Starting /dee2/code/volunteer_pipeline.sh SRR12951296 current disk space = 1543337689088 free memory = 1606421108 SRR12951296 SRAfilesize 188273a0be54293d91f31b02604883eb SRR12951296.sra SRR12951296.sra file validated SRR12951296 is paired end SRR12951296 is conventional basespace SRR12951296 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951296_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 57 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5115 37.0 37.0 37.0 37.0 37.0 2 36.206 37.0 37.0 37.0 37.0 37.0 3 36.478 37.0 37.0 37.0 37.0 37.0 4 36.537 37.0 37.0 37.0 37.0 37.0 5 36.6345 37.0 37.0 37.0 37.0 37.0 6 36.584 37.0 37.0 37.0 37.0 37.0 7 36.584 37.0 37.0 37.0 37.0 37.0 8 36.4535 37.0 37.0 37.0 37.0 37.0 9 36.6395 37.0 37.0 37.0 37.0 37.0 10-14 36.558099999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.5518 37.0 37.0 37.0 37.0 37.0 20-24 36.5121 37.0 37.0 37.0 37.0 37.0 25-29 36.4829 37.0 37.0 37.0 37.0 37.0 30-34 36.4806 37.0 37.0 37.0 37.0 37.0 35-39 36.4213 37.0 37.0 37.0 37.0 37.0 40-44 36.0347 37.0 37.0 37.0 34.6 37.0 45-49 34.7005 37.0 37.0 37.0 24.2 37.0 50-54 34.5377 37.0 37.0 37.0 24.2 37.0 55-59 33.1953 37.0 37.0 37.0 13.8 37.0 60-64 33.3771 37.0 37.0 37.0 16.6 37.0 65-69 33.0912 37.0 37.0 37.0 13.8 37.0 70-74 33.940099999999994 37.0 37.0 37.0 21.8 37.0 75-79 36.052099999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.2471 37.0 37.0 37.0 37.0 37.0 85-89 36.2299 37.0 37.0 37.0 37.0 37.0 90-94 36.2827 37.0 37.0 37.0 37.0 37.0 95-99 36.285000000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.2698 37.0 37.0 37.0 37.0 37.0 105-109 36.2238 37.0 37.0 37.0 37.0 37.0 110-114 36.189099999999996 37.0 37.0 37.0 37.0 37.0 115-119 36.1882 37.0 37.0 37.0 37.0 37.0 120-124 36.1431 37.0 37.0 37.0 37.0 37.0 125-129 36.073800000000006 37.0 37.0 37.0 37.0 37.0 130-134 36.002 37.0 37.0 37.0 37.0 37.0 135-139 35.9312 37.0 37.0 37.0 37.0 37.0 140-144 35.8351 37.0 37.0 37.0 37.0 37.0 145-149 35.7896 37.0 37.0 37.0 37.0 37.0 150-151 35.581 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 3.0 24 3.0 25 4.0 26 5.0 27 6.0 28 17.0 29 25.0 30 31.0 31 48.0 32 102.0 33 524.0 34 191.0 35 282.0 36 2370.0 37 387.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 58.95 8.125 4.3999999999999995 28.525 2 19.61770623742455 24.069416498993963 27.03722334004024 29.275653923541245 3 18.8 11.55 35.925000000000004 33.725 4 21.625 17.75 17.375 43.25 5 37.85 21.224999999999998 18.925 22.0 6 37.724999999999994 25.6 18.675 18.0 7 16.925 35.15 31.15 16.775000000000002 8 19.275000000000002 33.775 22.8 24.15 9 34.325 16.075 26.200000000000003 23.400000000000002 10-14 24.654999999999998 26.83 20.18 28.335 15-19 24.77 22.245 23.94 29.044999999999998 20-24 24.48 26.02 23.62 25.88 25-29 24.099999999999998 23.29 23.3 29.310000000000002 30-34 21.165 26.200000000000003 23.474999999999998 29.160000000000004 35-39 27.07 26.16 23.25 23.52 40-44 21.33 22.98 23.435 32.255 45-49 24.965 22.470000000000002 25.929999999999996 26.634999999999998 50-54 26.86 19.48 23.794999999999998 29.865000000000002 55-59 22.865 19.8 28.43 28.904999999999998 60-64 25.965 19.195 28.12 26.72 65-69 25.005 29.375 21.525 24.095 70-74 35.67 19.955000000000002 20.745 23.630000000000003 75-79 37.585 20.415 18.82 23.18 80-84 36.74 19.97 19.52 23.77 85-89 38.1 19.355 19.759999999999998 22.785 90-94 37.59 19.885 19.93 22.595000000000002 95-99 37.39 19.21 19.825 23.575 100-104 37.72 19.8 18.955 23.525 105-109 37.66 19.325 19.72 23.294999999999998 110-114 37.395 19.994999999999997 19.165 23.445 115-119 37.730000000000004 19.82 18.995 23.455000000000002 120-124 38.105 19.994999999999997 18.9 23.0 125-129 38.155 20.735 18.56 22.55 130-134 38.18 19.445 19.485 22.89 135-139 37.205 20.05 18.740000000000002 24.005000000000003 140-144 38.1 19.88 18.665000000000003 23.355 145-149 38.585 19.73 18.34 23.345 150-151 36.125 19.75 19.8625 24.2625 >>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 0.5 18 0.5 19 0.0 20 0.0 21 0.5 22 0.5 23 0.0 24 0.0 25 0.5 26 1.0 27 1.0 28 1.0 29 2.0 30 2.5 31 5.5 32 6.5 33 4.0 34 6.0 35 14.5 36 29.5 37 37.0 38 45.0 39 51.5 40 63.5 41 84.5 42 78.5 43 83.0 44 114.0 45 130.0 46 132.0 47 130.5 48 134.0 49 132.5 50 138.5 51 146.0 52 139.0 53 126.5 54 117.5 55 115.5 56 115.5 57 97.0 58 82.5 59 82.5 60 80.0 61 76.5 62 72.0 63 80.5 64 123.0 65 217.0 66 232.5 67 157.0 68 103.0 69 71.0 70 56.5 71 49.5 72 46.0 73 45.0 74 30.0 75 22.5 76 23.5 77 19.0 78 14.0 79 7.5 80 7.5 81 6.0 82 3.0 83 2.0 84 0.0 85 0.5 86 0.5 87 0.0 88 0.0 89 0.0 90 0.5 91 0.5 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 0.6 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 warn #Total Deduplicated Percentage 68.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 83.0707218761451 56.675 2 11.652620007328691 15.9 3 3.4811286185415904 7.124999999999999 4 0.8061561011359473 2.1999999999999997 5 0.29314767314034446 1.0 6 0.18321729571271528 0.75 7 0.21986075485525836 1.05 8 0.07328691828508611 0.4 9 0.0 0.0 >10 0.18321729571271528 2.5749999999999997 >50 0.0 0.0 >100 0.03664345914254306 12.325 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAATGCCATCTCGTAT 493 12.325 TruSeq Adapter, Index 2 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAATGCCATCGCGTAT 50 1.25 TruSeq Adapter, Index 2 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAATGCCATCTCGTTT 16 0.4 TruSeq Adapter, Index 2 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAATGCCATCTCGGAT 16 0.4 TruSeq Adapter, Index 2 (97% over 36bp) GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 11 0.27499999999999997 No Hit GCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTGCC 10 0.25 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 8 0.2 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 8 0.2 No Hit ACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGACG 7 0.17500000000000002 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 7 0.17500000000000002 No Hit GCCACATCCCGGCTCGGGAAATCTTAACCCGATTCCCTTTCGGGGGATAC 7 0.17500000000000002 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 7 0.17500000000000002 No Hit GCACTTGGAGTAGCGGAGGAGCCCGACGAGGGCGATCATGGAGGAAGTCC 7 0.17500000000000002 No Hit TGGACATTGATCATGGGCTTGTCACCAGGACCAGCAACAACCTTGAAGGG 7 0.17500000000000002 No Hit GTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCCCCCGA 6 0.15 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 6 0.15 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 6 0.15 No Hit GGGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGT 6 0.15 No Hit GNTCGGAAGAGCACACGTCTGAACTCCAGTCACAGAATGCCATCTCGTAT 6 0.15 TruSeq Adapter, Index 13 (97% over 35bp) CGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCAAGATCTGC 5 0.125 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 5 0.125 No Hit GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 5 0.125 No Hit TGCATATTTACATCGTCAGGATTTGATTGTAAACAAGCTCTCAATCTAAG 5 0.125 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 5 0.125 No Hit TTCTGATCTAGGGCGCCCAGCAGCATTCTGCTGCTCTCTAGCAGAATGCT 5 0.125 No Hit ATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGA 5 0.125 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.075 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 0.21250000000000002 0.0 0.0 0.0 0.0 68-69 0.2875 0.0 0.0 0.0 0.0 70-71 0.325 0.0 0.0 0.0 0.0 72-73 0.325 0.0 0.0 0.0 0.0 74-75 0.38749999999999996 0.0 0.0 0.0 0.0 76-77 0.425 0.0 0.0 0.0 0.0 78-79 0.5 0.0 0.0 0.0 0.0 80-81 0.575 0.0 0.0 0.0 0.0 82-83 0.6625000000000001 0.0 0.0 0.0 0.0 84-85 0.775 0.0 0.0 0.0 0.0 86-87 0.9375 0.0 0.0 0.0 0.0 88-89 1.275 0.0 0.0 0.0 0.0 90-91 1.5625 0.0 0.0 0.0 0.0 92-93 1.8875000000000002 0.0 0.0 0.0 0.0 94-95 2.0625 0.0 0.0 0.0 0.0 96-97 2.2249999999999996 0.0 0.0 0.0 0.0 98-99 2.4 0.0 0.0 0.0 0.0 100-101 2.6500000000000004 0.0 0.0 0.0 0.0 102-103 3.075 0.0 0.0 0.0 0.0 104-105 3.3875 0.0 0.0 0.0 0.0 106-107 3.8375 0.0 0.0 0.0 0.0 108-109 4.112500000000001 0.0 0.0 0.0 0.0 110-111 4.4 0.0 0.0 0.0 0.0 112-113 4.574999999999999 0.0 0.0 0.0 0.0 114-115 4.85 0.0 0.0 0.0 0.0 116-117 5.475 0.0 0.0 0.0 0.0 118-119 5.8125 0.0 0.0 0.0 0.0 120-121 6.175000000000001 0.0 0.0 0.0 0.0 122-123 6.7875 0.0 0.0 0.0 0.0 124-125 7.225 0.0 0.0 0.0 0.0 126-127 7.800000000000001 0.0 0.0 0.0 0.0 128-129 8.325 0.0 0.0 0.0 0.0 130-131 8.7625 0.0 0.0 0.0 0.0 132-133 9.4375 0.0 0.0 0.0 0.0 134-135 9.925 0.0 0.0 0.0 0.0 136-137 10.4375 0.0 0.0 0.0 0.0 138-139 11.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTA 10 0.006830828 145.0 4 TTCCTTT 10 0.006830828 145.0 8 GAGCACA 115 0.0 100.86957 9 TCGGAAG 120 0.0 96.666664 3 CGGAAGA 120 0.0 96.666664 4 AGAGCAC 120 0.0 96.666664 8 GATCGGA 130 0.0 94.807686 1 ATCGGAA 130 0.0 94.807686 2 AAGAGCA 125 0.0 92.799995 7 GAAGAGC 135 0.0 85.92592 6 GGAAGAG 135 0.0 85.92592 5 GAAAAGG 30 4.189703E-5 29.000002 65-69 TGAAAAG 30 4.189703E-5 29.000002 60-64 AAGGGGG 50 2.1536835E-9 29.0 65-69 AAAAGGG 35 3.5374105E-6 29.0 65-69 TGCTTGA 25 4.977651E-4 29.0 60-64 CTTGAAA 25 4.977651E-4 29.0 60-64 AAAGGGG 45 2.538036E-8 28.999998 65-69 CTTCTGC 55 5.9590093E-9 26.363636 55-59 CCATCTC 80 0.0 25.375 40-44 >>END_MODULE SRR12951296 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951296_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 59 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.07 37.0 37.0 37.0 37.0 37.0 2 35.9915 37.0 37.0 37.0 37.0 37.0 3 35.7405 37.0 37.0 37.0 37.0 37.0 4 35.906 37.0 37.0 37.0 37.0 37.0 5 35.96 37.0 37.0 37.0 37.0 37.0 6 36.052 37.0 37.0 37.0 37.0 37.0 7 35.3785 37.0 37.0 37.0 37.0 37.0 8 34.744 37.0 37.0 37.0 25.0 37.0 9 34.952 37.0 37.0 37.0 25.0 37.0 10-14 34.3198 37.0 37.0 37.0 25.0 37.0 15-19 34.3013 37.0 37.0 37.0 25.0 37.0 20-24 33.8793 37.0 37.0 37.0 22.2 37.0 25-29 32.8044 37.0 37.0 37.0 11.0 37.0 30-34 32.474599999999995 37.0 37.0 37.0 11.0 37.0 35-39 32.16289999999999 37.0 37.0 37.0 11.0 37.0 40-44 32.33290000000001 37.0 37.0 37.0 11.0 37.0 45-49 32.3327 37.0 37.0 37.0 11.0 37.0 50-54 32.4638 37.0 37.0 37.0 11.0 37.0 55-59 32.778000000000006 37.0 37.0 37.0 11.0 37.0 60-64 33.19970000000001 37.0 37.0 37.0 13.8 37.0 65-69 33.1082 37.0 37.0 37.0 13.8 37.0 70-74 32.533100000000005 37.0 37.0 37.0 11.0 37.0 75-79 32.243700000000004 37.0 37.0 37.0 11.0 37.0 80-84 32.5058 37.0 37.0 37.0 11.0 37.0 85-89 33.1961 37.0 37.0 37.0 16.6 37.0 90-94 34.21509999999999 37.0 37.0 37.0 25.0 37.0 95-99 34.676 37.0 37.0 37.0 25.0 37.0 100-104 34.94 37.0 37.0 37.0 25.0 37.0 105-109 35.0697 37.0 37.0 37.0 29.8 37.0 110-114 35.217600000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.2367 37.0 37.0 37.0 37.0 37.0 120-124 35.1986 37.0 37.0 37.0 37.0 37.0 125-129 35.221799999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.09439999999999 37.0 37.0 37.0 32.2 37.0 135-139 35.0377 37.0 37.0 37.0 32.2 37.0 140-144 34.9529 37.0 37.0 37.0 27.4 37.0 145-149 34.8437 37.0 37.0 37.0 25.0 37.0 150-151 34.6055 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 14.0 14 25.0 15 8.0 16 19.0 17 19.0 18 15.0 19 21.0 20 39.0 21 48.0 22 43.0 23 54.0 24 43.0 25 68.0 26 94.0 27 100.0 28 88.0 29 58.0 30 34.0 31 31.0 32 49.0 33 47.0 34 155.0 35 423.0 36 2253.0 37 250.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 57.275 17.8 5.775 19.15 2 42.699999999999996 19.45 19.325 18.525 3 37.35 19.7 21.6 21.349999999999998 4 40.025 25.124999999999996 15.174999999999999 19.675 5 41.099999999999994 26.174999999999997 15.45 17.275 6 38.550000000000004 25.75 16.375 19.325 7 38.0 17.375 25.424999999999997 19.2 8 36.35 18.15 19.75 25.75 9 38.35 17.974999999999998 20.875 22.8 10-14 40.02 20.575 17.71 21.695 15-19 38.975 20.4 19.05 21.575 20-24 38.21 21.205 19.265 21.32 25-29 37.614999999999995 21.279999999999998 19.45 21.654999999999998 30-34 36.125 21.085 21.105 21.685 35-39 33.37 22.355 22.615 21.66 40-44 36.845 21.52 20.05 21.584999999999997 45-49 35.06 21.735 21.37 21.834999999999997 50-54 36.05 21.044999999999998 21.029999999999998 21.875 55-59 36.945 21.654999999999998 20.005 21.395 60-64 38.605000000000004 21.205 19.03 21.16 65-69 38.05 21.04 19.38 21.529999999999998 70-74 37.72 21.75 19.1 21.43 75-79 35.745 22.56 19.585 22.11 80-84 36.504999999999995 21.335 20.47 21.69 85-89 38.01 20.215 19.485 22.29 90-94 38.415 20.47 19.325 21.790000000000003 95-99 39.085 20.51 19.265 21.14 100-104 39.945 21.145 18.81 20.1 105-109 40.03 20.21 18.915000000000003 20.845 110-114 40.315 20.71 18.315 20.66 115-119 40.475 20.03 18.505 20.990000000000002 120-124 40.38 20.585 18.41 20.625 125-129 40.095 20.685000000000002 17.54 21.68 130-134 41.22 20.53 17.825 20.424999999999997 135-139 41.355 20.28 18.17 20.195 140-144 41.52 20.97 17.72 19.79 145-149 42.76 20.57 16.865 19.805 150-151 43.3625 20.275000000000002 16.175 20.1875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 1.5 8 1.5 9 1.0 10 1.0 11 0.0 12 0.5 13 0.5 14 1.0 15 2.0 16 2.0 17 1.0 18 0.5 19 1.0 20 0.5 21 0.5 22 1.0 23 0.5 24 2.0 25 5.5 26 4.5 27 1.5 28 0.5 29 1.5 30 1.5 31 2.0 32 7.0 33 7.5 34 7.0 35 16.5 36 24.5 37 40.5 38 47.0 39 49.5 40 61.0 41 71.5 42 86.5 43 94.5 44 103.0 45 108.5 46 120.5 47 129.0 48 136.0 49 148.5 50 147.5 51 139.5 52 131.5 53 130.5 54 121.5 55 112.0 56 103.0 57 86.0 58 85.0 59 86.0 60 67.5 61 58.5 62 56.0 63 66.5 64 75.0 65 70.5 66 74.0 67 70.0 68 67.5 69 67.5 70 55.5 71 44.5 72 45.0 73 37.5 74 31.5 75 29.0 76 25.5 77 24.5 78 20.0 79 11.5 80 12.0 81 12.0 82 6.5 83 6.5 84 7.0 85 9.0 86 12.5 87 13.0 88 13.0 89 11.0 90 8.5 91 12.5 92 17.0 93 22.5 94 26.0 95 27.5 96 39.5 97 54.5 98 70.5 99 76.0 100 72.0 >>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 78.45 #Duplication Level Percentage of deduplicated Percentage of total 1 84.51242829827916 66.3 2 10.548119821542384 16.55 3 3.31421287444232 7.8 4 0.7648183556405354 2.4 5 0.3186743148502231 1.25 6 0.19120458891013384 0.8999999999999999 7 0.09560229445506692 0.525 8 0.03186743148502231 0.2 9 0.03186743148502231 0.22499999999999998 >10 0.15933715742511154 1.725 >50 0.03186743148502231 2.125 >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 fail #Sequence Count Percentage Possible Source GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 85 2.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGG 18 0.44999999999999996 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGG 16 0.4 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGG 15 0.375 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGGG 10 0.25 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGG 10 0.25 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAA 9 0.22499999999999998 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTGGGGGGGGGGG 8 0.2 No Hit ATCGACCTCGGCACGACGTACTCGTGCGTGGGCGTATGGCAGCACGACCG 7 0.17500000000000002 No Hit GGCCTGCCGCGGTCCGCGTCGCTGTGCCTGCGGGAGGTGCTCCTGGTGCT 7 0.17500000000000002 No Hit GTTAAAAAGCTCGTAGTTGGACTTTGGGCCGGGTCGGCCGGTCCGCCTCA 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGG 6 0.15 No Hit GCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTG 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 6 0.15 No Hit AGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGT 6 0.15 No Hit GAGACAGGTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCA 6 0.15 No Hit GTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGT 6 0.15 No Hit ATATTTTTCAACAATACGCCAATCTGCCAGACTCCGCTTTGCCTCGAACT 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGG 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGTGGGGGGGGGGG 5 0.125 No Hit GTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGT 5 0.125 No Hit GGGTACCATCCTGGAGTGTAGGTAGACCTGTAAATATTGTAGGGGCACTA 5 0.125 No Hit GTCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGT 5 0.125 No Hit CGTTATTTTACTTATTCCGTGGGTCGGAAGCGGGGCAAGTCCCCTCCTTT 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTGGGGGGGGGGGGG 5 0.125 No Hit GCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGCGAATGG 5 0.125 No Hit GCAGAACTGGCGATGCGGGATGAACCGGAAGCCGGGTTACGGTGCCCAAC 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 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.07500000000000001 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.2375 0.0 0.0 0.0 0.0 68-69 0.3125 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.45 0.0 0.0 0.0 0.0 78-79 0.525 0.0 0.0 0.0 0.0 80-81 0.6 0.0 0.0 0.0 0.0 82-83 0.6875 0.0 0.0 0.0 0.0 84-85 0.8 0.0 0.0 0.0 0.0 86-87 0.9624999999999999 0.0 0.0 0.0 0.0 88-89 1.3 0.0 0.0 0.0 0.0 90-91 1.5875 0.0 0.0 0.0 0.0 92-93 1.9125 0.0 0.0 0.0 0.0 94-95 2.0875000000000004 0.0 0.0 0.0 0.0 96-97 2.25 0.0 0.0 0.0 0.0 98-99 2.425 0.0 0.0 0.0 0.0 100-101 2.6875 0.0 0.0 0.0 0.0 102-103 3.125 0.0 0.0 0.0 0.0 104-105 3.425 0.0 0.0 0.0 0.0 106-107 3.8625 0.0 0.0 0.0 0.0 108-109 4.112500000000001 0.0 0.0 0.0 0.0 110-111 4.4 0.0 0.0 0.0 0.0 112-113 4.574999999999999 0.0 0.0 0.0 0.0 114-115 4.862500000000001 0.0 0.0 0.0 0.0 116-117 5.5 0.0 0.0 0.0 0.0 118-119 5.8375 0.0 0.0 0.0 0.0 120-121 6.15 0.0 0.0 0.0 0.0 122-123 6.7875 0.0 0.0 0.0 0.0 124-125 7.225 0.0 0.0 0.0 0.0 126-127 7.800000000000001 0.0 0.0 0.0 0.0 128-129 8.3375 0.0 0.0 0.0 0.0 130-131 8.8125 0.0 0.0 0.0 0.0 132-133 9.525 0.0 0.0 0.0 0.0 134-135 10.025 0.0 0.0 0.0 0.0 136-137 10.537500000000001 0.0 0.0 0.0 0.0 138-139 11.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGTG 170 0.007020358 7.6764703 30-34 >>END_MODULE Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005221 spots for SRR12951296.sra Written 2005221 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra Read 2005208 spots for SRR12951296.sra Written 2005208 spots for SRR12951296.sra SRR ids: ['SRR12951296.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bf8pk_6l SRR12951296.sra spots: 40104173 blocks: [[1, 2005208], [2005209, 4010416], [4010417, 6015624], [6015625, 8020832], [8020833, 10026040], [10026041, 12031248], [12031249, 14036456], [14036457, 16041664], [16041665, 18046872], [18046873, 20052080], [20052081, 22057288], [22057289, 24062496], [24062497, 26067704], [26067705, 28072912], [28072913, 30078120], [30078121, 32083328], [32083329, 34088536], [34088537, 36093744], [36093745, 38098952], [38098953, 40104173]] SRR12951296 file size 13607452 SRR12951296 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 SRR12951296 SRR12951296_1.fastq SRR12951296_2.fastq Input file: SRR12951296_1.fastq Paired file: SRR12951296_2.fastq trimmed: SRR12951296-trimmed-pair1.fastq, SRR12951296-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 10:58:22 2024 >> started Sat Dec 7 10:59:10 2024 >> done (47.469s) 40104173 read pairs processed; of these: 557 ( 0.00%) short read pairs filtered out after trimming by size control 5058541 (12.61%) empty read pairs filtered out after trimming by size control 35045075 (87.39%) read pairs available; of these: 6087148 (17.37%) trimmed read pairs available after processing 28957927 (82.63%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 32 0.00% 19 45 0.00% 20 61 0.00% 21 78 0.00% 22 100 0.00% 23 89 0.00% 24 123 0.00% 25 149 0.00% 26 159 0.00% 27 169 0.00% 28 236 0.00% 29 185 0.00% 30 227 0.00% 31 204 0.00% 32 263 0.00% 33 228 0.00% 34 271 0.00% 35 230 0.00% 36 265 0.00% 37 252 0.00% 38 307 0.00% 39 310 0.00% 40 301 0.00% 41 374 0.00% 42 411 0.00% 43 423 0.00% 44 419 0.00% 45 513 0.00% 46 482 0.00% 47 660 0.00% 48 693 0.00% 49 811 0.00% 50 899 0.00% 51 1016 0.00% 52 1160 0.00% 53 1247 0.00% 54 1446 0.00% 55 1679 0.00% 56 1796 0.01% 57 2062 0.01% 58 2547 0.01% 59 2776 0.01% 60 3226 0.01% 61 3638 0.01% 62 4362 0.01% 63 4873 0.01% 64 4891 0.01% 65 5431 0.02% 66 6078 0.02% 67 6684 0.02% 68 7852 0.02% 69 8357 0.02% 70 9589 0.03% 71 10453 0.03% 72 12097 0.03% 73 13159 0.04% 74 14002 0.04% 75 14657 0.04% 76 15929 0.05% 77 17290 0.05% 78 18178 0.05% 79 19816 0.06% 80 20891 0.06% 81 22795 0.07% 82 24463 0.07% 83 26181 0.07% 84 27611 0.08% 85 29269 0.08% 86 31804 0.09% 87 32319 0.09% 88 33905 0.10% 89 34350 0.10% 90 35991 0.10% 91 38616 0.11% 92 41074 0.12% 93 43569 0.12% 94 44750 0.13% 95 47224 0.13% 96 49401 0.14% 97 49177 0.14% 98 51924 0.15% 99 55358 0.16% 100 55706 0.16% 101 56964 0.16% 102 57361 0.16% 103 59752 0.17% 104 62785 0.18% 105 62731 0.18% 106 64846 0.19% 107 66597 0.19% 108 67192 0.19% 109 69048 0.20% 110 69652 0.20% 111 73601 0.21% 112 77108 0.22% 113 78024 0.22% 114 81548 0.23% 115 84028 0.24% 116 86241 0.25% 117 85555 0.24% 118 86634 0.25% 119 89831 0.26% 120 92972 0.27% 121 93463 0.27% 122 97415 0.28% 123 100366 0.29% 124 103540 0.30% 125 104355 0.30% 126 108592 0.31% 127 107160 0.31% 128 106578 0.30% 129 110349 0.31% 130 109410 0.31% 131 110463 0.32% 132 113507 0.32% 133 118601 0.34% 134 118758 0.34% 135 120655 0.34% 136 123288 0.35% 137 123133 0.35% 138 125317 0.36% 139 125513 0.36% 140 126788 0.36% 141 128354 0.37% 142 130762 0.37% 143 131593 0.38% 144 137644 0.39% 145 137146 0.39% 146 138355 0.39% 147 136327 0.39% 148 135696 0.39% 149 134910 0.38% 150 134002 0.38% 151 28957927 82.63% 35045075 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=2.71 fanout-score-rank=34 prefix-density=0.92 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.07 sequence-density-rank=33 fanout-score=179.52 fanout-score-rank=1 prefix-density=0.58 prefix-fanout=21.3 sequence=CCGCCGCCGCCACCACGGGACTGCGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCCCTCGATGGCGTCGCGCATCGACTGCTCGCTGGCGAAGGTGACGAAGCCGAACCCGCGGGAACGGCCAGTCTCCCTGTCGTTGATGATCTTGGAGTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCGTCGGTAGCCCAGGCGAGGCCGCCCACGAAGCAACGGTACTCAACTTCCGCCATTCCTCCCACTAAACCCTAACGAACCGGAACC criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=27 prefix-density=0.63 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.11 sequence-density-rank=16 fanout-score=124.40 fanout-score-rank=1 prefix-density=0.97 prefix-fanout=14.0 sequence=CGCCGCCGCCGC SRR12951296 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:59:57 Started mapping on | Dec 07 10:59:57 Finished on | Dec 07 11:05:30 Mapping speed, Million of reads per hour | 378.87 Number of input reads | 35045075 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 24515830 Uniquely mapped reads % | 69.96% Average mapped length | 291.05 Number of splices: Total | 20327212 Number of splices: Annotated (sjdb) | 18838992 Number of splices: GT/AG | 20067073 Number of splices: GC/AG | 223933 Number of splices: AT/AC | 11952 Number of splices: Non-canonical | 24254 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.56 Insertion rate per base | 0.00% Insertion average length | 1.14 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 233224 % of reads mapped to multiple loci | 0.67% Number of reads mapped to too many loci | 1287107 % of reads mapped to too many loci | 3.67% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.52% % of reads unmapped: other | 19.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10296021 10296021 10296021 N_multimapping 233224 233224 233224 N_noFeature 844650 23842044 1082191 N_ambiguous 524662 3379 88046 UnstrandedReadsAssigned:23146518 PositiveStrandReadsAssigned:670407 NegativeStrandReadsAssigned:23345593 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951296 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: SRR12951296-trimmed-pair1.fastq SRR12951296-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,045,075 reads, 24,126,735 reads pseudoaligned [quant] estimated average fragment length: 241.198 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,159 rounds 52973 SRR12951296.ke.tsv 35125 SRR12951296.se.tsv 88098 total ==> SRR12951296.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 696.258 0 0 PNS24247 1044 803.802 195.29 13.6146 PNS24249 1928 1687.8 505.516 16.7837 PNS24246 1044 803.802 195.29 13.6146 PNS24248 1044 803.802 195.29 13.6146 PNS24244 1471 1230.8 196.613 8.95152 PNS24243 293 108.644 0 0 KQK14069 1603 1362.8 25449.9 1046.47 KQK14071 474 251.949 618.368 137.533 ==> SRR12951296.se.tsv <== BRADI_1g14170v3 27134 BRADI_1g53295v3 128 BRADI_1g59795v3 416 BRADI_1g07683v3 0 BRADI_1g00485v3 45 BRADI_1g20270v3 753 BRADI_1g74790v3 2478 BRADI_1g09890v3 0 BRADI_1g77505v3 231 BRADI_1g48960v3 0 SRR12951296 completed mapping pipeline successfully