Starting /dee2/code/volunteer_pipeline.sh SRR7170845 current disk space = 3087467593728 free memory = 1540116540 SRR7170845 SRAfilesize 44a2261afafbead024a2716c52c1a2a1 SRR7170845.sra SRR7170845.sra file validated SRR7170845 is paired end SRR7170845 is conventional basespace SRR7170845 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170845_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 43 >>END_MODULE >>Per base sequence quality warn #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.84325 34.0 33.0 34.0 32.0 34.0 2 33.15775 34.0 33.0 34.0 32.0 34.0 3 33.11775 34.0 33.0 34.0 31.0 34.0 4 33.2725 34.0 33.0 34.0 32.0 34.0 5 33.42675 34.0 33.0 34.0 33.0 34.0 6 36.78925 38.0 37.0 38.0 35.0 38.0 7 37.07825 38.0 38.0 38.0 36.0 38.0 8 37.3085 38.0 38.0 38.0 37.0 38.0 9 37.41275 38.0 38.0 38.0 37.0 38.0 10-14 37.44125 38.0 38.0 38.0 37.0 38.0 15-19 37.43 38.0 38.0 38.0 37.0 38.0 20-24 37.357150000000004 38.0 38.0 38.0 37.0 38.0 25-29 37.29595 38.0 38.0 38.0 37.0 38.0 30-34 37.249649999999995 38.0 38.0 38.0 37.0 38.0 35-39 37.2113 38.0 38.0 38.0 36.8 38.0 40-44 36.581050000000005 38.0 38.0 38.0 34.2 38.0 45-49 36.97105 38.0 38.0 38.0 35.8 38.0 50-54 36.8581 38.0 38.0 38.0 35.8 38.0 55-59 36.6833 38.0 38.0 38.0 34.6 38.0 60-64 36.5499 38.0 38.0 38.0 34.2 38.0 65-69 36.62545 38.0 38.0 38.0 34.6 38.0 70-74 36.1188 38.0 38.0 38.0 33.8 38.0 75-79 33.0643 38.0 36.6 38.0 9.6 38.0 80-84 32.1876 38.0 36.0 38.0 2.0 38.0 85-89 32.00705000000001 38.0 35.6 38.0 2.0 38.0 90-94 31.8238 38.0 35.0 38.0 2.0 38.0 95-99 31.684800000000003 38.0 34.8 38.0 2.0 38.0 100-104 31.5627 38.0 34.4 38.0 2.0 38.0 105-109 31.360400000000006 38.0 34.2 38.0 2.0 38.0 110-114 31.34485 38.0 34.0 38.0 2.0 38.0 115-119 31.05985 38.0 33.8 38.0 2.0 38.0 120-124 30.796049999999997 38.0 32.8 38.0 2.0 38.0 125-129 30.441650000000003 38.0 31.0 38.0 2.0 38.0 130-134 30.067850000000004 38.0 31.0 38.0 2.0 38.0 135-139 29.5262 37.8 27.0 38.0 2.0 38.0 140-144 29.096449999999997 38.0 26.2 38.0 2.0 38.0 145-149 28.363800000000005 36.2 22.8 38.0 2.0 38.0 150-151 24.354625 33.5 7.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 3.0 8 2.0 9 1.0 10 3.0 11 1.0 12 4.0 13 4.0 14 6.0 15 5.0 16 30.0 17 46.0 18 129.0 19 279.0 20 28.0 21 14.0 22 14.0 23 18.0 24 10.0 25 14.0 26 15.0 27 30.0 28 19.0 29 43.0 30 53.0 31 64.0 32 73.0 33 101.0 34 148.0 35 243.0 36 684.0 37 1915.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.44736842105263 21.86842105263158 6.5 33.18421052631579 2 17.325 24.375 41.875 16.425 3 14.05 24.95 37.5 23.5 4 20.075000000000003 28.95 24.725 26.25 5 27.775 33.35 22.650000000000002 16.225 6 24.05 35.949999999999996 24.125 15.875 7 13.700000000000001 33.45 37.9 14.95 8 17.875 29.7 28.599999999999998 23.825 9 23.325000000000003 22.575 29.525000000000002 24.575 10-14 20.02 29.865000000000002 23.645 26.47 15-19 19.42 26.479999999999997 28.375 25.724999999999998 20-24 18.675 30.825000000000003 27.055 23.445 25-29 19.139999999999997 28.08 26.915 25.865 30-34 16.6 27.245 29.349999999999998 26.805 35-39 20.778116717507626 25.398809821473222 26.31394709206381 27.509126368955343 40-44 18.65 28.17 27.700000000000003 25.480000000000004 45-49 20.2970297029703 27.362736273627362 29.547954795479548 22.792279227922794 50-54 22.425 25.005 26.82 25.75 55-59 18.060000000000002 25.215 31.66 25.064999999999998 60-64 20.485 25.945 30.785 22.785 65-69 19.105 36.955 23.805 20.135 70-74 17.244999999999997 38.87 23.415 20.47 75-79 17.585 36.445 24.395 21.575 80-84 17.974999999999998 33.684999999999995 25.275 23.064999999999998 85-89 18.709999999999997 32.54 25.46 23.29 90-94 18.465 32.019999999999996 25.41 24.104999999999997 95-99 19.02 31.630000000000003 25.36 23.990000000000002 100-104 19.335 31.495 25.679999999999996 23.49 105-109 19.295 31.355 25.240000000000002 24.11 110-114 19.61 30.975 25.755 23.66 115-119 19.785 30.2 25.480000000000004 24.535 120-124 19.645000000000003 30.42 25.06 24.875 125-129 20.285 30.095 25.585 24.035 130-134 19.48 30.659999999999997 24.26 25.6 135-139 20.405 30.564999999999998 24.55 24.48 140-144 19.814999999999998 30.7 24.515 24.97 145-149 20.294999999999998 29.720000000000002 24.169999999999998 25.814999999999998 150-151 20.6125 30.3 24.087500000000002 25.0 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 1.0 2 0.5 3 0.5 4 0.5 5 0.0 6 1.0 7 1.0 8 0.5 9 0.5 10 1.0 11 1.5 12 0.5 13 0.0 14 1.0 15 2.5 16 2.0 17 0.5 18 0.0 19 0.0 20 0.5 21 2.5 22 3.5 23 3.5 24 4.0 25 8.5 26 9.0 27 9.5 28 12.0 29 19.5 30 31.5 31 37.0 32 47.5 33 53.5 34 57.5 35 78.5 36 96.5 37 113.0 38 138.5 39 165.5 40 195.5 41 245.5 42 275.0 43 292.5 44 301.0 45 261.5 46 239.5 47 232.5 48 196.5 49 164.0 50 147.5 51 117.0 52 90.5 53 79.5 54 68.5 55 56.5 56 47.5 57 32.0 58 17.0 59 11.0 60 6.0 61 3.5 62 2.5 63 3.0 64 2.5 65 1.5 66 1.5 67 0.5 68 0.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.5 97 0.5 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 5.0 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 0.015 40-44 0.0 45-49 0.01 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 86.5 #Duplication Level Percentage of deduplicated Percentage of total 1 99.16184971098266 85.775 2 0.46242774566473993 0.8 3 0.1445086705202312 0.375 4 0.028901734104046246 0.1 5 0.028901734104046246 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.08670520231213873 1.55 >50 0.05780346820809249 3.65 >100 0.028901734104046246 7.625 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTAT 305 7.625 TruSeq Adapter, Index 8 (97% over 36bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTATG 90 2.25 TruSeq Adapter, Index 8 (97% over 35bp) CGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTATGCC 56 1.4000000000000001 TruSeq Adapter, Index 8 (96% over 33bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTA 25 0.625 TruSeq Adapter, Index 8 (97% over 36bp) TCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTATGC 25 0.625 TruSeq Adapter, Index 8 (97% over 34bp) NATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTAT 12 0.3 TruSeq Adapter, Index 3 (97% over 34bp) GAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTATGCCGT 5 0.125 TruSeq Adapter, Index 8 (96% over 31bp) >>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 0.7 0.0 0.0 0.0 0.0 2 0.7 0.0 0.0 0.0 0.0 3 0.7 0.0 0.0 0.0 0.0 4 0.7 0.0 0.0 0.0 0.0 5 0.7 0.0 0.0 0.0 0.0 6 0.7 0.0 0.0 0.0 0.0 7 0.7 0.0 0.0 0.0 0.0 8 0.7 0.0 0.0 0.0 0.0 9 0.7 0.0 0.0 0.0 0.0 10-11 0.7 0.0 0.0 0.0 0.0 12-13 0.7 0.0 0.0 0.0 0.0 14-15 0.7 0.0 0.0 0.0 0.0 16-17 0.7 0.0 0.0 0.0 0.0 18-19 0.7 0.0 0.0 0.0 0.0 20-21 0.725 0.0 0.0 0.0 0.0 22-23 0.725 0.0 0.0 0.0 0.0 24-25 0.725 0.0 0.0 0.0 0.0 26-27 0.725 0.0 0.0 0.0 0.0 28-29 0.7375 0.0 0.0 0.0 0.0 30-31 0.75 0.0 0.0 0.0 0.0 32-33 0.75 0.0 0.0 0.0 0.0 34-35 0.75 0.0 0.0 0.0 0.0 36-37 0.75 0.0 0.0 0.0 0.0 38-39 0.75 0.0 0.0 0.0 0.0 40-41 0.775 0.0 0.0 0.0 0.0 42-43 0.775 0.0 0.0 0.0 0.0 44-45 0.775 0.0 0.0 0.0 0.0 46-47 0.775 0.0 0.0 0.0 0.0 48-49 0.7875000000000001 0.0 0.0 0.0 0.0 50-51 0.8 0.0 0.0 0.0 0.0 52-53 0.8125 0.0 0.0 0.0 0.0 54-55 0.825 0.0 0.0 0.0 0.0 56-57 0.825 0.0 0.0 0.0 0.0 58-59 0.8625 0.0 0.0 0.0 0.0 60-61 0.9625 0.0 0.0 0.0 0.0 62-63 1.075 0.0 0.0 0.0 0.0 64-65 1.15 0.0 0.0 0.0 0.0 66-67 1.2125 0.0 0.0 0.0 0.0 68-69 1.3125 0.0 0.0 0.0 0.0 70-71 1.325 0.0 0.0 0.0 0.0 72-73 1.375 0.0 0.0 0.0 0.0 74-75 1.425 0.0 0.0 0.0 0.0 76-77 1.4875 0.0 0.0 0.0 0.0 78-79 1.525 0.0 0.0 0.0 0.0 80-81 1.6 0.0 0.0 0.0 0.0 82-83 1.7625 0.0 0.0 0.0 0.0 84-85 1.9125 0.0 0.0 0.0 0.0 86-87 2.0875 0.0 0.0 0.0 0.0 88-89 2.2750000000000004 0.0 0.0 0.0 0.0 90-91 2.4875 0.0 0.0 0.0 0.0 92-93 2.75 0.0 0.0 0.0 0.0 94-95 3.1375 0.0 0.0 0.0 0.0 96-97 3.725 0.0 0.0 0.0 0.0 98-99 4.15 0.0 0.0 0.0 0.0 100-101 4.55 0.0 0.0 0.0 0.0 102-103 4.9625 0.0 0.0 0.0 0.0 104-105 5.4625 0.0 0.0 0.0 0.0 106-107 6.1 0.0 0.0 0.0 0.0 108-109 6.637499999999999 0.0 0.0 0.0 0.0 110-111 7.025 0.0 0.0 0.0 0.0 112-113 7.4625 0.0 0.0 0.0 0.0 114-115 7.975 0.0 0.0 0.0 0.0 116-117 8.5 0.0 0.0 0.0 0.0 118-119 9.162500000000001 0.0 0.0 0.0 0.0 120-121 9.825 0.0 0.0 0.0 0.0 122-123 10.6125 0.0 0.0 0.0 0.0 124-125 11.0125 0.0 0.0 0.0 0.0 126-127 11.5625 0.0 0.0 0.0 0.0 128-129 12.225 0.0 0.0 0.0 0.0 130-131 12.85 0.0 0.0 0.0 0.0 132-133 13.600000000000001 0.0 0.0 0.0 0.0 134-135 14.350000000000001 0.0 0.0 0.0 0.0 136-137 15.287500000000001 0.0 0.0 0.0 0.0 138-139 16.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCGGA 110 3.7307473E-8 49.82125 1 ATCGGAA 120 1.4092075E-7 42.24427 2 TCGGAAG 130 2.644083E-7 38.994713 3 GAAGAGC 135 3.5563062E-7 37.55046 6 CGGAAGA 135 3.5563062E-7 37.55046 4 GAGCACA 140 4.7310095E-7 36.209377 9 GGAAGAG 140 4.7310095E-7 36.209377 5 AGAGCAC 150 8.1256985E-7 33.795418 8 AAGAGCA 165 1.7131861E-6 30.723104 7 TTGAAAA 65 1.8189894E-12 28.967503 60-64 TGAAAAA 70 1.09139364E-10 24.829285 60-64 TCTGCTT 80 2.1827873E-11 23.536095 55-59 CTTGAAA 75 2.6193447E-10 23.174002 60-64 TCTCGTA 85 5.0931703E-11 22.151617 40-44 CTGCTTG 85 5.0931703E-11 22.151617 55-59 CGTCTTC 85 5.0931703E-11 22.151617 50-54 GCGCATC 90 1.05501385E-10 20.973406 35-39 TATGCCG 90 1.09139364E-10 20.92097 45-49 ATCTCGT 85 1.2496457E-9 20.447647 40-44 TTCTGCT 85 1.2496457E-9 20.447647 55-59 >>END_MODULE SRR7170845 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170845_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 43 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.29675 33.0 33.0 34.0 32.0 34.0 2 32.453 34.0 33.0 34.0 32.0 34.0 3 32.2225 34.0 33.0 34.0 31.0 34.0 4 32.22225 34.0 33.0 34.0 32.0 34.0 5 32.353 34.0 33.0 34.0 32.0 34.0 6 36.16525 38.0 38.0 38.0 35.0 38.0 7 36.45025 38.0 38.0 38.0 36.0 38.0 8 36.234 38.0 38.0 38.0 36.0 38.0 9 36.29275 38.0 38.0 38.0 36.0 38.0 10-14 36.18705 38.0 38.0 38.0 35.0 38.0 15-19 36.13145 38.0 38.0 38.0 35.2 38.0 20-24 36.14805 38.0 38.0 38.0 35.0 38.0 25-29 36.046350000000004 38.0 38.0 38.0 34.8 38.0 30-34 35.9562 38.0 38.0 38.0 34.0 38.0 35-39 35.93075 38.0 38.0 38.0 34.2 38.0 40-44 35.9127 38.0 38.0 38.0 34.4 38.0 45-49 35.711850000000005 38.0 38.0 38.0 33.4 38.0 50-54 35.74079999999999 38.0 38.0 38.0 33.2 38.0 55-59 35.501949999999994 38.0 38.0 38.0 31.2 38.0 60-64 35.32895 38.0 38.0 38.0 29.8 38.0 65-69 35.497749999999996 38.0 38.0 38.0 31.6 38.0 70-74 35.77095 38.0 38.0 38.0 33.8 38.0 75-79 35.60375 38.0 38.0 38.0 33.2 38.0 80-84 32.3371 38.0 36.8 38.0 2.0 38.0 85-89 31.9226 38.0 36.2 38.0 2.0 38.0 90-94 31.825100000000003 38.0 36.0 38.0 2.0 38.0 95-99 31.624200000000002 38.0 35.8 38.0 2.0 38.0 100-104 31.5824 38.0 35.6 38.0 2.0 38.0 105-109 31.410850000000003 38.0 35.0 38.0 2.0 38.0 110-114 31.245299999999997 38.0 34.6 38.0 2.0 38.0 115-119 31.0764 38.0 34.0 38.0 2.0 38.0 120-124 30.837049999999998 38.0 34.0 38.0 2.0 38.0 125-129 30.516399999999997 38.0 33.0 38.0 2.0 38.0 130-134 30.0952 38.0 31.0 38.0 2.0 38.0 135-139 29.411849999999998 38.0 27.8 38.0 2.0 38.0 140-144 28.885949999999998 38.0 25.0 38.0 2.0 38.0 145-149 28.123450000000002 37.8 20.2 38.0 2.0 38.0 150-151 23.728875 32.5 2.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 72.0 3 11.0 4 7.0 5 10.0 6 5.0 7 8.0 8 2.0 9 1.0 10 4.0 11 4.0 12 17.0 13 34.0 14 24.0 15 20.0 16 14.0 17 20.0 18 34.0 19 59.0 20 239.0 21 24.0 22 17.0 23 10.0 24 19.0 25 13.0 26 17.0 27 20.0 28 26.0 29 26.0 30 28.0 31 48.0 32 53.0 33 84.0 34 114.0 35 202.0 36 527.0 37 2187.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.9 26.1 7.575 24.425 2 20.9 29.349999999999998 36.75 13.0 3 15.475 25.0 39.7 19.825 4 20.375 32.025 22.8 24.8 5 30.725 33.650000000000006 18.95 16.675 6 27.500000000000004 35.675000000000004 20.674999999999997 16.150000000000002 7 18.0 28.65 34.625 18.725 8 19.075 30.675 27.025 23.225 9 27.275 23.95 27.250000000000004 21.525 10-14 25.979999999999997 26.38 25.85 21.790000000000003 15-19 25.369999999999997 25.89 28.82 19.919999999999998 20-24 27.925 29.035 25.224999999999998 17.815 25-29 25.505 31.314999999999998 24.75 18.43 30-34 25.124999999999996 25.155 31.3 18.42 35-39 23.02 29.635 27.26 20.085 40-44 25.34 26.075 28.515 20.07 45-49 23.335 28.999999999999996 27.544999999999998 20.119999999999997 50-54 26.08 24.645 28.22 21.055 55-59 27.605 24.39 26.669999999999998 21.335 60-64 23.97 26.924999999999997 26.700000000000003 22.405 65-69 20.979999999999997 27.894999999999996 30.65 20.474999999999998 70-74 21.185000000000002 36.34 24.415 18.060000000000002 75-79 20.75 36.24 24.875 18.135 80-84 21.59 35.415 24.755 18.240000000000002 85-89 22.35 33.96 24.654999999999998 19.035 90-94 22.770000000000003 32.440000000000005 25.380000000000003 19.41 95-99 23.805 31.05 25.86 19.285 100-104 24.55 29.815 25.874999999999996 19.759999999999998 105-109 24.3 29.945 26.05 19.705000000000002 110-114 23.205000000000002 31.180000000000003 25.945 19.67 115-119 23.625 32.5 24.834999999999997 19.040000000000003 120-124 23.400000000000002 32.74 24.825 19.035 125-129 23.595 32.49 24.805 19.11 130-134 24.224999999999998 30.669999999999998 25.705 19.400000000000002 135-139 24.415 30.964999999999996 25.580000000000002 19.040000000000003 140-144 23.965 31.5 25.330000000000002 19.205 145-149 24.745 31.64 24.725 18.89 150-151 25.2625 30.525000000000002 25.374999999999996 18.8375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.5 11 1.5 12 1.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 1.0 23 2.0 24 2.0 25 2.5 26 3.0 27 6.5 28 12.0 29 13.0 30 17.0 31 26.0 32 31.5 33 39.0 34 47.5 35 54.0 36 77.0 37 119.0 38 160.0 39 204.0 40 224.5 41 239.5 42 276.0 43 293.0 44 292.5 45 267.5 46 230.0 47 217.0 48 217.5 49 182.0 50 147.0 51 124.5 52 95.0 53 78.5 54 67.0 55 58.5 56 41.5 57 25.5 58 19.5 59 18.0 60 14.5 61 9.5 62 7.0 63 5.0 64 3.5 65 4.5 66 4.0 67 2.0 68 2.5 69 2.5 70 0.5 71 1.0 72 2.0 73 1.5 74 0.5 75 0.0 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 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 89.4 #Duplication Level Percentage of deduplicated Percentage of total 1 99.13310961968679 88.625 2 0.44742729306487694 0.8 3 0.16778523489932887 0.44999999999999996 4 0.05592841163310962 0.2 5 0.02796420581655481 0.125 6 0.0 0.0 7 0.0 0.0 8 0.02796420581655481 0.2 9 0.05592841163310962 0.44999999999999996 >10 0.05592841163310962 1.4000000000000001 >50 0.0 0.0 >100 0.02796420581655481 7.75 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCAGTACGTGTAGATCT 310 7.75 Illumina Single End PCR Primer 1 (96% over 32bp) AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCAGTACGTGTAGATC 28 0.7000000000000001 Illumina Single End PCR Primer 1 (96% over 33bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCAGTACGTGTAGATCTC 28 0.7000000000000001 Illumina Single End PCR Primer 1 (96% over 31bp) CGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCAGTACGTGTAGATCTCGG 9 0.22499999999999998 Illumina Single End PCR Primer 1 (96% over 29bp) AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 9 0.22499999999999998 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 8 0.2 No Hit AAGCAGAAGACGGCATACGAGATGCGCGAGAGTGACTGGAGTTCAGACGT 5 0.125 RNA PCR Primer, Index 26 (96% over 27bp) >>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 0.7 0.0 0.0 0.0 0.0 2 0.7 0.0 0.0 0.0 0.0 3 0.7 0.0 0.0 0.0 0.0 4 0.7 0.0 0.0 0.0 0.0 5 0.7 0.0 0.0 0.0 0.0 6 0.7 0.0 0.0 0.0 0.0 7 0.7 0.0 0.0 0.0 0.0 8 0.7 0.0 0.0 0.0 0.0 9 0.7 0.0 0.0 0.0 0.0 10-11 0.7 0.0 0.0 0.0 0.0 12-13 0.7 0.0 0.0 0.0 0.0 14-15 0.7 0.0 0.0 0.0 0.0 16-17 0.7 0.0 0.0 0.0 0.0 18-19 0.7 0.0 0.0 0.0 0.0 20-21 0.725 0.0 0.0 0.0 0.0 22-23 0.725 0.0 0.0 0.0 0.0 24-25 0.725 0.0 0.0 0.0 0.0 26-27 0.725 0.0 0.0 0.0 0.0 28-29 0.7375 0.0 0.0 0.0 0.0 30-31 0.75 0.0 0.0 0.0 0.0 32-33 0.75 0.0 0.0 0.0 0.0 34-35 0.75 0.0 0.0 0.0 0.0 36-37 0.75 0.0 0.0 0.0 0.0 38-39 0.75 0.0 0.0 0.0 0.0 40-41 0.775 0.0 0.0 0.0 0.0 42-43 0.775 0.0 0.0 0.0 0.0 44-45 0.775 0.0 0.0 0.0 0.0 46-47 0.775 0.0 0.0 0.0 0.0 48-49 0.775 0.0 0.0 0.0 0.0 50-51 0.775 0.0 0.0 0.0 0.0 52-53 0.7875000000000001 0.0 0.0 0.0 0.0 54-55 0.8 0.0 0.0 0.0 0.0 56-57 0.8 0.0 0.0 0.0 0.0 58-59 0.8125 0.0 0.0 0.0 0.0 60-61 0.8625 0.0 0.0 0.0 0.0 62-63 0.975 0.0 0.0 0.0 0.0 64-65 1.0125 0.0 0.0 0.0 0.0 66-67 1.0625 0.0 0.0 0.0 0.0 68-69 1.1625 0.0 0.0 0.0 0.0 70-71 1.175 0.0 0.0 0.0 0.0 72-73 1.225 0.0 0.0 0.0 0.0 74-75 1.275 0.0 0.0 0.0 0.0 76-77 1.3375 0.0 0.0 0.0 0.0 78-79 1.375 0.0 0.0 0.0 0.0 80-81 1.4625 0.0 0.0 0.0 0.0 82-83 1.6125 0.0 0.0 0.0 0.0 84-85 1.7625 0.0 0.0 0.0 0.0 86-87 1.9375 0.0 0.0 0.0 0.0 88-89 2.125 0.0 0.0 0.0 0.0 90-91 2.3375 0.0 0.0 0.0 0.0 92-93 2.6 0.0 0.0 0.0 0.0 94-95 3.0125 0.0 0.0 0.0 0.0 96-97 3.6 0.0 0.0 0.0 0.0 98-99 4.012499999999999 0.0 0.0 0.0 0.0 100-101 4.4125 0.0 0.0 0.0 0.0 102-103 4.8375 0.0 0.0 0.0 0.0 104-105 5.3375 0.0 0.0 0.0 0.0 106-107 5.9625 0.0 0.0 0.0 0.0 108-109 6.487500000000001 0.0 0.0 0.0 0.0 110-111 6.85 0.0 0.0 0.0 0.0 112-113 7.2875 0.0 0.0 0.0 0.0 114-115 7.800000000000001 0.0 0.0 0.0 0.0 116-117 8.2875 0.0 0.0 0.0 0.0 118-119 8.925 0.0 0.0 0.0 0.0 120-121 9.5375 0.0 0.0 0.0 0.0 122-123 10.3125 0.0 0.0 0.0 0.0 124-125 10.7375 0.0 0.0 0.0 0.0 126-127 11.2625 0.0 0.0 0.0 0.0 128-129 11.912500000000001 0.0 0.0 0.0 0.0 130-131 12.5625 0.0 0.0 0.0 0.0 132-133 13.3125 0.0 0.0 0.0 0.0 134-135 14.05 0.0 0.0 0.0 0.0 136-137 14.975 0.0 0.0 0.0 0.0 138-139 15.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGAGGAT 10 0.006830828 145.0 8 ACGAGGA 10 0.006830828 145.0 7 TGGACGC 10 0.006830828 145.0 145 GAGCGTC 115 9.9924364E-8 44.130436 9 GATCGGA 115 9.9924364E-8 44.130436 1 AGAGCGT 115 9.9924364E-8 44.130436 8 ATCGGAA 120 1.3968383E-7 42.291668 2 GGAAGAG 120 1.3968383E-7 42.291668 5 AAGAGCG 125 1.925655E-7 40.6 7 CGGAAGA 125 1.925655E-7 40.6 4 GAAGAGC 130 2.620891E-7 39.03846 6 TCGGAAG 130 2.620891E-7 39.03846 3 GTATCAT 55 1.1668232E-4 26.363638 145 CATTAAA 50 7.0600436E-8 26.1 65-69 ATCATTA 45 8.383813E-7 25.777777 60-64 TATCATT 40 9.990927E-6 25.375 60-64 CCGTATC 45 2.4877938E-5 22.555553 60-64 TCGCCGT 45 2.4877938E-5 22.555553 55-59 CGTATCA 45 2.4877938E-5 22.555553 60-64 CGCCGTA 45 2.4877938E-5 22.555553 55-59 >>END_MODULE Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788241 spots for SRR7170845.sra Written 788241 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra Read 788234 spots for SRR7170845.sra Written 788234 spots for SRR7170845.sra SRR ids: ['SRR7170845.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r99z8_jy SRR7170845.sra spots: 15764687 blocks: [[1, 788234], [788235, 1576468], [1576469, 2364702], [2364703, 3152936], [3152937, 3941170], [3941171, 4729404], [4729405, 5517638], [5517639, 6305872], [6305873, 7094106], [7094107, 7882340], [7882341, 8670574], [8670575, 9458808], [9458809, 10247042], [10247043, 11035276], [11035277, 11823510], [11823511, 12611744], [12611745, 13399978], [13399979, 14188212], [14188213, 14976446], [14976447, 15764687]] SRR7170845 file size 5320434 SRR7170845 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 SRR7170845 SRR7170845_1.fastq SRR7170845_2.fastq Input file: SRR7170845_1.fastq Paired file: SRR7170845_2.fastq trimmed: SRR7170845-trimmed-pair1.fastq, SRR7170845-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 Thu Feb 13 19:08:31 2025 >> started Thu Feb 13 19:08:48 2025 >> done (17.044s) 15764687 read pairs processed; of these: 98992 ( 0.63%) short read pairs filtered out after trimming by size control 1672968 (10.61%) empty read pairs filtered out after trimming by size control 13992727 (88.76%) read pairs available; of these: 9628198 (68.81%) trimmed read pairs available after processing 4364529 (31.19%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 117 0.00% 19 510 0.00% 20 158 0.00% 21 186 0.00% 22 229 0.00% 23 226 0.00% 24 275 0.00% 25 267 0.00% 26 324 0.00% 27 325 0.00% 28 332 0.00% 29 310 0.00% 30 343 0.00% 31 562 0.00% 32 347 0.00% 33 347 0.00% 34 371 0.00% 35 367 0.00% 36 362 0.00% 37 373 0.00% 38 422 0.00% 39 452 0.00% 40 508 0.00% 41 670 0.00% 42 648 0.00% 43 711 0.01% 44 876 0.01% 45 1741 0.01% 46 2511 0.02% 47 2674 0.02% 48 2481 0.02% 49 2781 0.02% 50 2760 0.02% 51 3003 0.02% 52 3157 0.02% 53 2843 0.02% 54 3076 0.02% 55 3331 0.02% 56 3342 0.02% 57 3945 0.03% 58 4456 0.03% 59 4416 0.03% 60 5306 0.04% 61 8315 0.06% 62 7700 0.06% 63 8217 0.06% 64 5030 0.04% 65 4689 0.03% 66 3975 0.03% 67 4237 0.03% 68 4528 0.03% 69 5194 0.04% 70 6351 0.05% 71 8878 0.06% 72 20827 0.15% 73 25010 0.18% 74 42753 0.31% 75 48386 0.35% 76 138550 0.99% 77 157661 1.13% 78 65781 0.47% 79 33330 0.24% 80 25191 0.18% 81 23094 0.17% 82 22891 0.16% 83 22349 0.16% 84 23148 0.17% 85 22763 0.16% 86 22583 0.16% 87 22727 0.16% 88 22826 0.16% 89 24241 0.17% 90 25469 0.18% 91 27640 0.20% 92 29493 0.21% 93 32369 0.23% 94 33515 0.24% 95 34762 0.25% 96 34192 0.24% 97 34159 0.24% 98 33924 0.24% 99 34165 0.24% 100 36579 0.26% 101 38344 0.27% 102 41789 0.30% 103 43964 0.31% 104 46501 0.33% 105 47205 0.34% 106 46715 0.33% 107 46146 0.33% 108 45536 0.33% 109 45521 0.33% 110 46495 0.33% 111 49093 0.35% 112 51765 0.37% 113 54889 0.39% 114 57503 0.41% 115 59654 0.43% 116 59537 0.43% 117 58646 0.42% 118 57983 0.41% 119 57030 0.41% 120 59163 0.42% 121 60551 0.43% 122 62484 0.45% 123 66172 0.47% 124 69838 0.50% 125 71609 0.51% 126 73525 0.53% 127 73425 0.52% 128 73626 0.53% 129 73392 0.52% 130 74696 0.53% 131 76482 0.55% 132 80191 0.57% 133 84966 0.61% 134 89860 0.64% 135 94684 0.68% 136 98298 0.70% 137 102821 0.73% 138 105532 0.75% 139 108702 0.78% 140 114810 0.82% 141 123271 0.88% 142 134555 0.96% 143 151931 1.09% 144 173559 1.24% 145 202010 1.44% 146 246843 1.76% 147 321966 2.30% 148 466434 3.33% 149 865143 6.18% 150 3023410 21.61% 151 4364529 31.19% 13992727 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=25 prefix-density=0.34 prefix-fanout=1.9 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.06 sequence-density-rank=29 fanout-score=17.04 fanout-score-rank=1 prefix-density=0.72 prefix-fanout=1.5 sequence=GTGCAAGTGGACAGGGGAGAGAAGACGATGGTAGCTAAGAGAATGCATGCGATAAGAAAGGCCTTCATCTTGGAAATATATGGGACTAACATGGTTATGCTCTCCT criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.84 fanout-score-rank=15 prefix-density=0.53 prefix-fanout=1.9 sequence=AACCGCACCCCGGCACA criterion=fanout-score sequence-density=0.06 sequence-density-rank=30 fanout-score=26.02 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=9.1 sequence=AAGGCCAAGATCCAGGACAAGGA SRR7170845 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 19:10:05 Started mapping on | Feb 13 19:10:05 Finished on | Feb 13 19:11:28 Mapping speed, Million of reads per hour | 606.91 Number of input reads | 13992727 Average input read length | 268 UNIQUE READS: Uniquely mapped reads number | 10366827 Uniquely mapped reads % | 74.09% Average mapped length | 278.57 Number of splices: Total | 9909258 Number of splices: Annotated (sjdb) | 9657399 Number of splices: GT/AG | 9714430 Number of splices: GC/AG | 146477 Number of splices: AT/AC | 7157 Number of splices: Non-canonical | 41194 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.03% Deletion average length | 2.62 Insertion rate per base | 0.02% Insertion average length | 2.05 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 350969 % of reads mapped to multiple loci | 2.51% Number of reads mapped to too many loci | 11206 % of reads mapped to too many loci | 0.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 23.28% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3292718 3292718 3292718 N_multimapping 350969 350969 350969 N_noFeature 397384 10163498 480847 N_ambiguous 331768 3337 209198 UnstrandedReadsAssigned:9637675 PositiveStrandReadsAssigned:199992 NegativeStrandReadsAssigned:9676782 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=130 echo kmer=125 SRR7170845 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7170845-trimmed-pair1.fastq SRR7170845-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,992,727 reads, 11,860,266 reads pseudoaligned [quant] estimated average fragment length: 199.253 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,063 rounds 52401 SRR7170845.ke.tsv 34699 SRR7170845.se.tsv 87100 total ==> SRR7170845.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1819.75 1011 42.2305 Potri.005G024800.1.v4.1 1035 836.747 368 33.4303 Potri.004G059700.1.v4.1 961 762.787 13 1.29547 Potri.007G009000.2.v4.1 1416 1217.75 0 0 Potri.003G141000.2.v4.1 2943 2744.75 513 14.207 Potri.016G087400.1.v4.1 270 108.798 918 641.367 Potri.015G069301.1.v4.1 564 370.514 0 0 Potri.010G195200.1.v4.1 1773 1574.75 438.952 21.1881 Potri.012G127500.1.v4.1 977 778.774 368 35.9189 ==> SRR7170845.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 534 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 373 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 16 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 4 SRR7170845 completed mapping pipeline successfully