 26095921 (83.42%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 18 0.00% 20 19 0.00% 21 28 0.00% 22 32 0.00% 23 31 0.00% 24 30 0.00% 25 60 0.00% 26 54 0.00% 27 60 0.00% 28 75 0.00% 29 59 0.00% 30 63 0.00% 31 70 0.00% 32 61 0.00% 33 81 0.00% 34 82 0.00% 35 61 0.00% 36 85 0.00% 37 103 0.00% 38 106 0.00% 39 101 0.00% 40 138 0.00% 41 119 0.00% 42 125 0.00% 43 148 0.00% 44 127 0.00% 45 162 0.00% 46 167 0.00% 47 179 0.00% 48 232 0.00% 49 290 0.00% 50 312 0.00% 51 353 0.00% 52 412 0.00% 53 383 0.00% 54 425 0.00% 55 526 0.00% 56 552 0.00% 57 664 0.00% 58 798 0.00% 59 845 0.00% 60 1037 0.00% 61 1256 0.00% 62 1385 0.00% 63 1567 0.01% 64 1611 0.01% 65 1929 0.01% 66 2016 0.01% 67 2228 0.01% 68 2620 0.01% 69 2965 0.01% 70 3592 0.01% 71 4040 0.01% 72 4899 0.02% 73 5295 0.02% 74 5973 0.02% 75 6572 0.02% 76 7027 0.02% 77 7623 0.02% 78 8522 0.03% 79 9603 0.03% 80 10634 0.03% 81 12111 0.04% 82 13948 0.04% 83 15475 0.05% 84 16221 0.05% 85 18231 0.06% 86 19048 0.06% 87 20004 0.06% 88 21504 0.07% 89 22927 0.07% 90 24987 0.08% 91 26983 0.09% 92 29619 0.09% 93 32025 0.10% 94 33827 0.11% 95 36325 0.12% 96 37958 0.12% 97 38822 0.12% 98 40223 0.13% 99 41691 0.13% 100 44203 0.14% 101 45825 0.15% 102 48057 0.15% 103 51809 0.17% 104 54256 0.17% 105 56266 0.18% 106 57969 0.19% 107 58883 0.19% 108 59674 0.19% 109 61291 0.20% 110 63071 0.20% 111 65727 0.21% 112 69001 0.22% 113 71269 0.23% 114 75117 0.24% 115 77217 0.25% 116 78581 0.25% 117 79240 0.25% 118 81315 0.26% 119 81625 0.26% 120 82282 0.26% 121 84431 0.27% 122 86467 0.28% 123 89472 0.29% 124 94032 0.30% 125 95012 0.30% 126 96936 0.31% 127 97713 0.31% 128 98231 0.31% 129 99811 0.32% 130 98501 0.31% 131 100342 0.32% 132 102615 0.33% 133 105434 0.34% 134 108387 0.35% 135 109722 0.35% 136 112390 0.36% 137 111318 0.36% 138 112184 0.36% 139 112988 0.36% 140 112935 0.36% 141 113463 0.36% 142 114753 0.37% 143 117201 0.37% 144 118276 0.38% 145 120544 0.39% 146 121998 0.39% 147 121699 0.39% 148 121725 0.39% 149 122436 0.39% 150 121988 0.39% 151 26095921 83.42% 31284179 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=12.81 fanout-score-rank=11 prefix-density=0.10 prefix-fanout=12.8 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTCAGTTATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.05 sequence-density-rank=27 fanout-score=252.57 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=21.6 sequence=CGCCGCCGCCACCACGGGACTGCGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCCCTCGATGGCGTCGCGCATCGACTGCTCGCTGGCGAAGGTGACGAAGCCGAACCCGCGGGAACGGCCAGTCTCCCTGTCGTTGATGATCTTGGAGTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCGTCGGTAGCCCAGGCGAGGCCGCCCACGAAGCAACGGTACTCAACTTCCGCCATTCCTCCCACTAAACCCTAACGAACCGGAACC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=34 prefix-density=0.67 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.09 sequence-density-rank=19 fanout-score=230.66 fanout-score-rank=1 prefix-density=0.97 prefix-fanout=22.1 sequence=CGCCGCCGCCGA SRR12951305 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:16:37 Started mapping on | Dec 07 11:16:37 Finished on | Dec 07 11:20:12 Mapping speed, Million of reads per hour | 523.83 Number of input reads | 31284179 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 28520045 Uniquely mapped reads % | 91.16% Average mapped length | 292.03 Number of splices: Total | 26238409 Number of splices: Annotated (sjdb) | 24246239 Number of splices: GT/AG | 25845634 Number of splices: GC/AG | 337558 Number of splices: AT/AC | 17467 Number of splices: Non-canonical | 37750 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.60 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 267753 % of reads mapped to multiple loci | 0.86% Number of reads mapped to too many loci | 121003 % of reads mapped to too many loci | 0.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.60% % of reads unmapped: other | 1.99% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2496381 2496381 2496381 N_multimapping 267753 267753 267753 N_noFeature 1394933 27659883 1707493 N_ambiguous 635321 4121 87733 UnstrandedReadsAssigned:26489791 PositiveStrandReadsAssigned:856041 NegativeStrandReadsAssigned:26724819 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951305 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: SRR12951305-trimmed-pair1.fastq SRR12951305-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,284,179 reads, 27,329,330 reads pseudoaligned [quant] estimated average fragment length: 244.89 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,201 rounds 52973 SRR12951305.ke.tsv 35125 SRR12951305.se.tsv 88098 total ==> SRR12951305.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 692.594 0 0 PNS24247 1044 800.11 186.313 12.5836 PNS24249 1928 1684.11 441.589 14.1696 PNS24246 1044 800.11 186.313 12.5836 PNS24248 1044 800.11 186.313 12.5836 PNS24244 1471 1227.11 217.472 9.577 PNS24243 293 107.102 0 0 KQK14069 1603 1359.11 61415 2441.91 KQK14071 474 249.779 367.943 79.6041 ==> SRR12951305.se.tsv <== BRADI_1g14170v3 61669 BRADI_1g53295v3 266 BRADI_1g59795v3 1016 BRADI_1g07683v3 0 BRADI_1g00485v3 28 BRADI_1g20270v3 615 BRADI_1g74790v3 2413 BRADI_1g09890v3 0 BRADI_1g77505v3 396 BRADI_1g48960v3 0 SRR12951305 completed mapping pipeline successfully