Starting /dee2/code/volunteer_pipeline.sh SRR12951314 current disk space = 1543070588928 free memory = 1598057348 SRR12951314 SRAfilesize 72ee6aff399b3c0a3ec73b07ef6e227c SRR12951314.sra SRR12951314.sra file validated SRR12951314 is paired end SRR12951314 is conventional basespace SRR12951314 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951314_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5345 37.0 37.0 37.0 37.0 37.0 2 36.24425 37.0 37.0 37.0 37.0 37.0 3 36.4705 37.0 37.0 37.0 37.0 37.0 4 36.5445 37.0 37.0 37.0 37.0 37.0 5 36.605 37.0 37.0 37.0 37.0 37.0 6 36.608 37.0 37.0 37.0 37.0 37.0 7 36.5835 37.0 37.0 37.0 37.0 37.0 8 36.555 37.0 37.0 37.0 37.0 37.0 9 36.5995 37.0 37.0 37.0 37.0 37.0 10-14 36.540800000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.5445 37.0 37.0 37.0 37.0 37.0 20-24 36.50170000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.487 37.0 37.0 37.0 37.0 37.0 30-34 36.4356 37.0 37.0 37.0 37.0 37.0 35-39 36.4054 37.0 37.0 37.0 37.0 37.0 40-44 36.4279 37.0 37.0 37.0 37.0 37.0 45-49 36.32039999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.3595 37.0 37.0 37.0 37.0 37.0 55-59 36.339999999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.3208 37.0 37.0 37.0 37.0 37.0 65-69 36.209999999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.20309999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.2096 37.0 37.0 37.0 37.0 37.0 80-84 36.2208 37.0 37.0 37.0 37.0 37.0 85-89 36.1854 37.0 37.0 37.0 37.0 37.0 90-94 36.17100000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.1015 37.0 37.0 37.0 37.0 37.0 100-104 36.1435 37.0 37.0 37.0 37.0 37.0 105-109 36.096500000000006 37.0 37.0 37.0 37.0 37.0 110-114 36.073899999999995 37.0 37.0 37.0 37.0 37.0 115-119 36.132 37.0 37.0 37.0 37.0 37.0 120-124 36.101600000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.9302 37.0 37.0 37.0 37.0 37.0 130-134 35.9473 37.0 37.0 37.0 37.0 37.0 135-139 35.9149 37.0 37.0 37.0 37.0 37.0 140-144 35.899800000000006 37.0 37.0 37.0 37.0 37.0 145-149 35.8459 37.0 37.0 37.0 37.0 37.0 150-151 35.655 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 2.0 23 3.0 24 8.0 25 5.0 26 8.0 27 8.0 28 15.0 29 16.0 30 23.0 31 37.0 32 43.0 33 78.0 34 128.0 35 282.0 36 2867.0 37 476.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.75 11.375 5.575 35.3 2 23.196783111334508 9.977381251570746 30.811761749183216 36.014073887911536 3 20.1 14.899999999999999 26.25 38.75 4 25.8 20.849999999999998 22.175 31.175000000000004 5 27.05 25.224999999999998 22.325 25.4 6 24.925 30.475 22.475 22.125 7 21.075 23.75 35.325 19.85 8 21.4 23.925 28.725 25.95 9 21.15 21.875 29.2 27.775 10-14 24.3 25.89 23.84 25.97 15-19 24.235 24.654999999999998 24.66 26.450000000000003 20-24 23.805 25.040000000000003 24.865000000000002 26.290000000000003 25-29 24.755 24.455 24.165 26.625 30-34 24.610000000000003 24.72 24.145 26.525 35-39 24.18 24.13 24.63 27.060000000000002 40-44 24.79 24.585 23.82 26.805 45-49 24.195 24.884999999999998 24.715 26.205000000000002 50-54 24.685000000000002 24.295 24.815 26.205000000000002 55-59 24.834999999999997 24.25 24.515 26.400000000000002 60-64 24.6 24.695 23.625 27.08 65-69 24.73 24.63 23.985 26.655 70-74 24.695 24.55 24.035 26.72 75-79 24.775 24.625 23.735 26.865 80-84 25.5 24.805 23.16 26.534999999999997 85-89 25.56 24.585 23.400000000000002 26.455000000000002 90-94 25.105 24.295 23.974999999999998 26.625 95-99 24.44 24.81 23.77 26.979999999999997 100-104 25.174999999999997 24.445 23.775 26.605 105-109 25.264999999999997 24.115000000000002 23.765 26.855 110-114 25.275 24.47 23.724999999999998 26.529999999999998 115-119 25.430000000000003 24.45 23.9 26.22 120-124 25.009999999999998 24.435000000000002 23.605 26.950000000000003 125-129 24.965 24.86 23.555 26.619999999999997 130-134 25.25 25.365 22.785 26.6 135-139 25.27 24.295 23.59 26.845000000000002 140-144 25.540000000000003 24.13 23.965 26.365 145-149 25.69 24.135 23.799999999999997 26.375 150-151 25.974999999999998 24.825 22.8625 26.337500000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 1.0 6 1.0 7 0.5 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 0.5 23 0.5 24 1.0 25 2.5 26 2.5 27 1.0 28 1.5 29 3.0 30 6.0 31 6.5 32 5.5 33 8.5 34 19.0 35 31.5 36 38.0 37 45.0 38 65.5 39 83.5 40 93.0 41 114.5 42 140.0 43 152.5 44 164.5 45 170.0 46 180.0 47 193.0 48 191.0 49 177.5 50 155.5 51 145.5 52 146.0 53 127.0 54 97.5 55 92.5 56 104.0 57 103.5 58 85.0 59 72.5 60 74.5 61 70.5 62 64.5 63 67.5 64 70.5 65 81.5 66 77.5 67 71.0 68 68.5 69 58.0 70 47.5 71 35.0 72 34.5 73 31.0 74 25.0 75 24.5 76 19.0 77 11.5 78 7.0 79 8.5 80 7.0 81 3.0 82 4.0 83 3.0 84 1.0 85 0.5 86 0.5 87 0.5 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 0.525 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 82.875 #Duplication Level Percentage of deduplicated Percentage of total 1 84.0422322775264 69.65 2 12.458521870286576 20.65 3 2.6847662141779787 6.675000000000001 4 0.603318250377074 2.0 5 0.12066365007541478 0.5 6 0.06033182503770739 0.3 7 0.0 0.0 8 0.0 0.0 9 0.030165912518853696 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAACGACATCTCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 19 (97% over 37bp) GCATTATTAATAGTACAGTTCGGTCCGACAGACGTCGACACAACCATTAG 6 0.15 No Hit GGGGAAGGGAGCTTCGAGGCGGCCGGACGCGGCTCGTCGGCCGGAACGGC 6 0.15 No Hit GGTCGCCTCCATCCCTGTAGATAGATAACCATAAAGACCAACAAACATGG 5 0.125 No Hit ACCGGCACCAAGAACAGATCCGACTAATACATTCCTTGCACGCCACATTG 5 0.125 No Hit GTCGCAGCACTTCGGCCAATACCCCACGGCATTCACCTCTGCAAGGATTC 5 0.125 No Hit GTCCCTCTCACCGGCAGTGAGGATGGCCCCGACGCCGCCGTCTGTGGTGG 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 0.0125 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.037500000000000006 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.2875 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 0.5 0.0 0.0 0.0 0.0 92-93 0.6125 0.0 0.0 0.0 0.0 94-95 0.775 0.0 0.0 0.0 0.0 96-97 0.875 0.0 0.0 0.0 0.0 98-99 1.05 0.0 0.0 0.0 0.0 100-101 1.25 0.0 0.0 0.0 0.0 102-103 1.4375 0.0 0.0 0.0 0.0 104-105 1.5875 0.0 0.0 0.0 0.0 106-107 1.7625 0.0 0.0 0.0 0.0 108-109 2.0 0.0 0.0 0.0 0.0 110-111 2.2875 0.0 0.0 0.0 0.0 112-113 2.5125 0.0 0.0 0.0 0.0 114-115 2.7125 0.0 0.0 0.0 0.0 116-117 3.0625 0.0 0.0 0.0 0.0 118-119 3.425 0.0 0.0 0.0 0.0 120-121 3.9250000000000003 0.0 0.0 0.0 0.0 122-123 4.425000000000001 0.0 0.0 0.0 0.0 124-125 4.95 0.0 0.0 0.0 0.0 126-127 5.5375 0.0 0.0 0.0 0.0 128-129 5.987500000000001 0.0 0.0 0.0 0.0 130-131 6.4625 0.0 0.0 0.0 0.0 132-133 6.9375 0.0 0.0 0.0 0.0 134-135 7.6125 0.0 0.0 0.0 0.0 136-137 8.0375 0.0 0.0 0.0 0.0 138-139 8.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12951314 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951314_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2035 37.0 37.0 37.0 37.0 37.0 2 36.153 37.0 37.0 37.0 37.0 37.0 3 36.248 37.0 37.0 37.0 37.0 37.0 4 36.218 37.0 37.0 37.0 37.0 37.0 5 36.179 37.0 37.0 37.0 37.0 37.0 6 36.2095 37.0 37.0 37.0 37.0 37.0 7 36.134 37.0 37.0 37.0 37.0 37.0 8 36.1945 37.0 37.0 37.0 37.0 37.0 9 36.141 37.0 37.0 37.0 37.0 37.0 10-14 36.1567 37.0 37.0 37.0 37.0 37.0 15-19 36.09009999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.0508 37.0 37.0 37.0 37.0 37.0 25-29 35.9675 37.0 37.0 37.0 37.0 37.0 30-34 35.940099999999994 37.0 37.0 37.0 37.0 37.0 35-39 35.8767 37.0 37.0 37.0 37.0 37.0 40-44 35.8837 37.0 37.0 37.0 37.0 37.0 45-49 35.8553 37.0 37.0 37.0 37.0 37.0 50-54 35.8689 37.0 37.0 37.0 37.0 37.0 55-59 35.8594 37.0 37.0 37.0 37.0 37.0 60-64 35.8621 37.0 37.0 37.0 37.0 37.0 65-69 35.811 37.0 37.0 37.0 37.0 37.0 70-74 35.7536 37.0 37.0 37.0 37.0 37.0 75-79 35.7689 37.0 37.0 37.0 37.0 37.0 80-84 35.696000000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.693799999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.7043 37.0 37.0 37.0 37.0 37.0 95-99 35.6947 37.0 37.0 37.0 37.0 37.0 100-104 35.6856 37.0 37.0 37.0 37.0 37.0 105-109 35.571000000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.60719999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.6643 37.0 37.0 37.0 37.0 37.0 120-124 35.6358 37.0 37.0 37.0 37.0 37.0 125-129 35.5306 37.0 37.0 37.0 37.0 37.0 130-134 35.530899999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.470000000000006 37.0 37.0 37.0 37.0 37.0 140-144 35.42379999999999 37.0 37.0 37.0 37.0 37.0 145-149 35.346 37.0 37.0 37.0 37.0 37.0 150-151 35.1635 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 13.0 14 9.0 15 9.0 16 2.0 17 2.0 18 4.0 19 5.0 20 5.0 21 11.0 22 9.0 23 12.0 24 8.0 25 5.0 26 12.0 27 16.0 28 15.0 29 15.0 30 23.0 31 32.0 32 38.0 33 70.0 34 138.0 35 463.0 36 2721.0 37 363.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.1 21.349999999999998 7.775 27.775 2 30.3 23.150000000000002 24.5 22.05 3 25.724999999999998 24.175 27.875 22.225 4 27.675 29.925 18.95 23.45 5 29.5 31.125000000000004 17.925 21.45 6 25.4 34.0 18.05 22.55 7 23.849999999999998 19.275000000000002 32.9 23.974999999999998 8 25.525 22.625 23.425 28.425 9 25.35 22.05 26.275 26.325 10-14 27.800000000000004 24.015 21.935 26.25 15-19 28.000000000000004 25.085 21.97 24.945 20-24 27.3 24.69 22.505 25.505 25-29 26.845000000000002 24.54 22.985 25.629999999999995 30-34 26.93 24.335 23.48 25.255 35-39 26.875 24.675 22.75 25.7 40-44 26.834999999999997 24.25 23.075000000000003 25.840000000000003 45-49 26.974999999999998 24.855 23.09 25.080000000000002 50-54 27.13 24.415 23.474999999999998 24.98 55-59 27.195000000000004 24.77 22.845 25.19 60-64 27.735 24.325 23.18 24.759999999999998 65-69 27.26 24.32 23.195 25.224999999999998 70-74 27.345000000000002 24.635 22.8 25.22 75-79 27.255000000000003 24.315 23.005 25.424999999999997 80-84 27.655 23.665 23.405 25.275 85-89 27.310000000000002 23.84 23.849999999999998 25.0 90-94 27.810000000000002 24.0 23.72 24.47 95-99 27.565 24.495 23.745 24.195 100-104 27.450000000000003 24.62 23.150000000000002 24.779999999999998 105-109 28.000000000000004 23.685000000000002 23.73 24.585 110-114 27.41 24.990000000000002 23.31 24.29 115-119 28.43 24.2 23.16 24.21 120-124 27.779999999999998 25.335 22.425 24.46 125-129 27.634999999999998 24.959999999999997 23.43 23.974999999999998 130-134 28.235 25.014999999999997 23.275000000000002 23.474999999999998 135-139 28.505000000000003 24.25 23.145 24.099999999999998 140-144 28.93 24.825 22.725 23.52 145-149 30.0 24.740000000000002 22.455 22.805 150-151 28.9 24.637500000000003 22.537499999999998 23.925 >>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 0.5 8 0.5 9 0.0 10 0.0 11 1.0 12 1.5 13 0.5 14 0.5 15 1.5 16 1.0 17 0.0 18 0.5 19 1.0 20 0.5 21 0.5 22 1.0 23 0.5 24 0.5 25 1.0 26 1.0 27 2.5 28 2.0 29 2.0 30 3.5 31 5.5 32 8.5 33 9.0 34 15.0 35 23.5 36 30.5 37 34.5 38 55.0 39 85.0 40 103.0 41 111.0 42 120.5 43 149.5 44 162.0 45 163.5 46 165.5 47 161.5 48 149.5 49 142.5 50 158.0 51 162.5 52 136.5 53 111.5 54 108.0 55 115.0 56 109.5 57 96.0 58 100.0 59 101.0 60 92.5 61 84.0 62 76.0 63 71.5 64 74.0 65 82.0 66 86.5 67 76.5 68 54.5 69 42.0 70 50.0 71 52.5 72 46.5 73 38.5 74 34.0 75 33.5 76 18.5 77 7.5 78 9.0 79 8.5 80 5.5 81 4.0 82 5.0 83 3.5 84 1.0 85 1.0 86 1.0 87 1.5 88 1.5 89 0.5 90 0.5 91 0.5 92 0.5 93 1.0 94 1.5 95 1.5 96 1.5 97 2.0 98 2.0 99 1.5 100 4.0 >>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 83.275 #Duplication Level Percentage of deduplicated Percentage of total 1 84.53917742419694 70.39999999999999 2 11.978384869408586 19.950000000000003 3 2.6718703092164517 6.675000000000001 4 0.6604623236265386 2.1999999999999997 5 0.09006304413089163 0.375 6 0.03002101471029721 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.03002101471029721 0.25 >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 10 0.25 No Hit CAAGGAGAGGTACGAGAGGGAGTTCGAGGAGCTCGCCCGGGGCGCCGGGT 6 0.15 No Hit CGGGACAATCACCACGACCTCGAGCCGCTCCGTCTCCGTTCCTCCGCTTG 5 0.125 No Hit GAGACGCAATGGAGAAGAGATTCATCCGGGTTGCCAAAGGCTCACTAGTT 5 0.125 No Hit AGAAAGTATGGCAGCAGGAAGCAAGGCCGAGAGAAAAGCAGCAATAGATG 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 0.0125 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.037500000000000006 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.2875 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 0.475 0.0 0.0 0.0 0.0 92-93 0.5875 0.0 0.0 0.0 0.0 94-95 0.75 0.0 0.0 0.0 0.0 96-97 0.8500000000000001 0.0 0.0 0.0 0.0 98-99 1.025 0.0 0.0 0.0 0.0 100-101 1.225 0.0 0.0 0.0 0.0 102-103 1.4125 0.0 0.0 0.0 0.0 104-105 1.5625 0.0 0.0 0.0 0.0 106-107 1.7375 0.0 0.0 0.0 0.0 108-109 1.975 0.0 0.0 0.0 0.0 110-111 2.2625 0.0 0.0 0.0 0.0 112-113 2.4875 0.0 0.0 0.0 0.0 114-115 2.675 0.0 0.0 0.0 0.0 116-117 3.0 0.0 0.0 0.0 0.0 118-119 3.3375000000000004 0.0 0.0 0.0 0.0 120-121 3.825 0.0 0.0 0.0 0.0 122-123 4.324999999999999 0.0 0.0 0.0 0.0 124-125 4.85 0.0 0.0 0.0 0.0 126-127 5.4375 0.0 0.0 0.0 0.0 128-129 5.9125 0.0 0.0 0.0 0.0 130-131 6.387499999999999 0.0 0.0 0.0 0.0 132-133 6.875 0.0 0.0 0.0 0.0 134-135 7.5375 0.0 0.0 0.0 0.0 136-137 7.975 0.0 0.0 0.0 0.0 138-139 8.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTACTG 10 0.006830828 145.0 1 >>END_MODULE Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472543 spots for SRR12951314.sra Written 1472543 spots for SRR12951314.sra Read 1472551 spots for SRR12951314.sra Written 1472551 spots for SRR12951314.sra SRR ids: ['SRR12951314.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jc8xzbin SRR12951314.sra spots: 29450868 blocks: [[1, 1472543], [1472544, 2945086], [2945087, 4417629], [4417630, 5890172], [5890173, 7362715], [7362716, 8835258], [8835259, 10307801], [10307802, 11780344], [11780345, 13252887], [13252888, 14725430], [14725431, 16197973], [16197974, 17670516], [17670517, 19143059], [19143060, 20615602], [20615603, 22088145], [22088146, 23560688], [23560689, 25033231], [25033232, 26505774], [26505775, 27978317], [27978318, 29450868]] SRR12951314 file size 9986993 SRR12951314 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 SRR12951314 SRR12951314_1.fastq SRR12951314_2.fastq Input file: SRR12951314_1.fastq Paired file: SRR12951314_2.fastq trimmed: SRR12951314-trimmed-pair1.fastq, SRR12951314-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 11:35:11 2024 >> started Sat Dec 7 11:35:49 2024 >> done (37.947s) 29450868 read pairs processed; of these: 153 ( 0.00%) short read pairs filtered out after trimming by size control 48517 ( 0.16%) empty read pairs filtered out after trimming by size control 29402198 (99.83%) read pairs available; of these: 3385015 (11.51%) trimmed read pairs available after processing 26017183 (88.49%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 13 0.00% 20 18 0.00% 21 16 0.00% 22 34 0.00% 23 28 0.00% 24 50 0.00% 25 54 0.00% 26 50 0.00% 27 75 0.00% 28 70 0.00% 29 74 0.00% 30 71 0.00% 31 87 0.00% 32 59 0.00% 33 80 0.00% 34 103 0.00% 35 90 0.00% 36 86 0.00% 37 80 0.00% 38 111 0.00% 39 88 0.00% 40 88 0.00% 41 114 0.00% 42 105 0.00% 43 124 0.00% 44 133 0.00% 45 136 0.00% 46 137 0.00% 47 141 0.00% 48 187 0.00% 49 175 0.00% 50 192 0.00% 51 224 0.00% 52 265 0.00% 53 266 0.00% 54 251 0.00% 55 283 0.00% 56 309 0.00% 57 336 0.00% 58 398 0.00% 59 436 0.00% 60 538 0.00% 61 622 0.00% 62 640 0.00% 63 697 0.00% 64 797 0.00% 65 857 0.00% 66 932 0.00% 67 1001 0.00% 68 1047 0.00% 69 1314 0.00% 70 1466 0.00% 71 1694 0.01% 72 1968 0.01% 73 2255 0.01% 74 2396 0.01% 75 2644 0.01% 76 2939 0.01% 77 3219 0.01% 78 3523 0.01% 79 4012 0.01% 80 4419 0.02% 81 5009 0.02% 82 5894 0.02% 83 6396 0.02% 84 7267 0.02% 85 7749 0.03% 86 8611 0.03% 87 8996 0.03% 88 9809 0.03% 89 10524 0.04% 90 11613 0.04% 91 12764 0.04% 92 13791 0.05% 93 15156 0.05% 94 16430 0.06% 95 17625 0.06% 96 18452 0.06% 97 19355 0.07% 98 20555 0.07% 99 21770 0.07% 100 22861 0.08% 101 24266 0.08% 102 25440 0.09% 103 27426 0.09% 104 28866 0.10% 105 30508 0.10% 106 31793 0.11% 107 33372 0.11% 108 33587 0.11% 109 35240 0.12% 110 36391 0.12% 111 38267 0.13% 112 39842 0.14% 113 41844 0.14% 114 44082 0.15% 115 46047 0.16% 116 47085 0.16% 117 48462 0.16% 118 49940 0.17% 119 50730 0.17% 120 52403 0.18% 121 53337 0.18% 122 55434 0.19% 123 57455 0.20% 124 60717 0.21% 125 61216 0.21% 126 63268 0.22% 127 64982 0.22% 128 65288 0.22% 129 67971 0.23% 130 67587 0.23% 131 69315 0.24% 132 71234 0.24% 133 74359 0.25% 134 76173 0.26% 135 78654 0.27% 136 79319 0.27% 137 81083 0.28% 138 81678 0.28% 139 83767 0.28% 140 83879 0.29% 141 85712 0.29% 142 87090 0.30% 143 88367 0.30% 144 90515 0.31% 145 92453 0.31% 146 93029 0.32% 147 93811 0.32% 148 94689 0.32% 149 94488 0.32% 150 97298 0.33% 151 26017183 88.49% 29402198 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=4.37 fanout-score-rank=28 prefix-density=0.32 prefix-fanout=3.1 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.06 sequence-density-rank=32 fanout-score=215.67 fanout-score-rank=1 prefix-density=0.75 prefix-fanout=15.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=1.08 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=33 prefix-density=1.08 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=11 fanout-score=190.79 fanout-score-rank=1 prefix-density=1.04 prefix-fanout=23.0 sequence=CGCCGCCGCCGC SRR12951314 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:36:29 Started mapping on | Dec 07 11:36:30 Finished on | Dec 07 11:40:07 Mapping speed, Million of reads per hour | 487.78 Number of input reads | 29402198 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 26895393 Uniquely mapped reads % | 91.47% Average mapped length | 295.41 Number of splices: Total | 25642929 Number of splices: Annotated (sjdb) | 23966331 Number of splices: GT/AG | 25274429 Number of splices: GC/AG | 313038 Number of splices: AT/AC | 15863 Number of splices: Non-canonical | 39599 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.32 Insertion rate per base | 0.01% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 297407 % of reads mapped to multiple loci | 1.01% Number of reads mapped to too many loci | 123548 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.64% % of reads unmapped: other | 2.46% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2209398 2209398 2209398 N_multimapping 297407 297407 297407 N_noFeature 896054 26178284 1129801 N_ambiguous 567687 3583 84965 UnstrandedReadsAssigned:25431652 PositiveStrandReadsAssigned:713526 NegativeStrandReadsAssigned:25680627 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951314 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: SRR12951314-trimmed-pair1.fastq SRR12951314-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 29,402,198 reads, 26,219,762 reads pseudoaligned [quant] estimated average fragment length: 263.344 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,185 rounds 52973 SRR12951314.ke.tsv 35125 SRR12951314.se.tsv 88098 total ==> SRR12951314.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 674.307 0 0 PNS24247 1044 781.656 119.76 7.99379 PNS24249 1928 1665.66 393.79 12.3349 PNS24246 1044 781.656 119.76 7.99379 PNS24248 1044 781.656 119.76 7.99379 PNS24244 1471 1208.66 204.931 8.84632 PNS24243 293 98.2775 0 0 KQK14069 1603 1340.66 64380 2505.48 KQK14071 474 235.693 312.715 69.2246 ==> SRR12951314.se.tsv <== BRADI_1g14170v3 64904 BRADI_1g53295v3 221 BRADI_1g59795v3 501 BRADI_1g07683v3 0 BRADI_1g00485v3 13 BRADI_1g20270v3 700 BRADI_1g74790v3 2331 BRADI_1g09890v3 0 BRADI_1g77505v3 383 BRADI_1g48960v3 0 SRR12951314 completed mapping pipeline successfully