Starting /dee2/code/volunteer_pipeline.sh SRR7814839 current disk space = 1551358119936 free memory = 1605392616 SRR7814839 SRAfilesize 2c4ef619754d9066ee04f4319ef42759 SRR7814839.sra SRR7814839.sra file validated SRR7814839 is paired end SRR7814839 is conventional basespace SRR7814839 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814839_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2445 37.0 37.0 37.0 37.0 37.0 2 36.25175 37.0 37.0 37.0 37.0 37.0 3 36.371 37.0 37.0 37.0 37.0 37.0 4 36.4015 37.0 37.0 37.0 37.0 37.0 5 36.4425 37.0 37.0 37.0 37.0 37.0 6 36.48 37.0 37.0 37.0 37.0 37.0 7 36.3775 37.0 37.0 37.0 37.0 37.0 8 36.573 37.0 37.0 37.0 37.0 37.0 9 36.4275 37.0 37.0 37.0 37.0 37.0 10-14 36.482800000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.483000000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.481500000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.3622 37.0 37.0 37.0 37.0 37.0 30-34 36.3983 37.0 37.0 37.0 37.0 37.0 35-39 36.3686 37.0 37.0 37.0 37.0 37.0 40-44 36.1845 37.0 37.0 37.0 37.0 37.0 45-49 35.259 37.0 37.0 37.0 32.2 37.0 50-54 34.8532 37.0 37.0 37.0 29.8 37.0 55-59 34.543 37.0 37.0 37.0 25.0 37.0 60-64 34.709500000000006 37.0 37.0 37.0 27.4 37.0 65-69 34.589600000000004 37.0 37.0 37.0 27.4 37.0 70-74 34.9541 37.0 37.0 37.0 29.8 37.0 75-79 35.8846 37.0 37.0 37.0 37.0 37.0 80-84 36.030199999999994 37.0 37.0 37.0 37.0 37.0 85-89 36.0158 37.0 37.0 37.0 37.0 37.0 90-94 36.0205 37.0 37.0 37.0 37.0 37.0 95-99 35.865500000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.8758 37.0 37.0 37.0 37.0 37.0 105-109 35.9536 37.0 37.0 37.0 37.0 37.0 110-114 35.8746 37.0 37.0 37.0 37.0 37.0 115-119 35.754999999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.6774 37.0 37.0 37.0 37.0 37.0 125-129 35.6885 37.0 37.0 37.0 37.0 37.0 130-134 35.598699999999994 37.0 37.0 37.0 37.0 37.0 135-139 35.4671 37.0 37.0 37.0 37.0 37.0 140-144 35.431 37.0 37.0 37.0 37.0 37.0 145-149 35.0972 37.0 37.0 37.0 27.4 37.0 150-151 34.47525 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 2.0 20 0.0 21 0.0 22 1.0 23 2.0 24 8.0 25 7.0 26 9.0 27 15.0 28 19.0 29 32.0 30 44.0 31 66.0 32 258.0 33 124.0 34 159.0 35 390.0 36 2646.0 37 218.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 57.31096644967452 10.41562343515273 3.780671006509765 28.492739108662995 2 23.730932733183295 18.479619904976243 29.257314328582147 28.532133033258315 3 20.65 17.925 30.175 31.25 4 27.150000000000002 23.275000000000002 19.650000000000002 29.925 5 31.225 29.425 19.7 19.650000000000002 6 27.750000000000004 29.45 21.6 21.2 7 17.95 27.825 35.125 19.1 8 18.425 27.500000000000004 27.800000000000004 26.275 9 26.400000000000002 19.15 30.675 23.775 10-14 24.01 27.325 22.255 26.41 15-19 23.880000000000003 24.97 24.22 26.93 20-24 23.265 27.255000000000003 24.48 25.0 25-29 23.895 25.045 24.705 26.355 30-34 22.13 26.179999999999996 24.37 27.32 35-39 22.53 24.67 24.14 28.660000000000004 40-44 22.35 26.19 24.310000000000002 27.150000000000002 45-49 25.53 23.494999999999997 24.5 26.474999999999998 50-54 26.455000000000002 23.515 23.855 26.174999999999997 55-59 26.669999999999998 22.795 24.93 25.605 60-64 27.339999999999996 23.419999999999998 24.785 24.455 65-69 26.045 25.105 23.76 25.09 70-74 28.384999999999998 24.15 22.86 24.605 75-79 29.544999999999998 22.814999999999998 23.380000000000003 24.26 80-84 29.404999999999998 23.0 22.88 24.715 85-89 29.435 23.47 22.455 24.64 90-94 29.294999999999998 22.61 22.86 25.235000000000003 95-99 29.885 22.615 23.119999999999997 24.38 100-104 30.15 23.119999999999997 22.375 24.355 105-109 29.445 22.695 22.845 25.014999999999997 110-114 29.465000000000003 23.380000000000003 22.655 24.5 115-119 29.98 23.13 22.495 24.395 120-124 29.975 23.425 21.78 24.82 125-129 29.78 23.65 22.45 24.12 130-134 29.635 22.725 22.84 24.8 135-139 29.709999999999997 22.485 22.695 25.11 140-144 29.885 23.494999999999997 22.125 24.495 145-149 30.25 23.015 22.075 24.66 150-151 29.625 22.75 22.3875 25.2375 >>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 0.5 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 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 0.5 26 0.0 27 1.0 28 1.0 29 1.0 30 4.0 31 9.0 32 13.5 33 16.5 34 23.5 35 28.5 36 39.0 37 56.5 38 64.5 39 74.0 40 94.0 41 117.5 42 140.0 43 158.0 44 164.0 45 165.5 46 167.5 47 171.5 48 175.0 49 168.5 50 167.0 51 164.5 52 138.5 53 120.0 54 115.0 55 101.5 56 96.5 57 81.0 58 64.0 59 71.0 60 66.5 61 57.0 62 57.5 63 51.5 64 50.0 65 68.0 66 77.0 67 66.0 68 61.0 69 59.5 70 64.5 71 74.5 72 76.0 73 65.5 74 41.5 75 30.5 76 25.5 77 12.5 78 8.0 79 5.5 80 1.5 81 1.5 82 1.5 83 0.0 84 0.5 85 0.5 86 0.5 87 0.5 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 0.15 2 0.025 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 89.75 #Duplication Level Percentage of deduplicated Percentage of total 1 95.18105849582173 85.425 2 4.345403899721449 7.8 3 0.22284122562674097 0.6 4 0.02785515320334262 0.1 5 0.02785515320334262 0.125 6 0.02785515320334262 0.15 7 0.0 0.0 8 0.0 0.0 9 0.02785515320334262 0.22499999999999998 >10 0.11142061281337048 3.4000000000000004 >50 0.02785515320334262 2.175 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCTCGGTT 87 2.175 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCGCGGGT 44 1.0999999999999999 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCTCGGGT 39 0.975 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCGCGGTT 35 0.8750000000000001 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCTCGTTT 18 0.44999999999999996 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCGCGTTT 9 0.22499999999999998 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCTCGTAT 6 0.15 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACACCATCCAATCTCGGAT 5 0.125 TruSeq Adapter, Index 1 (97% over 37bp) >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.1 0.0 0.0 0.0 0.0 2 0.1 0.0 0.0 0.0 0.0 3 0.1 0.0 0.0 0.0 0.0 4 0.1 0.0 0.0 0.0 0.0 5 0.1 0.0 0.0 0.0 0.0 6 0.1 0.0 0.0 0.0 0.0 7 0.1 0.0 0.0 0.0 0.0 8 0.1 0.0 0.0 0.0 0.0 9 0.1 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.1 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.15 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.3125 0.0 0.0 0.0 0.0 88-89 0.42500000000000004 0.0 0.0 0.0 0.0 90-91 0.4625 0.0 0.0 0.0 0.0 92-93 0.4875 0.0 0.0 0.0 0.0 94-95 0.5625 0.0 0.0 0.0 0.0 96-97 0.6125 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.9125 0.0 0.0 0.0 0.0 102-103 1.1875 0.0 0.0 0.0 0.0 104-105 1.275 0.0 0.0 0.0 0.0 106-107 1.4249999999999998 0.0 0.0 0.0 0.0 108-109 1.6125 0.0 0.0 0.0 0.0 110-111 1.7875 0.0 0.0 0.0 0.0 112-113 1.925 0.0 0.0 0.0 0.0 114-115 2.125 0.0 0.0 0.0 0.0 116-117 2.2125 0.0 0.0 0.0 0.0 118-119 2.6 0.0 0.0 0.0 0.0 120-121 2.925 0.0 0.0 0.0 0.0 122-123 3.25 0.0 0.0 0.0 0.0 124-125 3.5875 0.0 0.0 0.0 0.0 126-127 3.875 0.0 0.0 0.0 0.0 128-129 4.275 0.0 0.0 0.0 0.0 130-131 4.6375 0.0 0.0 0.0 0.0 132-133 5.2125 0.0 0.0 0.0 0.0 134-135 5.675 0.0 0.0 0.0 0.0 136-137 6.125 0.0 0.0 0.0 0.0 138-139 6.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCGGA 85 1.07320375E-10 68.2353 1 TCGGAAG 85 1.07320375E-10 68.2353 3 GAGCACA 85 1.07320375E-10 68.2353 9 ATCGGAA 85 1.07320375E-10 68.2353 2 GAAGAGC 90 1.8007995E-10 64.44444 6 CGGAAGA 90 1.8007995E-10 64.44444 4 AGAGCAC 90 1.8007995E-10 64.44444 8 AAGAGCA 95 2.910383E-10 61.052635 7 GGAAGAG 95 2.910383E-10 61.052635 5 AATCTCG 40 2.9585467E-4 21.75 40-44 CAATCTC 40 2.9585467E-4 21.75 40-44 TCCAATC 60 4.1126805E-7 21.75 35-39 AGTCACA 65 8.8818524E-7 20.076923 25-29 ATCCAAT 60 1.0196794E-5 19.333334 35-39 CATCCAA 60 1.0196794E-5 19.333334 35-39 ACTCCAG 70 1.807628E-6 18.642857 20-24 CACCATC 80 3.1520904E-7 18.125 30-34 GTCACAC 65 2.0332325E-5 17.846153 25-29 ACCATCC 65 2.0332325E-5 17.846153 30-34 ACACCAT 65 2.0332325E-5 17.846153 30-34 >>END_MODULE SRR7814839 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814839_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 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2455 37.0 37.0 37.0 37.0 37.0 2 35.813 37.0 37.0 37.0 37.0 37.0 3 35.7845 37.0 37.0 37.0 37.0 37.0 4 35.697 37.0 37.0 37.0 37.0 37.0 5 36.0825 37.0 37.0 37.0 37.0 37.0 6 35.9705 37.0 37.0 37.0 37.0 37.0 7 35.6115 37.0 37.0 37.0 37.0 37.0 8 35.3135 37.0 37.0 37.0 37.0 37.0 9 35.2935 37.0 37.0 37.0 37.0 37.0 10-14 35.1354 37.0 37.0 37.0 34.6 37.0 15-19 35.0595 37.0 37.0 37.0 32.2 37.0 20-24 34.9698 37.0 37.0 37.0 29.8 37.0 25-29 34.6582 37.0 37.0 37.0 25.0 37.0 30-34 34.52759999999999 37.0 37.0 37.0 25.0 37.0 35-39 34.7256 37.0 37.0 37.0 27.4 37.0 40-44 34.61569999999999 37.0 37.0 37.0 25.0 37.0 45-49 34.672900000000006 37.0 37.0 37.0 25.0 37.0 50-54 34.543099999999995 37.0 37.0 37.0 25.0 37.0 55-59 34.4085 37.0 37.0 37.0 25.0 37.0 60-64 34.391200000000005 37.0 37.0 37.0 25.0 37.0 65-69 34.3137 37.0 37.0 37.0 25.0 37.0 70-74 34.4368 37.0 37.0 37.0 25.0 37.0 75-79 34.406 37.0 37.0 37.0 25.0 37.0 80-84 34.2881 37.0 37.0 37.0 25.0 37.0 85-89 34.584999999999994 37.0 37.0 37.0 25.0 37.0 90-94 34.9134 37.0 37.0 37.0 27.4 37.0 95-99 34.9007 37.0 37.0 37.0 25.0 37.0 100-104 35.0144 37.0 37.0 37.0 25.0 37.0 105-109 35.0461 37.0 37.0 37.0 27.4 37.0 110-114 34.981899999999996 37.0 37.0 37.0 25.0 37.0 115-119 35.0726 37.0 37.0 37.0 25.0 37.0 120-124 34.92810000000001 37.0 37.0 37.0 25.0 37.0 125-129 34.909000000000006 37.0 37.0 37.0 25.0 37.0 130-134 34.822199999999995 37.0 37.0 37.0 25.0 37.0 135-139 34.6043 37.0 37.0 37.0 25.0 37.0 140-144 34.512 37.0 37.0 37.0 25.0 37.0 145-149 34.48989999999999 37.0 37.0 37.0 25.0 37.0 150-151 33.9365 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 1.0 14 3.0 15 2.0 16 6.0 17 1.0 18 5.0 19 21.0 20 22.0 21 35.0 22 33.0 23 47.0 24 57.0 25 69.0 26 35.0 27 22.0 28 27.0 29 24.0 30 28.0 31 49.0 32 77.0 33 122.0 34 221.0 35 637.0 36 2304.0 37 151.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.525 18.4 5.949999999999999 24.125 2 33.575 20.825 24.474999999999998 21.125 3 28.549999999999997 22.025 26.35 23.075000000000003 4 32.05 28.999999999999996 18.825 20.125 5 32.125 31.175000000000004 17.375 19.325 6 28.825 31.55 18.425 21.2 7 27.825 17.75 32.675 21.75 8 27.125 22.45 21.975 28.449999999999996 9 29.725 20.75 23.45 26.075 10-14 30.54 24.125 20.78 24.555 15-19 30.25 23.455000000000002 22.07 24.224999999999998 20-24 29.785 24.265 21.88 24.07 25-29 28.595 24.93 22.31 24.165 30-34 28.09 25.135 23.195 23.580000000000002 35-39 26.229999999999997 27.965 21.735 24.07 40-44 26.224999999999998 27.755000000000003 22.095000000000002 23.925 45-49 26.305 27.465 22.97 23.26 50-54 27.405 26.51 22.115000000000002 23.97 55-59 28.645 25.06 22.895 23.400000000000002 60-64 29.75 24.59 22.38 23.28 65-69 28.939999999999998 25.575 22.095000000000002 23.39 70-74 27.46 26.705000000000002 22.345000000000002 23.49 75-79 27.560000000000002 26.11 22.655 23.674999999999997 80-84 29.14 25.319999999999997 23.005 22.535 85-89 30.264999999999997 24.310000000000002 22.400000000000002 23.025000000000002 90-94 30.625000000000004 23.79 22.02 23.565 95-99 31.31 23.474999999999998 22.305 22.91 100-104 31.485000000000003 23.47 21.825 23.22 105-109 31.119999999999997 23.09 22.650000000000002 23.14 110-114 31.345 23.974999999999998 21.94 22.74 115-119 31.635 23.385 22.02 22.96 120-124 31.374999999999996 23.7 22.125 22.8 125-129 31.28 23.919999999999998 22.195 22.605 130-134 32.32 23.68 21.525 22.475 135-139 31.7 23.94 22.215 22.145 140-144 32.07 23.61 21.975 22.345000000000002 145-149 32.35 24.01 21.425 22.215 150-151 32.2125 24.125 21.95 21.712500000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.5 5 2.0 6 1.5 7 0.5 8 1.5 9 2.5 10 4.0 11 2.5 12 2.0 13 3.0 14 2.5 15 1.5 16 0.5 17 1.0 18 1.0 19 2.5 20 2.0 21 0.5 22 2.0 23 2.5 24 1.5 25 1.5 26 3.5 27 5.0 28 4.0 29 4.0 30 6.0 31 7.0 32 7.5 33 12.0 34 22.0 35 26.0 36 31.5 37 49.0 38 65.0 39 78.5 40 92.0 41 117.5 42 133.0 43 137.5 44 159.0 45 162.5 46 154.0 47 160.0 48 162.0 49 157.0 50 142.0 51 128.0 52 128.5 53 123.0 54 115.5 55 108.0 56 82.5 57 76.5 58 95.0 59 84.5 60 74.5 61 83.5 62 78.0 63 72.5 64 76.5 65 65.0 66 64.0 67 72.0 68 69.0 69 60.0 70 48.0 71 49.5 72 41.5 73 32.5 74 31.0 75 22.0 76 19.5 77 16.0 78 10.5 79 9.5 80 10.0 81 11.0 82 9.0 83 7.5 84 7.0 85 5.5 86 5.5 87 6.0 88 8.0 89 9.5 90 8.5 91 9.0 92 6.0 93 4.0 94 2.5 95 2.5 96 3.5 97 1.0 98 1.5 99 2.0 100 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 0.0 145-149 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 95.45 #Duplication Level Percentage of deduplicated Percentage of total 1 95.67836563645888 91.325 2 4.033525405971713 7.7 3 0.23572551073860662 0.675 4 0.026191723415400735 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.026191723415400735 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.1 0.0 0.0 0.0 0.0 2 0.1 0.0 0.0 0.0 0.0 3 0.1 0.0 0.0 0.0 0.0 4 0.1 0.0 0.0 0.0 0.0 5 0.1 0.0 0.0 0.0 0.0 6 0.1 0.0 0.0 0.0 0.0 7 0.1 0.0 0.0 0.0 0.0 8 0.1 0.0 0.0 0.0 0.0 9 0.1 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.1 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 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 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.16249999999999998 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.2125 0.0 0.0 0.0 0.0 86-87 0.2625 0.0 0.0 0.0 0.0 88-89 0.375 0.0 0.0 0.0 0.0 90-91 0.42500000000000004 0.0 0.0 0.0 0.0 92-93 0.4625 0.0 0.0 0.0 0.0 94-95 0.5375000000000001 0.0 0.0 0.0 0.0 96-97 0.5874999999999999 0.0 0.0 0.0 0.0 98-99 0.7375 0.0 0.0 0.0 0.0 100-101 0.8875 0.0 0.0 0.0 0.0 102-103 1.1625 0.0 0.0 0.0 0.0 104-105 1.275 0.0 0.0 0.0 0.0 106-107 1.4249999999999998 0.0 0.0 0.0 0.0 108-109 1.6125 0.0 0.0 0.0 0.0 110-111 1.7875 0.0 0.0 0.0 0.0 112-113 1.925 0.0 0.0 0.0 0.0 114-115 2.125 0.0 0.0 0.0 0.0 116-117 2.2125 0.0 0.0 0.0 0.0 118-119 2.575 0.0 0.0 0.0 0.0 120-121 2.9125 0.0 0.0 0.0 0.0 122-123 3.25 0.0 0.0 0.0 0.0 124-125 3.625 0.0 0.0 0.0 0.0 126-127 3.9250000000000003 0.0 0.0 0.0 0.0 128-129 4.324999999999999 0.0 0.0 0.0 0.0 130-131 4.675000000000001 0.0 0.0 0.0 0.0 132-133 5.1875 0.0 0.0 0.0 0.0 134-135 5.65 0.0 0.0 0.0 0.0 136-137 6.125 0.0 0.0 0.0 0.0 138-139 6.5375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGAGAG 35 0.0035366106 20.714287 45-49 >>END_MODULE Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861257 spots for SRR7814839.sra Written 1861257 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra Read 1861251 spots for SRR7814839.sra Written 1861251 spots for SRR7814839.sra SRR ids: ['SRR7814839.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rmgu6bcc SRR7814839.sra spots: 37225026 blocks: [[1, 1861251], [1861252, 3722502], [3722503, 5583753], [5583754, 7445004], [7445005, 9306255], [9306256, 11167506], [11167507, 13028757], [13028758, 14890008], [14890009, 16751259], [16751260, 18612510], [18612511, 20473761], [20473762, 22335012], [22335013, 24196263], [24196264, 26057514], [26057515, 27918765], [27918766, 29780016], [29780017, 31641267], [31641268, 33502518], [33502519, 35363769], [35363770, 37225026]] SRR7814839 file size 12592639 SRR7814839 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 SRR7814839 SRR7814839_1.fastq SRR7814839_2.fastq Input file: SRR7814839_1.fastq Paired file: SRR7814839_2.fastq trimmed: SRR7814839-trimmed-pair1.fastq, SRR7814839-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 12:02:47 2024 >> started Fri Dec 6 12:03:42 2024 >> done (55.093s) 37225026 read pairs processed; of these: 970 ( 0.00%) short read pairs filtered out after trimming by size control 2377510 ( 6.39%) empty read pairs filtered out after trimming by size control 34846546 (93.61%) read pairs available; of these: 3681661 (10.57%) trimmed read pairs available after processing 31164885 (89.43%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 33 0.00% 20 23 0.00% 21 40 0.00% 22 30 0.00% 23 38 0.00% 24 47 0.00% 25 44 0.00% 26 60 0.00% 27 65 0.00% 28 70 0.00% 29 82 0.00% 30 66 0.00% 31 59 0.00% 32 88 0.00% 33 80 0.00% 34 63 0.00% 35 83 0.00% 36 71 0.00% 37 77 0.00% 38 122 0.00% 39 109 0.00% 40 120 0.00% 41 102 0.00% 42 99 0.00% 43 130 0.00% 44 114 0.00% 45 127 0.00% 46 163 0.00% 47 160 0.00% 48 201 0.00% 49 226 0.00% 50 243 0.00% 51 231 0.00% 52 251 0.00% 53 282 0.00% 54 308 0.00% 55 327 0.00% 56 323 0.00% 57 372 0.00% 58 445 0.00% 59 538 0.00% 60 577 0.00% 61 558 0.00% 62 659 0.00% 63 762 0.00% 64 747 0.00% 65 822 0.00% 66 936 0.00% 67 1086 0.00% 68 1188 0.00% 69 1368 0.00% 70 1573 0.00% 71 1846 0.01% 72 1881 0.01% 73 2253 0.01% 74 2370 0.01% 75 2822 0.01% 76 2918 0.01% 77 3253 0.01% 78 3811 0.01% 79 4226 0.01% 80 4646 0.01% 81 5250 0.02% 82 5903 0.02% 83 6613 0.02% 84 7463 0.02% 85 8284 0.02% 86 8723 0.03% 87 9599 0.03% 88 10481 0.03% 89 11454 0.03% 90 12638 0.04% 91 13866 0.04% 92 15114 0.04% 93 16635 0.05% 94 17834 0.05% 95 18808 0.05% 96 20378 0.06% 97 21739 0.06% 98 23005 0.07% 99 24730 0.07% 100 25977 0.07% 101 27553 0.08% 102 29480 0.08% 103 30936 0.09% 104 33016 0.09% 105 34621 0.10% 106 35864 0.10% 107 36975 0.11% 108 39150 0.11% 109 40787 0.12% 110 41941 0.12% 111 43930 0.13% 112 46089 0.13% 113 47558 0.14% 114 50032 0.14% 115 51466 0.15% 116 52901 0.15% 117 54588 0.16% 118 55570 0.16% 119 56591 0.16% 120 58350 0.17% 121 59917 0.17% 122 61208 0.18% 123 64483 0.19% 124 66455 0.19% 125 67598 0.19% 126 69155 0.20% 127 70299 0.20% 128 71104 0.20% 129 72322 0.21% 130 74126 0.21% 131 75259 0.22% 132 77140 0.22% 133 79823 0.23% 134 81636 0.23% 135 83790 0.24% 136 84638 0.24% 137 84732 0.24% 138 86769 0.25% 139 87485 0.25% 140 88185 0.25% 141 90130 0.26% 142 92056 0.26% 143 93674 0.27% 144 97026 0.28% 145 99010 0.28% 146 99001 0.28% 147 100787 0.29% 148 101147 0.29% 149 101164 0.29% 150 103224 0.30% 151 31164885 89.43% 34846546 reads passed initial QC criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=4.40 fanout-score-rank=26 prefix-density=0.20 prefix-fanout=3.5 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.02 sequence-density-rank=34 fanout-score=594.97 fanout-score-rank=1 prefix-density=0.57 prefix-fanout=21.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=2.42 fanout-score-rank=35 prefix-density=0.31 prefix-fanout=2.3 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=34 fanout-score=634.32 fanout-score-rank=1 prefix-density=0.98 prefix-fanout=20.8 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR7814839 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 12:05:35 Started mapping on | Dec 06 12:05:35 Finished on | Dec 06 12:10:07 Mapping speed, Million of reads per hour | 461.20 Number of input reads | 34846546 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 32120771 Uniquely mapped reads % | 92.18% Average mapped length | 295.19 Number of splices: Total | 32187008 Number of splices: Annotated (sjdb) | 30296877 Number of splices: GT/AG | 31748802 Number of splices: GC/AG | 346266 Number of splices: AT/AC | 23279 Number of splices: Non-canonical | 68661 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 3.07 Insertion rate per base | 0.02% Insertion average length | 2.74 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 546700 % of reads mapped to multiple loci | 1.57% Number of reads mapped to too many loci | 38954 % of reads mapped to too many loci | 0.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.49% % of reads unmapped: other | 0.66% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2179075 2179075 2179075 N_multimapping 546700 546700 546700 N_noFeature 898162 31353568 1181378 N_ambiguous 561884 3954 77995 UnstrandedReadsAssigned:30660725 PositiveStrandReadsAssigned:763249 NegativeStrandReadsAssigned:30861398 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7814839 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: SRR7814839-trimmed-pair1.fastq SRR7814839-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 34,846,546 reads, 31,355,221 reads pseudoaligned [quant] estimated average fragment length: 266.104 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,196 rounds 52973 SRR7814839.ke.tsv 35125 SRR7814839.se.tsv 88098 total ==> SRR7814839.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 671.622 0 0 PNS24247 1044 778.896 80.8047 4.70486 PNS24249 1928 1662.9 392.795 10.7125 PNS24246 1044 778.896 80.8047 4.70486 PNS24248 1044 778.896 80.8047 4.70486 PNS24244 1471 1205.9 135.791 5.10682 PNS24243 293 94.4929 2 0.959888 KQK14069 1603 1337.9 4662.09 158.033 KQK14071 474 233.948 4.31349 0.836179 ==> SRR7814839.se.tsv <== BRADI_1g14170v3 4687 BRADI_1g53295v3 842 BRADI_1g59795v3 124 BRADI_1g07683v3 0 BRADI_1g00485v3 88 BRADI_1g20270v3 3149 BRADI_1g74790v3 74 BRADI_1g09890v3 0 BRADI_1g77505v3 383 BRADI_1g48960v3 2 SRR7814839 completed mapping pipeline successfully