Starting /dee2/code/volunteer_pipeline.sh SRR12670168 current disk space = 3055686881280 free memory = 1485884796 SRR12670168 SRAfilesize 78dcd0ff59b151c0582270606452069a SRR12670168.sra SRR12670168.sra file validated SRR12670168 is paired end SRR12670168 is conventional basespace SRR12670168 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670168_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6075 37.0 37.0 37.0 37.0 37.0 2 36.5065 37.0 37.0 37.0 37.0 37.0 3 36.63 37.0 37.0 37.0 37.0 37.0 4 36.657 37.0 37.0 37.0 37.0 37.0 5 36.7155 37.0 37.0 37.0 37.0 37.0 6 36.653 37.0 37.0 37.0 37.0 37.0 7 36.572 37.0 37.0 37.0 37.0 37.0 8 36.6825 37.0 37.0 37.0 37.0 37.0 9 36.6155 37.0 37.0 37.0 37.0 37.0 10-14 36.6443 37.0 37.0 37.0 37.0 37.0 15-19 36.57340000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.5698 37.0 37.0 37.0 37.0 37.0 25-29 36.5438 37.0 37.0 37.0 37.0 37.0 30-34 36.549400000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.515100000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.4325 37.0 37.0 37.0 37.0 37.0 45-49 36.085 37.0 37.0 37.0 37.0 37.0 50-54 36.370900000000006 37.0 37.0 37.0 37.0 37.0 55-59 35.9053 37.0 37.0 37.0 37.0 37.0 60-64 35.9003 37.0 37.0 37.0 37.0 37.0 65-69 35.75580000000001 37.0 37.0 37.0 37.0 37.0 70-74 35.939499999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.293899999999994 37.0 37.0 37.0 37.0 37.0 80-84 36.338499999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.28830000000001 37.0 37.0 37.0 37.0 37.0 90-94 36.364 37.0 37.0 37.0 37.0 37.0 95-99 36.258700000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.2859 37.0 37.0 37.0 37.0 37.0 105-109 36.24980000000001 37.0 37.0 37.0 37.0 37.0 110-114 36.2444 37.0 37.0 37.0 37.0 37.0 115-119 36.214299999999994 37.0 37.0 37.0 37.0 37.0 120-124 36.0783 37.0 37.0 37.0 37.0 37.0 125-129 35.9862 37.0 37.0 37.0 37.0 37.0 130-134 35.9151 37.0 37.0 37.0 37.0 37.0 135-139 35.7959 37.0 37.0 37.0 37.0 37.0 140-144 35.5918 37.0 37.0 37.0 37.0 37.0 145-149 35.536699999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.34875 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 1.0 20 1.0 21 0.0 22 1.0 23 0.0 24 0.0 25 2.0 26 4.0 27 4.0 28 8.0 29 13.0 30 18.0 31 36.0 32 56.0 33 66.0 34 252.0 35 362.0 36 2820.0 37 355.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 49.825 10.875 5.8500000000000005 33.45 2 18.061122244488978 15.98196392785571 35.54609218436874 30.410821643286575 3 16.950000000000003 20.5 32.175 30.375000000000004 4 21.2 26.224999999999998 24.325 28.249999999999996 5 24.474999999999998 34.075 22.125 19.325 6 22.15 35.025 23.3 19.525000000000002 7 14.95 26.450000000000003 42.5 16.1 8 16.75 27.775 30.525000000000002 24.95 9 19.825 21.475 34.1 24.6 10-14 20.495 29.205 26.085 24.215 15-19 21.04 28.055000000000003 26.900000000000002 24.005000000000003 20-24 20.835 28.335 27.46 23.369999999999997 25-29 20.405 28.249999999999996 27.0 24.345 30-34 20.28 26.69 27.860000000000003 25.169999999999998 35-39 20.595 28.175 28.315 22.915 40-44 19.785 27.639999999999997 28.444999999999997 24.13 45-49 20.61 27.465 28.17 23.755000000000003 50-54 21.099999999999998 26.875 28.51 23.515 55-59 19.755 27.175 29.255 23.815 60-64 20.95 27.505000000000003 28.575 22.97 65-69 20.285 28.965000000000003 27.400000000000002 23.35 70-74 24.044999999999998 27.55 26.505000000000003 21.9 75-79 23.895 27.595 26.105 22.405 80-84 23.595 26.810000000000002 26.72 22.875 85-89 23.57 27.505000000000003 26.39 22.535 90-94 24.165 27.24 26.295 22.3 95-99 23.830000000000002 27.38 26.119999999999997 22.67 100-104 24.435000000000002 27.3 26.27 21.995 105-109 24.709999999999997 27.105 25.180000000000003 23.005 110-114 24.29 27.474999999999998 25.7 22.535 115-119 24.3 27.765 24.395 23.54 120-124 24.32 26.685 26.150000000000002 22.845 125-129 23.919999999999998 26.055 25.874999999999996 24.15 130-134 23.825 26.634999999999998 25.95 23.59 135-139 24.16 26.72 25.52 23.599999999999998 140-144 24.895 25.395 25.72 23.990000000000002 145-149 25.555 25.624999999999996 25.445 23.375 150-151 25.224999999999998 24.65 26.3125 23.8125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 1.0 8 1.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.5 23 1.5 24 2.5 25 4.5 26 6.5 27 6.5 28 6.0 29 15.0 30 26.5 31 26.5 32 27.5 33 32.5 34 33.5 35 53.5 36 74.5 37 83.5 38 109.0 39 138.0 40 179.0 41 203.5 42 228.0 43 241.5 44 248.0 45 264.5 46 259.0 47 239.5 48 227.0 49 233.5 50 203.5 51 150.5 52 115.0 53 95.5 54 81.0 55 63.5 56 50.5 57 33.0 58 19.5 59 23.0 60 18.0 61 9.5 62 7.5 63 6.0 64 12.0 65 40.5 66 48.0 67 26.0 68 11.5 69 4.0 70 1.5 71 0.5 72 1.0 73 0.5 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 0.0 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 0.2 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.325 #Duplication Level Percentage of deduplicated Percentage of total 1 81.26396425151611 63.65 2 14.873922757740186 23.3 3 3.127992339610597 7.35 4 0.4149377593360996 1.3 5 0.1915097350781998 0.75 6 0.06383657835939993 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.031918289179699966 0.75 >50 0.0 0.0 >100 0.031918289179699966 2.6 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTGATCATCTCGTAT 104 2.6 TruSeq Adapter, Index 18 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTGATCATCGCGTAT 30 0.75 TruSeq Adapter, Index 18 (97% over 38bp) GCGAATTTCATCATCAGTCATCTTCAAGAAATTTCTTGACATTTCAGTTG 6 0.15 No Hit GTTCCATGCTGACGTATCTGTGTGGCACACTGCTACAGCTTTAGCCTTTG 6 0.15 No Hit CATCGATTCCTTCTTCATAGACCCCGTGAGTTGAGGGATATGTAACCATA 5 0.125 No Hit GTCATGGATAACCTTGGCCAAGGGGGCAAGACAGTTTGTAGTGCAGCTAG 5 0.125 No Hit CCATAGTTACTCTTTCAATTTCTTCCTCAAATGCTTTCTGCTGCCTTTCA 5 0.125 No Hit CTAGCATTATCCGGGTCAAGGATGACTTTGTTTGAGATGTATAACGTAGC 5 0.125 No Hit GTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCT 5 0.125 No Hit GTATAATAAAACTTCTTCAGCTCAAGAAAGCTGTCCACAGTCAGCAACAG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0125 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 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 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.0875 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 0.1375 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.1875 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.25 0.0 0.0 0.0 0.0 62-63 0.35 0.0 0.0 0.0 0.0 64-65 0.4625 0.0 0.0 0.0 0.0 66-67 0.575 0.0 0.0 0.0 0.0 68-69 0.6875 0.0 0.0 0.0 0.0 70-71 1.0875 0.0 0.0 0.0 0.0 72-73 1.2875 0.0 0.0 0.0 0.0 74-75 1.6 0.0 0.0 0.0 0.0 76-77 1.8625 0.0 0.0 0.0 0.0 78-79 2.2249999999999996 0.0 0.0 0.0 0.0 80-81 2.45 0.0 0.0 0.0 0.0 82-83 2.8375000000000004 0.0 0.0 0.0 0.0 84-85 3.3625 0.0 0.0 0.0 0.0 86-87 3.8375 0.0 0.0 0.0 0.0 88-89 4.2125 0.0 0.0 0.0 0.0 90-91 4.762499999999999 0.0 0.0 0.0 0.0 92-93 5.5 0.0 0.0 0.0 0.0 94-95 6.15 0.0 0.0 0.0 0.0 96-97 6.824999999999999 0.0 0.0 0.0 0.0 98-99 7.550000000000001 0.0 0.0 0.0 0.0 100-101 8.25 0.0 0.0 0.0 0.0 102-103 9.3125 0.0 0.0 0.0 0.0 104-105 10.2875 0.0 0.0 0.0 0.0 106-107 11.0625 0.0 0.0 0.0 0.0 108-109 11.85 0.0 0.0 0.0 0.0 110-111 12.9 0.0 0.0 0.0 0.0 112-113 13.6 0.0 0.0 0.0 0.0 114-115 14.6875 0.0 0.0 0.0 0.0 116-117 15.7 0.0 0.0 0.0 0.0 118-119 16.5 0.0 0.0 0.0 0.0 120-121 17.475 0.0 0.0 0.0 0.0 122-123 18.15 0.0 0.0 0.0 0.0 124-125 19.025 0.0 0.0 0.0 0.0 126-127 19.7875 0.0 0.0 0.0 0.0 128-129 20.725 0.0 0.0 0.0 0.0 130-131 21.5875 0.0 0.0 0.0 0.0 132-133 22.4 0.0 0.0 0.0 0.0 134-135 23.1875 0.0 0.0 0.0 0.0 136-137 24.325 0.0 0.0 0.0 0.0 138-139 25.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670168 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670168_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.457 37.0 37.0 37.0 37.0 37.0 2 36.2335 37.0 37.0 37.0 37.0 37.0 3 36.1725 37.0 37.0 37.0 37.0 37.0 4 36.27 37.0 37.0 37.0 37.0 37.0 5 36.3865 37.0 37.0 37.0 37.0 37.0 6 36.4085 37.0 37.0 37.0 37.0 37.0 7 36.211 37.0 37.0 37.0 37.0 37.0 8 35.9825 37.0 37.0 37.0 37.0 37.0 9 36.1405 37.0 37.0 37.0 37.0 37.0 10-14 35.9645 37.0 37.0 37.0 37.0 37.0 15-19 36.0472 37.0 37.0 37.0 37.0 37.0 20-24 35.882799999999996 37.0 37.0 37.0 37.0 37.0 25-29 35.6364 37.0 37.0 37.0 37.0 37.0 30-34 35.5117 37.0 37.0 37.0 37.0 37.0 35-39 35.467200000000005 37.0 37.0 37.0 37.0 37.0 40-44 35.455200000000005 37.0 37.0 37.0 37.0 37.0 45-49 35.435500000000005 37.0 37.0 37.0 37.0 37.0 50-54 35.3928 37.0 37.0 37.0 37.0 37.0 55-59 35.484500000000004 37.0 37.0 37.0 37.0 37.0 60-64 35.559900000000006 37.0 37.0 37.0 37.0 37.0 65-69 35.54260000000001 37.0 37.0 37.0 37.0 37.0 70-74 35.25150000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.251400000000004 37.0 37.0 37.0 37.0 37.0 80-84 35.2981 37.0 37.0 37.0 37.0 37.0 85-89 35.4009 37.0 37.0 37.0 37.0 37.0 90-94 35.609700000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.6992 37.0 37.0 37.0 37.0 37.0 100-104 35.7307 37.0 37.0 37.0 37.0 37.0 105-109 35.70399999999999 37.0 37.0 37.0 37.0 37.0 110-114 35.602199999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.5312 37.0 37.0 37.0 37.0 37.0 120-124 35.35080000000001 37.0 37.0 37.0 34.6 37.0 125-129 35.207800000000006 37.0 37.0 37.0 32.2 37.0 130-134 34.9974 37.0 37.0 37.0 25.0 37.0 135-139 34.7589 37.0 37.0 37.0 25.0 37.0 140-144 34.4298 37.0 37.0 37.0 25.0 37.0 145-149 34.0543 37.0 37.0 37.0 25.0 37.0 150-151 33.88475 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 4.0 13 5.0 14 1.0 15 3.0 16 3.0 17 2.0 18 2.0 19 7.0 20 9.0 21 13.0 22 11.0 23 14.0 24 13.0 25 25.0 26 32.0 27 25.0 28 25.0 29 22.0 30 33.0 31 60.0 32 86.0 33 121.0 34 227.0 35 493.0 36 2474.0 37 290.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.575 22.325 8.025 21.075 2 29.425 23.549999999999997 28.849999999999998 18.175 3 24.025 26.474999999999998 30.45 19.05 4 27.650000000000002 32.324999999999996 21.625 18.4 5 26.900000000000002 36.25 20.1 16.75 6 24.975 38.45 20.45 16.125 7 23.0 20.95 37.4 18.65 8 23.974999999999998 23.35 28.425 24.25 9 24.15 23.775 28.499999999999996 23.575 10-14 26.16 27.925 25.624999999999996 20.29 15-19 25.874999999999996 27.089999999999996 26.455000000000002 20.580000000000002 20-24 25.240000000000002 27.47 27.205000000000002 20.085 25-29 25.674999999999997 27.08 27.200000000000003 20.044999999999998 30-34 24.685000000000002 27.1 28.34 19.875 35-39 24.69 27.245 27.775 20.29 40-44 25.11 27.71 27.38 19.8 45-49 24.975 27.05 27.965 20.01 50-54 25.009999999999998 27.52 27.975 19.495 55-59 25.445 27.18 27.250000000000004 20.125 60-64 26.255 26.47 26.895000000000003 20.380000000000003 65-69 26.150000000000002 26.919999999999998 26.46 20.47 70-74 25.22 27.515 26.915 20.349999999999998 75-79 25.34 27.62 26.715 20.325 80-84 26.305 27.644999999999996 25.385 20.665 85-89 26.555 26.634999999999998 26.52 20.29 90-94 27.245 27.48 25.885 19.39 95-99 26.919999999999998 27.744999999999997 25.645 19.689999999999998 100-104 28.28 27.11 25.135 19.475 105-109 28.785 27.255000000000003 25.56 18.4 110-114 28.615000000000002 26.779999999999998 25.555 19.05 115-119 30.025000000000002 26.965 25.180000000000003 17.83 120-124 30.349999999999998 26.96 24.709999999999997 17.98 125-129 31.195 26.14 24.64 18.025 130-134 32.025 25.715 25.285000000000004 16.975 135-139 32.34 25.555 24.995 17.11 140-144 33.845 25.275 23.935000000000002 16.945 145-149 35.08 24.67 24.395 15.855 150-151 35.8875 22.8875 24.462500000000002 16.7625 >>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 0.5 9 0.5 10 0.0 11 0.5 12 1.0 13 1.0 14 1.5 15 1.5 16 1.0 17 0.5 18 0.0 19 1.0 20 2.5 21 3.0 22 2.5 23 2.0 24 3.5 25 2.5 26 2.0 27 8.0 28 12.0 29 13.0 30 20.5 31 23.0 32 20.5 33 27.5 34 40.0 35 65.0 36 96.0 37 112.0 38 130.0 39 139.0 40 151.5 41 188.0 42 237.5 43 255.5 44 244.0 45 254.0 46 256.0 47 243.5 48 224.5 49 206.0 50 175.0 51 142.5 52 114.0 53 95.5 54 89.5 55 73.0 56 50.5 57 38.5 58 29.0 59 13.5 60 11.5 61 8.0 62 2.5 63 3.0 64 2.5 65 3.5 66 4.0 67 3.0 68 2.5 69 1.0 70 1.5 71 2.0 72 2.0 73 1.0 74 1.5 75 2.5 76 1.5 77 2.0 78 2.0 79 1.5 80 2.0 81 1.0 82 1.0 83 1.5 84 2.0 85 1.5 86 1.0 87 2.0 88 3.0 89 4.5 90 4.0 91 3.0 92 5.5 93 8.0 94 7.5 95 8.0 96 10.0 97 12.5 98 12.5 99 11.5 100 14.5 >>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 80.825 #Duplication Level Percentage of deduplicated Percentage of total 1 81.93628209093721 66.225 2 14.382926074853078 23.25 3 2.9075162387875038 7.049999999999999 4 0.37117228580266004 1.2 5 0.24744819053510672 1.0 6 0.06186204763377668 0.3 7 0.06186204763377668 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.03093102381688834 0.625 >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 25 0.625 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 7 0.17500000000000002 No Hit CGTCAAGTCGCCGATTCAATACCCTTTTCATCTGACAAATTGCCAGAAAT 6 0.15 No Hit GAAAACCAACATGGTTGATGTTTCCATGTCTGAATTCGAGGAAGTCATTA 6 0.15 No Hit AATATGTTGAAATTAAAGGAGGAATTTGATTACAAAAGTTTGTCTAGAAG 5 0.125 No Hit GTTTGGAAGAGTAGTGGAGGGTCTGGATGTTGTGAAGGCTATAGAGAAGT 5 0.125 No Hit GTTTGATATGGTTATGATAAAAGATAATCATATATCAATAGCTGGAGGTA 5 0.125 No Hit AGCTTCGACCCACTGGGCTTGGCTGATGATCCAGAGGCATTCGCTGAGTT 5 0.125 No Hit AGGACATCTACTTGGGCTTGCTCACAGTAGTGATTCCAATGCCGTTATGT 5 0.125 No Hit GCTCAAGCCGGTGCTGAGTTTGTCGTTGAGTCCACTGGAGTTTTCACAGA 5 0.125 No Hit GGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTATG 5 0.125 No Hit GCACCCTTTTGCTCCTACTGAACAGTCTCAAGGTTACCAGGAAATGTTCG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0125 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 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 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.0875 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 0.1375 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.1875 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.25 0.0 0.0 0.0 0.0 62-63 0.35 0.0 0.0 0.0 0.0 64-65 0.44999999999999996 0.0 0.0 0.0 0.0 66-67 0.55 0.0 0.0 0.0 0.0 68-69 0.6625 0.0 0.0 0.0 0.0 70-71 1.0625 0.0 0.0 0.0 0.0 72-73 1.2625 0.0 0.0 0.0 0.0 74-75 1.575 0.0 0.0 0.0 0.0 76-77 1.8375 0.0 0.0 0.0 0.0 78-79 2.2 0.0 0.0 0.0 0.0 80-81 2.425 0.0 0.0 0.0 0.0 82-83 2.8125 0.0 0.0 0.0 0.0 84-85 3.325 0.0 0.0 0.0 0.0 86-87 3.8125 0.0 0.0 0.0 0.0 88-89 4.1875 0.0 0.0 0.0 0.0 90-91 4.725 0.0 0.0 0.0 0.0 92-93 5.449999999999999 0.0 0.0 0.0 0.0 94-95 6.1 0.0 0.0 0.0 0.0 96-97 6.775 0.0 0.0 0.0 0.0 98-99 7.5 0.0 0.0 0.0 0.0 100-101 8.225 0.0 0.0 0.0 0.0 102-103 9.3375 0.0 0.0 0.0 0.0 104-105 10.2625 0.0 0.0 0.0 0.0 106-107 11.0875 0.0 0.0 0.0 0.0 108-109 11.875 0.0 0.0 0.0 0.0 110-111 12.9 0.0 0.0 0.0 0.0 112-113 13.5625 0.0 0.0 0.0 0.0 114-115 14.649999999999999 0.0 0.0 0.0 0.0 116-117 15.6875 0.0 0.0 0.0 0.0 118-119 16.5 0.0 0.0 0.0 0.0 120-121 17.475 0.0 0.0 0.0 0.0 122-123 18.15 0.0 0.0 0.0 0.0 124-125 19.025 0.0 0.0 0.0 0.0 126-127 19.775 0.0 0.0 0.0 0.0 128-129 20.6875 0.0 0.0 0.0 0.0 130-131 21.5875 0.0 0.0 0.0 0.0 132-133 22.4 0.0 0.0 0.0 0.0 134-135 23.2125 0.0 0.0 0.0 0.0 136-137 24.375 0.0 0.0 0.0 0.0 138-139 25.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701120 spots for SRR12670168.sra Written 701120 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra Read 701115 spots for SRR12670168.sra Written 701115 spots for SRR12670168.sra SRR ids: ['SRR12670168.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_nl14snlw SRR12670168.sra spots: 14022305 blocks: [[1, 701115], [701116, 1402230], [1402231, 2103345], [2103346, 2804460], [2804461, 3505575], [3505576, 4206690], [4206691, 4907805], [4907806, 5608920], [5608921, 6310035], [6310036, 7011150], [7011151, 7712265], [7712266, 8413380], [8413381, 9114495], [9114496, 9815610], [9815611, 10516725], [10516726, 11217840], [11217841, 11918955], [11918956, 12620070], [12620071, 13321185], [13321186, 14022305]] SRR12670168 file size 4743692 SRR12670168 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 SRR12670168 SRR12670168_1.fastq SRR12670168_2.fastq Input file: SRR12670168_1.fastq Paired file: SRR12670168_2.fastq trimmed: SRR12670168-trimmed-pair1.fastq, SRR12670168-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 Tue Feb 11 08:35:07 2025 >> started Tue Feb 11 08:35:22 2025 >> done (15.401s) 14022305 read pairs processed; of these: 213 ( 0.00%) short read pairs filtered out after trimming by size control 469654 ( 3.35%) empty read pairs filtered out after trimming by size control 13552438 (96.65%) read pairs available; of these: 4052602 (29.90%) trimmed read pairs available after processing 9499836 (70.10%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 27 0.00% 20 29 0.00% 21 45 0.00% 22 63 0.00% 23 81 0.00% 24 98 0.00% 25 99 0.00% 26 101 0.00% 27 127 0.00% 28 140 0.00% 29 124 0.00% 30 148 0.00% 31 165 0.00% 32 145 0.00% 33 139 0.00% 34 182 0.00% 35 201 0.00% 36 226 0.00% 37 261 0.00% 38 281 0.00% 39 306 0.00% 40 358 0.00% 41 376 0.00% 42 405 0.00% 43 447 0.00% 44 558 0.00% 45 569 0.00% 46 615 0.00% 47 711 0.01% 48 866 0.01% 49 1003 0.01% 50 1123 0.01% 51 1319 0.01% 52 1388 0.01% 53 1519 0.01% 54 1573 0.01% 55 1729 0.01% 56 1889 0.01% 57 2243 0.02% 58 2470 0.02% 59 2998 0.02% 60 3420 0.03% 61 3863 0.03% 62 4085 0.03% 63 4470 0.03% 64 4782 0.04% 65 5133 0.04% 66 5645 0.04% 67 6228 0.05% 68 6998 0.05% 69 7968 0.06% 70 9073 0.07% 71 10238 0.08% 72 11623 0.09% 73 12730 0.09% 74 13405 0.10% 75 14527 0.11% 76 15455 0.11% 77 16158 0.12% 78 17477 0.13% 79 19297 0.14% 80 21366 0.16% 81 23903 0.18% 82 26505 0.20% 83 28066 0.21% 84 30119 0.22% 85 30900 0.23% 86 31937 0.24% 87 32740 0.24% 88 33960 0.25% 89 35269 0.26% 90 38237 0.28% 91 40957 0.30% 92 43353 0.32% 93 45955 0.34% 94 47627 0.35% 95 48611 0.36% 96 48774 0.36% 97 49543 0.37% 98 48669 0.36% 99 50783 0.37% 100 51864 0.38% 101 53265 0.39% 102 56852 0.42% 103 58013 0.43% 104 59644 0.44% 105 59399 0.44% 106 59461 0.44% 107 58059 0.43% 108 57354 0.42% 109 57047 0.42% 110 57674 0.43% 111 59334 0.44% 112 60745 0.45% 113 61932 0.46% 114 63273 0.47% 115 63382 0.47% 116 62806 0.46% 117 62685 0.46% 118 61799 0.46% 119 60153 0.44% 120 60368 0.45% 121 61466 0.45% 122 62155 0.46% 123 63718 0.47% 124 65479 0.48% 125 63356 0.47% 126 64474 0.48% 127 63368 0.47% 128 61745 0.46% 129 60167 0.44% 130 60445 0.45% 131 59446 0.44% 132 60326 0.45% 133 61441 0.45% 134 62250 0.46% 135 63367 0.47% 136 62841 0.46% 137 61330 0.45% 138 60772 0.45% 139 60718 0.45% 140 58585 0.43% 141 58487 0.43% 142 59090 0.44% 143 59226 0.44% 144 60555 0.45% 145 60252 0.44% 146 60263 0.44% 147 60456 0.45% 148 59724 0.44% 149 57934 0.43% 150 57044 0.42% 151 9499836 70.10% 13552438 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=32 prefix-density=0.36 prefix-fanout=2.0 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCAT criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=119.78 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=13.8 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.99 fanout-score-rank=28 prefix-density=0.44 prefix-fanout=2.6 sequence=ATGGTGGCACCATTCAATGGTCTCAAGTCTGCCGCAGCTTTCCCAGTCAGTACCAGAAAGGCTAATGACATTACTTCCATTGCAAGCAATGGTGGACGAGTTCAATGCATGCAGGTGTGGCCACCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCACAGAGGAGGAATTGGCCAAGGAAATTGATTACCTTCTTCGCTCGAAGTGGGTTCCTTGCTTGGAATTCGAGTTGGAGAAAGGTTGGGTCTACCGTGAGCACCACAGCTCACCAGGGTACTATGATGGACGCTACTGGACTATGTGGAAGCTACCCATGTTTGGATGCACTGAGGCATCTCAAGTGTTGCTTGAGCTTGAGGAGGCAAAGAAAGCTTACCCTAACGCCTTTATCCGTATAATCGGATTCGACAACACGCGTCAAGTGCAGTGCATCAGCTTTATTGCCGCCAAGCCGAAAGGTGTCTAAGTCGTCCCAGAACTTGATGTGTCCCTAGCTA criterion=fanout-score sequence-density=0.08 sequence-density-rank=31 fanout-score=65.92 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=9.5 sequence=AAAAGAAAAGAAAA SRR12670168 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:36:04 Started mapping on | Feb 11 08:36:04 Finished on | Feb 11 08:37:25 Mapping speed, Million of reads per hour | 602.33 Number of input reads | 13552438 Average input read length | 280 UNIQUE READS: Uniquely mapped reads number | 12392444 Uniquely mapped reads % | 91.44% Average mapped length | 278.59 Number of splices: Total | 11742747 Number of splices: Annotated (sjdb) | 11453925 Number of splices: GT/AG | 11497768 Number of splices: GC/AG | 190252 Number of splices: AT/AC | 8119 Number of splices: Non-canonical | 46608 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 297201 % of reads mapped to multiple loci | 2.19% Number of reads mapped to too many loci | 65583 % of reads mapped to too many loci | 0.48% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.61% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 862793 862793 862793 N_multimapping 297201 297201 297201 N_noFeature 484471 12208658 566112 N_ambiguous 176077 763 73481 UnstrandedReadsAssigned:11731896 PositiveStrandReadsAssigned:183023 NegativeStrandReadsAssigned:11752851 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=128 echo kmer=123 SRR12670168 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: SRR12670168-trimmed-pair1.fastq SRR12670168-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,552,438 reads, 11,826,341 reads pseudoaligned [quant] estimated average fragment length: 198.624 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,042 rounds 52401 SRR12670168.ke.tsv 34699 SRR12670168.se.tsv 87100 total ==> SRR12670168.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.38 500 24.2087 Potri.005G024800.1.v4.1 1035 837.376 142 14.9462 Potri.004G059700.1.v4.1 961 763.442 9 1.03903 Potri.007G009000.2.v4.1 1416 1218.38 0 0 Potri.003G141000.2.v4.1 2943 2745.38 662 21.253 Potri.016G087400.1.v4.1 270 114.376 466 359.098 Potri.015G069301.1.v4.1 564 372.942 0 0 Potri.010G195200.1.v4.1 1773 1575.38 55 3.0771 Potri.012G127500.1.v4.1 977 779.407 55 6.21959 ==> SRR12670168.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 130 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 171 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 7 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR12670168 completed mapping pipeline successfully