Starting /dee2/code/volunteer_pipeline.sh SRR12666370 current disk space = 1543171289088 free memory = 1606489624 SRR12666370 SRAfilesize 78bb29b4e381cec06021ec9651079ca0 SRR12666370.sra SRR12666370.sra file validated SRR12666370 is paired end SRR12666370 is conventional basespace SRR12666370 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666370_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4165 37.0 37.0 37.0 37.0 37.0 2 36.2425 37.0 37.0 37.0 37.0 37.0 3 36.3695 37.0 37.0 37.0 37.0 37.0 4 36.536 37.0 37.0 37.0 37.0 37.0 5 36.5715 37.0 37.0 37.0 37.0 37.0 6 36.5705 37.0 37.0 37.0 37.0 37.0 7 36.476 37.0 37.0 37.0 37.0 37.0 8 36.5835 37.0 37.0 37.0 37.0 37.0 9 36.5285 37.0 37.0 37.0 37.0 37.0 10-14 36.535900000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.5054 37.0 37.0 37.0 37.0 37.0 20-24 36.4844 37.0 37.0 37.0 37.0 37.0 25-29 36.4007 37.0 37.0 37.0 37.0 37.0 30-34 36.4311 37.0 37.0 37.0 37.0 37.0 35-39 36.3603 37.0 37.0 37.0 37.0 37.0 40-44 36.343199999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.33200000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.356300000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.2993 37.0 37.0 37.0 37.0 37.0 60-64 36.341300000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.294200000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.2657 37.0 37.0 37.0 37.0 37.0 75-79 36.248400000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.1991 37.0 37.0 37.0 37.0 37.0 85-89 36.1774 37.0 37.0 37.0 37.0 37.0 90-94 36.135999999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.093399999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.098200000000006 37.0 37.0 37.0 37.0 37.0 105-109 36.1367 37.0 37.0 37.0 37.0 37.0 110-114 36.005100000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.970200000000006 37.0 37.0 37.0 37.0 37.0 120-124 35.9815 37.0 37.0 37.0 37.0 37.0 125-129 35.941500000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.9236 37.0 37.0 37.0 37.0 37.0 135-139 35.8926 37.0 37.0 37.0 37.0 37.0 140-144 35.7105 37.0 37.0 37.0 37.0 37.0 145-149 35.54350000000001 37.0 37.0 37.0 37.0 37.0 150-151 35.2885 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 3.0 24 2.0 25 5.0 26 4.0 27 8.0 28 18.0 29 18.0 30 27.0 31 27.0 32 59.0 33 92.0 34 157.0 35 313.0 36 2832.0 37 431.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 49.5 12.925 7.124999999999999 30.45 2 22.011005502751377 16.633316658329164 33.991995997999 27.363681840920464 3 20.225 24.2 27.575 28.000000000000004 4 23.799999999999997 31.0 22.175 23.025000000000002 5 24.45 33.2 21.675 20.674999999999997 6 21.75 33.6 23.549999999999997 21.099999999999998 7 17.5 22.3 40.2 20.0 8 20.375 22.75 28.499999999999996 28.375 9 20.375 20.75 30.4 28.475 10-14 23.305 26.275 24.6 25.82 15-19 23.155 25.21 25.490000000000002 26.145000000000003 20-24 22.93 26.055 25.72 25.295 25-29 23.119999999999997 25.605 25.645 25.629999999999995 30-34 22.795 25.825 25.64 25.740000000000002 35-39 22.720000000000002 25.779999999999998 26.040000000000003 25.46 40-44 22.775000000000002 26.55 25.135 25.540000000000003 45-49 22.97 25.44 25.41 26.179999999999996 50-54 22.975 25.905 25.215 25.905 55-59 22.945 25.874999999999996 25.455 25.724999999999998 60-64 23.375 26.314999999999998 24.575 25.735000000000003 65-69 23.244999999999997 26.045 24.805 25.905 70-74 23.11 26.415 25.025 25.45 75-79 23.73 25.545 24.89 25.835 80-84 23.49 25.874999999999996 24.560000000000002 26.075 85-89 23.599999999999998 25.369999999999997 25.4 25.629999999999995 90-94 23.32 24.965 25.124999999999996 26.590000000000003 95-99 23.549999999999997 26.05 24.725 25.674999999999997 100-104 24.0 25.740000000000002 25.019999999999996 25.240000000000002 105-109 23.89 25.724999999999998 24.42 25.965 110-114 23.35 26.215 24.59 25.845000000000002 115-119 23.599999999999998 26.005 24.935 25.46 120-124 23.474999999999998 25.45 24.66 26.415 125-129 24.485 25.205 24.635 25.674999999999997 130-134 24.32 25.380000000000003 24.295 26.005 135-139 24.18 26.31 23.880000000000003 25.629999999999995 140-144 23.715 25.845000000000002 24.545 25.895000000000003 145-149 24.055 25.305 24.425 26.215 150-151 23.575 25.412499999999998 24.887500000000003 26.125 >>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 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.0 21 0.0 22 0.5 23 0.5 24 0.5 25 0.5 26 1.0 27 2.5 28 4.0 29 3.5 30 5.0 31 11.5 32 19.0 33 25.0 34 27.0 35 35.0 36 44.0 37 55.0 38 80.0 39 97.5 40 120.0 41 149.0 42 170.0 43 180.5 44 196.0 45 206.5 46 210.5 47 209.0 48 187.0 49 184.0 50 179.0 51 155.0 52 134.0 53 127.5 54 128.5 55 113.0 56 93.5 57 88.0 58 89.0 59 71.0 60 63.0 61 67.5 62 63.5 63 60.0 64 51.5 65 48.0 66 45.5 67 40.0 68 38.5 69 30.5 70 18.0 71 17.0 72 15.5 73 11.0 74 7.5 75 7.5 76 6.0 77 2.0 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 0.05 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 92.325 #Duplication Level Percentage of deduplicated Percentage of total 1 92.30977525047386 85.225 2 7.1215813701597614 13.15 3 0.5415651232060655 1.5 4 0.0 0.0 5 0.027078256160303276 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 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 GTAGTGTAGTACGGGTAGAGGCATCAGAGGCTGCTGCTTCAGTGGCCGCA 5 0.125 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 0.0 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.30000000000000004 0.0 0.0 0.0 0.0 88-89 0.35 0.0 0.0 0.0 0.0 90-91 0.4 0.0 0.0 0.0 0.0 92-93 0.44999999999999996 0.0 0.0 0.0 0.0 94-95 0.5 0.0 0.0 0.0 0.0 96-97 0.6125 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 1.075 0.0 0.0 0.0 0.0 102-103 1.2625000000000002 0.0 0.0 0.0 0.0 104-105 1.4500000000000002 0.0 0.0 0.0 0.0 106-107 1.6875 0.0 0.0 0.0 0.0 108-109 2.0625 0.0 0.0 0.0 0.0 110-111 2.4875 0.0 0.0 0.0 0.0 112-113 2.775 0.0 0.0 0.0 0.0 114-115 2.9375 0.0 0.0 0.0 0.0 116-117 3.1625 0.0 0.0 0.0 0.0 118-119 3.3625 0.0 0.0 0.0 0.0 120-121 3.625 0.0 0.0 0.0 0.0 122-123 3.8625 0.0 0.0 0.0 0.0 124-125 4.2125 0.0 0.0 0.0 0.0 126-127 4.5375 0.0 0.0 0.0 0.0 128-129 4.8625 0.0 0.0 0.0 0.0 130-131 5.375 0.0 0.0 0.0 0.0 132-133 5.8125 0.0 0.0 0.0 0.0 134-135 6.425000000000001 0.0 0.0 0.0 0.0 136-137 6.9125 0.0 0.0 0.0 0.0 138-139 7.4875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AACCGTC 10 0.006830828 145.0 6 GTTCTAG 10 0.006830828 145.0 5 TCGTTCT 10 0.006830828 145.0 3 TTCTAGG 10 0.006830828 145.0 6 ATCGTTC 10 0.006830828 145.0 2 TAGGGCG 10 0.006830828 145.0 9 CATCGTT 10 0.006830828 145.0 1 CGTTCTA 10 0.006830828 145.0 4 >>END_MODULE SRR12666370 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666370_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.078 37.0 37.0 37.0 37.0 37.0 2 35.916 37.0 37.0 37.0 37.0 37.0 3 36.2045 37.0 37.0 37.0 37.0 37.0 4 36.2805 37.0 37.0 37.0 37.0 37.0 5 36.288 37.0 37.0 37.0 37.0 37.0 6 36.1585 37.0 37.0 37.0 37.0 37.0 7 36.215 37.0 37.0 37.0 37.0 37.0 8 36.2965 37.0 37.0 37.0 37.0 37.0 9 36.224 37.0 37.0 37.0 37.0 37.0 10-14 36.2986 37.0 37.0 37.0 37.0 37.0 15-19 36.2434 37.0 37.0 37.0 37.0 37.0 20-24 36.172999999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.187599999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.152499999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.1074 37.0 37.0 37.0 37.0 37.0 40-44 36.111599999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.12030000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.028499999999994 37.0 37.0 37.0 37.0 37.0 55-59 36.076299999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.029700000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.0025 37.0 37.0 37.0 37.0 37.0 70-74 35.9981 37.0 37.0 37.0 37.0 37.0 75-79 35.959199999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.93470000000001 37.0 37.0 37.0 37.0 37.0 85-89 35.8724 37.0 37.0 37.0 37.0 37.0 90-94 35.85809999999999 37.0 37.0 37.0 37.0 37.0 95-99 35.86750000000001 37.0 37.0 37.0 37.0 37.0 100-104 35.8927 37.0 37.0 37.0 37.0 37.0 105-109 35.782300000000006 37.0 37.0 37.0 37.0 37.0 110-114 35.767199999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.756299999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.733 37.0 37.0 37.0 37.0 37.0 125-129 35.7224 37.0 37.0 37.0 37.0 37.0 130-134 35.662400000000005 37.0 37.0 37.0 37.0 37.0 135-139 35.5517 37.0 37.0 37.0 37.0 37.0 140-144 35.470099999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.3424 37.0 37.0 37.0 37.0 37.0 150-151 34.9285 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 4.0 14 12.0 15 4.0 16 0.0 17 0.0 18 1.0 19 4.0 20 3.0 21 1.0 22 4.0 23 6.0 24 5.0 25 9.0 26 8.0 27 10.0 28 15.0 29 21.0 30 35.0 31 35.0 32 49.0 33 93.0 34 162.0 35 414.0 36 2610.0 37 493.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.925000000000004 17.150000000000002 8.625 24.3 2 29.099999999999998 20.349999999999998 27.700000000000003 22.85 3 24.85 23.1 29.075 22.975 4 27.400000000000002 30.725 18.5 23.375 5 26.0 35.4 18.075 20.525 6 22.975 34.025 18.05 24.95 7 21.85 17.775 35.8 24.575 8 23.0 21.55 24.325 31.125000000000004 9 24.099999999999998 21.65 24.425 29.825000000000003 10-14 25.825 25.040000000000003 23.18 25.955000000000002 15-19 26.16 24.535 23.845 25.46 20-24 25.645 24.75 24.605 25.0 25-29 26.235000000000003 25.105 23.785 24.875 30-34 25.83 24.815 24.145 25.21 35-39 25.345000000000002 24.625 25.06 24.97 40-44 26.095000000000002 24.85 23.875 25.180000000000003 45-49 26.645000000000003 25.080000000000002 23.810000000000002 24.465 50-54 25.935000000000002 25.900000000000002 23.945 24.22 55-59 26.5 25.124999999999996 24.46 23.915 60-64 26.105 25.165 24.325 24.404999999999998 65-69 25.745 25.319999999999997 24.755 24.18 70-74 26.369999999999997 24.59 24.7 24.34 75-79 26.465 25.055 24.735 23.745 80-84 26.08 25.045 24.745 24.13 85-89 27.250000000000004 24.66 24.62 23.47 90-94 26.46 24.87 24.63 24.04 95-99 26.245 24.22 25.330000000000002 24.205 100-104 26.14 25.75 24.125 23.985 105-109 26.44 25.224999999999998 24.715 23.62 110-114 26.75 25.874999999999996 24.13 23.244999999999997 115-119 26.875 24.715 25.275 23.135 120-124 26.685 25.595000000000002 24.07 23.65 125-129 26.805 25.445 24.865000000000002 22.884999999999998 130-134 27.16 26.490000000000002 24.295 22.055 135-139 26.83 26.355 24.2 22.615 140-144 27.26 25.795 24.2 22.745 145-149 27.834999999999997 25.56 24.47 22.134999999999998 150-151 28.262500000000003 25.0125 24.0 22.725 >>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 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 1.0 14 0.5 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 2.5 27 3.0 28 1.0 29 2.0 30 4.5 31 4.5 32 3.5 33 9.5 34 20.5 35 24.0 36 31.5 37 48.5 38 69.5 39 93.0 40 104.5 41 110.0 42 122.0 43 155.0 44 176.0 45 199.5 46 213.0 47 197.5 48 186.0 49 180.5 50 165.0 51 149.0 52 130.5 53 120.0 54 128.5 55 122.0 56 105.0 57 100.0 58 98.0 59 87.5 60 81.0 61 74.0 62 77.5 63 81.0 64 76.5 65 67.0 66 55.0 67 52.5 68 59.0 69 46.5 70 33.5 71 37.5 72 29.5 73 14.0 74 8.5 75 6.0 76 4.5 77 3.0 78 1.5 79 0.5 80 0.0 81 0.0 82 0.5 83 1.0 84 0.5 85 0.5 86 1.0 87 1.0 88 1.0 89 0.5 90 1.0 91 1.0 92 0.0 93 0.5 94 1.0 95 1.5 96 1.0 97 0.0 98 0.0 99 0.0 100 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 91.925 #Duplication Level Percentage of deduplicated Percentage of total 1 92.22192004351373 84.775 2 7.070981778623878 13.0 3 0.6255099265705739 1.725 4 0.0 0.0 5 0.027196083763937992 0.125 6 0.027196083763937992 0.15 7 0.0 0.0 8 0.0 0.0 9 0.027196083763937992 0.22499999999999998 >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 9 0.22499999999999998 No Hit GGTTGACACCGAGAAGAGCCACTTCGAGGTGCAGGAGTCCGCGGCGGAGA 6 0.15 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 5 0.125 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 0.0 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.30000000000000004 0.0 0.0 0.0 0.0 88-89 0.35 0.0 0.0 0.0 0.0 90-91 0.4 0.0 0.0 0.0 0.0 92-93 0.44999999999999996 0.0 0.0 0.0 0.0 94-95 0.5 0.0 0.0 0.0 0.0 96-97 0.6125 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 1.075 0.0 0.0 0.0 0.0 102-103 1.275 0.0 0.0 0.0 0.0 104-105 1.475 0.0 0.0 0.0 0.0 106-107 1.7125 0.0 0.0 0.0 0.0 108-109 2.0875 0.0 0.0 0.0 0.0 110-111 2.5125 0.0 0.0 0.0 0.0 112-113 2.8125 0.0 0.0 0.0 0.0 114-115 2.9875 0.0 0.0 0.0 0.0 116-117 3.1875 0.0 0.0 0.0 0.0 118-119 3.3875 0.0 0.0 0.0 0.0 120-121 3.6500000000000004 0.0 0.0 0.0 0.0 122-123 3.8875 0.0 0.0 0.0 0.0 124-125 4.25 0.0 0.0 0.0 0.0 126-127 4.5875 0.0 0.0 0.0 0.0 128-129 4.925000000000001 0.0 0.0 0.0 0.0 130-131 5.4625 0.0 0.0 0.0 0.0 132-133 5.9375 0.0 0.0 0.0 0.0 134-135 6.5625 0.0 0.0 0.0 0.0 136-137 7.0875 0.0 0.0 0.0 0.0 138-139 7.6625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCTAGGT 10 0.006830828 145.0 7 GTCTGAA 10 0.006830828 145.0 6 CTAGGTT 10 0.006830828 145.0 8 GCCAGGA 10 0.006830828 145.0 145 TAGGTTT 10 0.006830828 145.0 9 AGTGTGA 25 8.7132835E-4 87.0 145 >>END_MODULE Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405105 spots for SRR12666370.sra Written 1405105 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra Read 1405104 spots for SRR12666370.sra Written 1405104 spots for SRR12666370.sra SRR ids: ['SRR12666370.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_s6ssibd9 SRR12666370.sra spots: 28102081 blocks: [[1, 1405104], [1405105, 2810208], [2810209, 4215312], [4215313, 5620416], [5620417, 7025520], [7025521, 8430624], [8430625, 9835728], [9835729, 11240832], [11240833, 12645936], [12645937, 14051040], [14051041, 15456144], [15456145, 16861248], [16861249, 18266352], [18266353, 19671456], [19671457, 21076560], [21076561, 22481664], [22481665, 23886768], [23886769, 25291872], [25291873, 26696976], [26696977, 28102081]] SRR12666370 file size 9528616 SRR12666370 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 SRR12666370 SRR12666370_1.fastq SRR12666370_2.fastq Input file: SRR12666370_1.fastq Paired file: SRR12666370_2.fastq trimmed: SRR12666370-trimmed-pair1.fastq, SRR12666370-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 13:21:55 2024 >> started Sat Dec 7 13:22:27 2024 >> done (31.818s) 28102081 read pairs processed; of these: 61 ( 0.00%) short read pairs filtered out after trimming by size control 10046 ( 0.04%) empty read pairs filtered out after trimming by size control 28091974 (99.96%) read pairs available; of these: 3031238 (10.79%) trimmed read pairs available after processing 25060736 (89.21%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 15 0.00% 20 13 0.00% 21 12 0.00% 22 17 0.00% 23 17 0.00% 24 16 0.00% 25 23 0.00% 26 20 0.00% 27 26 0.00% 28 24 0.00% 29 24 0.00% 30 37 0.00% 31 29 0.00% 32 35 0.00% 33 20 0.00% 34 34 0.00% 35 34 0.00% 36 48 0.00% 37 45 0.00% 38 51 0.00% 39 51 0.00% 40 53 0.00% 41 59 0.00% 42 46 0.00% 43 60 0.00% 44 62 0.00% 45 57 0.00% 46 69 0.00% 47 60 0.00% 48 88 0.00% 49 71 0.00% 50 81 0.00% 51 120 0.00% 52 102 0.00% 53 118 0.00% 54 105 0.00% 55 121 0.00% 56 144 0.00% 57 167 0.00% 58 176 0.00% 59 188 0.00% 60 231 0.00% 61 245 0.00% 62 306 0.00% 63 299 0.00% 64 360 0.00% 65 406 0.00% 66 452 0.00% 67 491 0.00% 68 591 0.00% 69 753 0.00% 70 797 0.00% 71 972 0.00% 72 1072 0.00% 73 1320 0.00% 74 1456 0.01% 75 1511 0.01% 76 1703 0.01% 77 1874 0.01% 78 2224 0.01% 79 2631 0.01% 80 2934 0.01% 81 3385 0.01% 82 4057 0.01% 83 4497 0.02% 84 5015 0.02% 85 5590 0.02% 86 5906 0.02% 87 6631 0.02% 88 7068 0.03% 89 7938 0.03% 90 8728 0.03% 91 10061 0.04% 92 10946 0.04% 93 12267 0.04% 94 13313 0.05% 95 14084 0.05% 96 14820 0.05% 97 15905 0.06% 98 16370 0.06% 99 17870 0.06% 100 18801 0.07% 101 20709 0.07% 102 22683 0.08% 103 24454 0.09% 104 25845 0.09% 105 27304 0.10% 106 27849 0.10% 107 28830 0.10% 108 29676 0.11% 109 31127 0.11% 110 32015 0.11% 111 34093 0.12% 112 36281 0.13% 113 38614 0.14% 114 41303 0.15% 115 41957 0.15% 116 43193 0.15% 117 43951 0.16% 118 44187 0.16% 119 45350 0.16% 120 46464 0.17% 121 48165 0.17% 122 51128 0.18% 123 53316 0.19% 124 56376 0.20% 125 57711 0.21% 126 58682 0.21% 127 59440 0.21% 128 59497 0.21% 129 59689 0.21% 130 61118 0.22% 131 62281 0.22% 132 65520 0.23% 133 67448 0.24% 134 71022 0.25% 135 73099 0.26% 136 73325 0.26% 137 74340 0.26% 138 74307 0.26% 139 74899 0.27% 140 74451 0.27% 141 76443 0.27% 142 77305 0.28% 143 80070 0.29% 144 84585 0.30% 145 86115 0.31% 146 87001 0.31% 147 88485 0.31% 148 86664 0.31% 149 87388 0.31% 150 87058 0.31% 151 25060736 89.21% 28091974 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=4.79 fanout-score-rank=25 prefix-density=0.23 prefix-fanout=3.8 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.04 sequence-density-rank=29 fanout-score=154.19 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=15.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.23 fanout-score-rank=33 prefix-density=0.51 prefix-fanout=2.1 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=33 fanout-score=597.23 fanout-score-rank=1 prefix-density=0.84 prefix-fanout=19.8 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGACTGTGCCGTGCTTATCATTGACTCCACGACTGGAGGTTTTGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCATGCCCTCCTTGCTTTCACTCTTGGAGTGAAGCAGATGATCTGCTGCTGCAACAAGATGGA SRR12666370 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:23:13 Started mapping on | Dec 07 13:23:14 Finished on | Dec 07 13:26:06 Mapping speed, Million of reads per hour | 587.97 Number of input reads | 28091974 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 26413323 Uniquely mapped reads % | 94.02% Average mapped length | 295.96 Number of splices: Total | 28391613 Number of splices: Annotated (sjdb) | 26638621 Number of splices: GT/AG | 28002330 Number of splices: GC/AG | 321892 Number of splices: AT/AC | 19927 Number of splices: Non-canonical | 47464 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.50 Insertion rate per base | 0.01% Insertion average length | 1.96 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 358535 % of reads mapped to multiple loci | 1.28% Number of reads mapped to too many loci | 47252 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.61% % of reads unmapped: other | 0.92% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1320116 1320116 1320116 N_multimapping 358535 358535 358535 N_noFeature 847771 25778728 1052274 N_ambiguous 506538 3552 78462 UnstrandedReadsAssigned:25059014 PositiveStrandReadsAssigned:631043 NegativeStrandReadsAssigned:25282587 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666370 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: SRR12666370-trimmed-pair1.fastq SRR12666370-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,091,974 reads, 25,721,663 reads pseudoaligned [quant] estimated average fragment length: 276.684 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,136 rounds 52973 SRR12666370.ke.tsv 35125 SRR12666370.se.tsv 88098 total ==> SRR12666370.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 661.344 0 0 PNS24247 1044 768.316 116.971 9.104 PNS24249 1928 1652.32 140.966 5.10168 PNS24246 1044 768.316 116.971 9.104 PNS24248 1044 768.316 116.971 9.104 PNS24244 1471 1195.32 249.12 12.4628 PNS24243 293 97.1543 0 0 KQK14069 1603 1327.32 5176.44 233.211 KQK14071 474 233.095 103.896 26.6536 ==> SRR12666370.se.tsv <== BRADI_1g14170v3 5914 BRADI_1g53295v3 122 BRADI_1g59795v3 600 BRADI_1g07683v3 0 BRADI_1g00485v3 93 BRADI_1g20270v3 2159 BRADI_1g74790v3 52 BRADI_1g09890v3 0 BRADI_1g77505v3 172 BRADI_1g48960v3 0 SRR12666370 completed mapping pipeline successfully