Starting /dee2/code/volunteer_pipeline.sh SRR12671350 current disk space = 3050112000000 free memory = 1443437240 SRR12671350 SRAfilesize 8d12f3d736d34a0e0ce6573dc5b28313 SRR12671350.sra SRR12671350.sra file validated SRR12671350 is paired end SRR12671350 is conventional basespace SRR12671350 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671350_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5555 37.0 37.0 37.0 37.0 37.0 2 36.43175 37.0 37.0 37.0 37.0 37.0 3 36.61 37.0 37.0 37.0 37.0 37.0 4 36.6915 37.0 37.0 37.0 37.0 37.0 5 36.651 37.0 37.0 37.0 37.0 37.0 6 36.659 37.0 37.0 37.0 37.0 37.0 7 36.471 37.0 37.0 37.0 37.0 37.0 8 36.6535 37.0 37.0 37.0 37.0 37.0 9 36.6815 37.0 37.0 37.0 37.0 37.0 10-14 36.6364 37.0 37.0 37.0 37.0 37.0 15-19 36.627500000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.6141 37.0 37.0 37.0 37.0 37.0 25-29 36.6222 37.0 37.0 37.0 37.0 37.0 30-34 36.6109 37.0 37.0 37.0 37.0 37.0 35-39 36.56420000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.58200000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.5142 37.0 37.0 37.0 37.0 37.0 50-54 36.519800000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.4752 37.0 37.0 37.0 37.0 37.0 60-64 36.471799999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.400400000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.4247 37.0 37.0 37.0 37.0 37.0 75-79 36.4298 37.0 37.0 37.0 37.0 37.0 80-84 36.3488 37.0 37.0 37.0 37.0 37.0 85-89 36.364 37.0 37.0 37.0 37.0 37.0 90-94 36.3602 37.0 37.0 37.0 37.0 37.0 95-99 36.28830000000001 37.0 37.0 37.0 37.0 37.0 100-104 36.334500000000006 37.0 37.0 37.0 37.0 37.0 105-109 36.2838 37.0 37.0 37.0 37.0 37.0 110-114 36.223 37.0 37.0 37.0 37.0 37.0 115-119 36.2578 37.0 37.0 37.0 37.0 37.0 120-124 36.1357 37.0 37.0 37.0 37.0 37.0 125-129 36.224900000000005 37.0 37.0 37.0 37.0 37.0 130-134 36.1431 37.0 37.0 37.0 37.0 37.0 135-139 36.0999 37.0 37.0 37.0 37.0 37.0 140-144 36.0166 37.0 37.0 37.0 37.0 37.0 145-149 35.9338 37.0 37.0 37.0 37.0 37.0 150-151 35.8545 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 2.0 24 1.0 25 1.0 26 3.0 27 6.0 28 7.0 29 11.0 30 18.0 31 24.0 32 40.0 33 69.0 34 106.0 35 231.0 36 3024.0 37 456.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.425 12.15 4.35 36.075 2 19.68898921494858 12.139453222974668 40.25583145221972 27.915726109857037 3 18.5 17.974999999999998 27.800000000000004 35.725 4 23.875 23.625 22.650000000000002 29.849999999999998 5 23.9 32.225 24.025 19.85 6 19.025 34.725 23.65 22.6 7 15.4 26.224999999999998 42.699999999999996 15.675 8 15.950000000000001 24.925 34.300000000000004 24.825 9 16.650000000000002 22.650000000000002 36.475 24.224999999999998 10-14 19.64 30.64 27.47 22.25 15-19 20.03 28.084999999999997 27.725 24.16 20-24 20.28 28.939999999999998 27.395000000000003 23.385 25-29 20.25 28.689999999999998 27.884999999999998 23.175 30-34 20.265 28.92 27.49 23.325000000000003 35-39 19.255 28.71 28.16 23.875 40-44 19.96 29.035 27.74 23.265 45-49 19.91 27.71 27.48 24.9 50-54 20.125 28.294999999999998 27.405 24.175 55-59 19.89 28.475 27.74 23.895 60-64 19.91 28.815 27.815 23.46 65-69 21.12 27.37 28.16 23.35 70-74 20.465 28.825 27.310000000000002 23.400000000000002 75-79 20.36 28.175 28.22 23.244999999999997 80-84 20.075000000000003 28.835 27.265 23.825 85-89 21.37 28.98 26.855 22.795 90-94 20.27 28.875 27.025 23.830000000000002 95-99 20.11 27.715 28.42 23.755000000000003 100-104 20.535 28.904999999999998 26.640000000000004 23.919999999999998 105-109 20.66 27.765 28.005000000000003 23.57 110-114 19.975 28.24 28.02 23.765 115-119 20.345 29.104999999999997 26.955000000000002 23.595 120-124 20.735 28.599999999999998 27.025 23.64 125-129 21.025 28.025 27.115000000000002 23.835 130-134 20.3 28.134999999999998 27.775 23.79 135-139 21.395 28.050000000000004 27.24 23.315 140-144 21.09 28.055000000000003 27.37 23.485 145-149 20.830000000000002 27.400000000000002 28.205000000000002 23.565 150-151 21.224999999999998 27.962500000000002 27.487499999999997 23.325000000000003 >>END_MODULE >>Per sequence GC content pass #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 0.0 12 0.5 13 0.5 14 0.0 15 1.0 16 1.5 17 1.0 18 0.5 19 0.5 20 1.5 21 3.5 22 2.5 23 1.5 24 2.0 25 1.0 26 2.5 27 6.0 28 9.5 29 11.5 30 13.5 31 21.0 32 32.5 33 45.5 34 67.0 35 90.0 36 103.0 37 111.0 38 117.0 39 151.5 40 185.5 41 193.5 42 226.0 43 240.0 44 262.5 45 290.0 46 258.0 47 229.0 48 225.0 49 213.5 50 174.0 51 144.5 52 126.5 53 107.0 54 87.5 55 65.0 56 51.0 57 36.0 58 27.0 59 20.0 60 13.5 61 10.0 62 5.5 63 4.0 64 3.5 65 1.5 66 0.5 67 0.0 68 0.5 69 0.5 70 0.0 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 0.0 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 0.325 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 83.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 84.97316636851521 71.25 2 11.866428145497913 19.900000000000002 3 2.3553965414430533 5.925 4 0.5664877757901015 1.9 5 0.20870602265951102 0.8750000000000001 6 0.02981514609421586 0.15 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 CCGCAAGGTGAAGTACAGATAAGCTTCTTAAATTTTCTAAAGATGCAACT 6 0.15 No Hit CTCCCTTTTCAAAACTAAGAAAGAACCATCAGAAGTTTCAAAGAATCTCA 5 0.125 No Hit ATTCAATGTGTGATGTCTTAGTAGATTCCAGGAACAATCCTGTAGCGAAC 5 0.125 No Hit GTAGACGTGACAGGACCCCAGAAGCTCGATATTCCTCCCTCAGCCATTCT 5 0.125 No Hit CCTAACTCAGGGTCCTGGACAACAGTTCCATTGCAGCAGAACTCTTTCTT 5 0.125 No Hit GTAAATTTTATTTTCAGTGATAATCATATACTTGTTGTCCACCCAAGTCG 5 0.125 No Hit GTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGG 5 0.125 No Hit GTTTCCCATTGAACAGGAGAAGTCACTTGGCGTGCCAAGATCTTCTTAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0125 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.07500000000000001 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.16249999999999998 0.0 0.0 0.0 0.0 84-85 0.1875 0.0 0.0 0.0 0.0 86-87 0.25 0.0 0.0 0.0 0.0 88-89 0.30000000000000004 0.0 0.0 0.0 0.0 90-91 0.375 0.0 0.0 0.0 0.0 92-93 0.45 0.0 0.0 0.0 0.0 94-95 0.48750000000000004 0.0 0.0 0.0 0.0 96-97 0.7 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.9125 0.0 0.0 0.0 0.0 102-103 1.0125 0.0 0.0 0.0 0.0 104-105 1.125 0.0 0.0 0.0 0.0 106-107 1.2125 0.0 0.0 0.0 0.0 108-109 1.2875 0.0 0.0 0.0 0.0 110-111 1.3625 0.0 0.0 0.0 0.0 112-113 1.5 0.0 0.0 0.0 0.0 114-115 1.6625 0.0 0.0 0.0 0.0 116-117 1.85 0.0 0.0 0.0 0.0 118-119 1.9625 0.0 0.0 0.0 0.0 120-121 2.125 0.0 0.0 0.0 0.0 122-123 2.3125 0.0 0.0 0.0 0.0 124-125 2.4625 0.0 0.0 0.0 0.0 126-127 2.6375 0.0 0.0 0.0 0.0 128-129 2.8375 0.0 0.0 0.0 0.0 130-131 3.0250000000000004 0.0 0.0 0.0 0.0 132-133 3.325 0.0 0.0 0.0 0.0 134-135 3.5 0.0 0.0 0.0 0.0 136-137 3.7375 0.0 0.0 0.0 0.0 138-139 4.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671350 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671350_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.374 37.0 37.0 37.0 37.0 37.0 2 36.1395 37.0 37.0 37.0 37.0 37.0 3 36.222 37.0 37.0 37.0 37.0 37.0 4 36.321 37.0 37.0 37.0 37.0 37.0 5 36.2625 37.0 37.0 37.0 37.0 37.0 6 36.2755 37.0 37.0 37.0 37.0 37.0 7 36.274 37.0 37.0 37.0 37.0 37.0 8 36.4175 37.0 37.0 37.0 37.0 37.0 9 36.292 37.0 37.0 37.0 37.0 37.0 10-14 36.33819999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.3081 37.0 37.0 37.0 37.0 37.0 20-24 36.2871 37.0 37.0 37.0 37.0 37.0 25-29 36.2445 37.0 37.0 37.0 37.0 37.0 30-34 36.2068 37.0 37.0 37.0 37.0 37.0 35-39 36.2385 37.0 37.0 37.0 37.0 37.0 40-44 36.1888 37.0 37.0 37.0 37.0 37.0 45-49 36.1617 37.0 37.0 37.0 37.0 37.0 50-54 36.15070000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.1143 37.0 37.0 37.0 37.0 37.0 60-64 36.084199999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.08970000000001 37.0 37.0 37.0 37.0 37.0 70-74 36.0774 37.0 37.0 37.0 37.0 37.0 75-79 36.0612 37.0 37.0 37.0 37.0 37.0 80-84 36.0186 37.0 37.0 37.0 37.0 37.0 85-89 36.036500000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.9799 37.0 37.0 37.0 37.0 37.0 95-99 35.9941 37.0 37.0 37.0 37.0 37.0 100-104 35.8902 37.0 37.0 37.0 37.0 37.0 105-109 35.838800000000006 37.0 37.0 37.0 37.0 37.0 110-114 35.7333 37.0 37.0 37.0 37.0 37.0 115-119 35.8899 37.0 37.0 37.0 37.0 37.0 120-124 35.7718 37.0 37.0 37.0 37.0 37.0 125-129 35.7338 37.0 37.0 37.0 37.0 37.0 130-134 35.716100000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.5715 37.0 37.0 37.0 37.0 37.0 140-144 35.6293 37.0 37.0 37.0 37.0 37.0 145-149 35.5486 37.0 37.0 37.0 37.0 37.0 150-151 35.28275 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 4.0 15 0.0 16 0.0 17 1.0 18 0.0 19 0.0 20 0.0 21 2.0 22 8.0 23 7.0 24 6.0 25 7.0 26 7.0 27 6.0 28 12.0 29 13.0 30 24.0 31 42.0 32 52.0 33 75.0 34 174.0 35 474.0 36 2803.0 37 280.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.175 25.55 8.5 24.775 2 27.05 25.8 31.424999999999997 15.725 3 19.925 27.6 34.425 18.05 4 24.6 35.25 22.1 18.05 5 24.2 38.875 21.975 14.95 6 19.375 38.625 22.725 19.275000000000002 7 18.5 22.55 40.150000000000006 18.8 8 19.400000000000002 24.8 30.15 25.650000000000002 9 20.8 23.625 31.724999999999998 23.849999999999998 10-14 22.675 28.835 27.365000000000002 21.125 15-19 22.755 28.655 27.93 20.66 20-24 21.975 29.099999999999998 27.72 21.205 25-29 22.155 28.525 28.255000000000003 21.065 30-34 22.775000000000002 27.98 28.455000000000002 20.79 35-39 22.37 28.63 28.025 20.974999999999998 40-44 22.325 27.38 28.945 21.349999999999998 45-49 21.795 28.53 27.975 21.7 50-54 22.25 27.61 28.175 21.965 55-59 22.495 28.255000000000003 27.93 21.32 60-64 22.67 27.16 28.68 21.490000000000002 65-69 23.189999999999998 27.694999999999997 28.345 20.77 70-74 22.745 28.22 27.495000000000005 21.54 75-79 22.665 27.725 28.144999999999996 21.465 80-84 23.34 27.925 27.365000000000002 21.37 85-89 23.330000000000002 28.29 27.735 20.645 90-94 23.39 27.865000000000002 27.639999999999997 21.105 95-99 23.119999999999997 27.58 27.99 21.310000000000002 100-104 23.9 27.52 27.884999999999998 20.695 105-109 24.05 27.07 27.675 21.205 110-114 23.225 28.335 27.834999999999997 20.605 115-119 23.285 27.785 28.185 20.745 120-124 23.544999999999998 28.375 27.43 20.65 125-129 23.89 27.250000000000004 28.050000000000004 20.810000000000002 130-134 24.065 27.915 27.450000000000003 20.57 135-139 24.015 27.525 27.939999999999998 20.52 140-144 24.265 28.134999999999998 27.495000000000005 20.105 145-149 24.785 27.950000000000003 27.66 19.605 150-151 24.75 28.1625 26.474999999999998 20.6125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.5 7 0.5 8 0.5 9 1.5 10 1.5 11 0.5 12 0.0 13 0.0 14 1.0 15 1.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 2.0 22 3.5 23 3.5 24 2.5 25 5.5 26 9.0 27 12.5 28 12.0 29 10.0 30 18.0 31 27.0 32 31.0 33 39.0 34 51.0 35 79.5 36 97.0 37 109.0 38 133.0 39 167.5 40 198.0 41 218.0 42 241.5 43 252.5 44 265.5 45 271.0 46 267.0 47 244.5 48 214.0 49 204.5 50 177.0 51 133.5 52 92.0 53 80.0 54 83.5 55 64.5 56 52.0 57 40.0 58 27.5 59 20.0 60 9.5 61 5.5 62 4.5 63 1.0 64 1.0 65 1.0 66 1.0 67 1.0 68 1.0 69 1.0 70 0.5 71 0.0 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.5 79 0.5 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 0.5 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 1.0 >>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 83.75 #Duplication Level Percentage of deduplicated Percentage of total 1 85.01492537313433 71.2 2 11.761194029850747 19.7 3 2.3582089552238807 5.925 4 0.5671641791044777 1.9 5 0.26865671641791045 1.125 6 0.029850746268656716 0.15 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 GAATAATCATCTTTTTGGTCCGATTACTTTTATCGAAAACTTGACGAGAT 6 0.15 No Hit AAAGAAACCCAAATTTCATCTCTCATCTTTCTTGGGTTTTCTTGCTTTGT 5 0.125 No Hit GCCAATCAAGAAGTTGATGAAGCTGATAGAGTTCAGATTGCAAATTACCT 5 0.125 No Hit GCAGCTGCTACCTTGCCTCGCCTCTCGAAATGCCGAAAACAGAATCTCCT 5 0.125 No Hit GGATACCCCATCAGCGGTTATCTTCTTTTTCCATTTTCACTCAACAACTC 5 0.125 No Hit CTATAGTGAAGAAAAACAAAAAAGAAATGGATGCCAAAGCTCTCTTCTTC 5 0.125 No Hit CTTCAATCGTAAATCACAAATACATACACGTTTACTCATCAGCTCGAAAA 5 0.125 No Hit TGTATCCCTCTCTTCTTCCATTTCTCTAAAGATAGACCCCTTCAGGTCTC 5 0.125 No Hit GTCATCTTTTGATGATGCAAATCAGCAAGGGGAAGATGTTGATTCATCTG 5 0.125 No Hit GCCTTCTGTCTGCTCAGGGGATCCATTTCTACTTCTTGCTATTTCAAGGG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0125 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.07500000000000001 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.16249999999999998 0.0 0.0 0.0 0.0 84-85 0.1875 0.0 0.0 0.0 0.0 86-87 0.25 0.0 0.0 0.0 0.0 88-89 0.30000000000000004 0.0 0.0 0.0 0.0 90-91 0.375 0.0 0.0 0.0 0.0 92-93 0.45 0.0 0.0 0.0 0.0 94-95 0.48750000000000004 0.0 0.0 0.0 0.0 96-97 0.7 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.9125 0.0 0.0 0.0 0.0 102-103 1.0125 0.0 0.0 0.0 0.0 104-105 1.125 0.0 0.0 0.0 0.0 106-107 1.2125 0.0 0.0 0.0 0.0 108-109 1.2875 0.0 0.0 0.0 0.0 110-111 1.3625 0.0 0.0 0.0 0.0 112-113 1.5 0.0 0.0 0.0 0.0 114-115 1.6749999999999998 0.0 0.0 0.0 0.0 116-117 1.8624999999999998 0.0 0.0 0.0 0.0 118-119 1.9625 0.0 0.0 0.0 0.0 120-121 2.125 0.0 0.0 0.0 0.0 122-123 2.3125 0.0 0.0 0.0 0.0 124-125 2.45 0.0 0.0 0.0 0.0 126-127 2.6125 0.0 0.0 0.0 0.0 128-129 2.825 0.0 0.0 0.0 0.0 130-131 3.0250000000000004 0.0 0.0 0.0 0.0 132-133 3.325 0.0 0.0 0.0 0.0 134-135 3.5 0.0 0.0 0.0 0.0 136-137 3.7375 0.0 0.0 0.0 0.0 138-139 4.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAATCTT 10 0.006830828 145.0 3 TACAAGA 10 0.006830828 145.0 2 >>END_MODULE Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786949 spots for SRR12671350.sra Written 786949 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra Read 786938 spots for SRR12671350.sra Written 786938 spots for SRR12671350.sra SRR ids: ['SRR12671350.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_l3ahnytk SRR12671350.sra spots: 15738771 blocks: [[1, 786938], [786939, 1573876], [1573877, 2360814], [2360815, 3147752], [3147753, 3934690], [3934691, 4721628], [4721629, 5508566], [5508567, 6295504], [6295505, 7082442], [7082443, 7869380], [7869381, 8656318], [8656319, 9443256], [9443257, 10230194], [10230195, 11017132], [11017133, 11804070], [11804071, 12591008], [12591009, 13377946], [13377947, 14164884], [14164885, 14951822], [14951823, 15738771]] SRR12671350 file size 5327022 SRR12671350 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 SRR12671350 SRR12671350_1.fastq SRR12671350_2.fastq Input file: SRR12671350_1.fastq Paired file: SRR12671350_2.fastq trimmed: SRR12671350-trimmed-pair1.fastq, SRR12671350-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 17:33:48 2025 >> started Tue Feb 11 17:34:06 2025 >> done (17.540s) 15738771 read pairs processed; of these: 88 ( 0.00%) short read pairs filtered out after trimming by size control 2731 ( 0.02%) empty read pairs filtered out after trimming by size control 15735952 (99.98%) read pairs available; of these: 885298 ( 5.63%) trimmed read pairs available after processing 14850654 (94.37%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 7 0.00% 20 6 0.00% 21 14 0.00% 22 19 0.00% 23 15 0.00% 24 19 0.00% 25 20 0.00% 26 17 0.00% 27 22 0.00% 28 27 0.00% 29 19 0.00% 30 22 0.00% 31 19 0.00% 32 26 0.00% 33 31 0.00% 34 16 0.00% 35 44 0.00% 36 31 0.00% 37 29 0.00% 38 24 0.00% 39 43 0.00% 40 41 0.00% 41 41 0.00% 42 33 0.00% 43 53 0.00% 44 44 0.00% 45 59 0.00% 46 45 0.00% 47 71 0.00% 48 96 0.00% 49 95 0.00% 50 105 0.00% 51 104 0.00% 52 115 0.00% 53 117 0.00% 54 120 0.00% 55 139 0.00% 56 180 0.00% 57 188 0.00% 58 256 0.00% 59 276 0.00% 60 276 0.00% 61 346 0.00% 62 395 0.00% 63 436 0.00% 64 474 0.00% 65 494 0.00% 66 584 0.00% 67 645 0.00% 68 718 0.00% 69 812 0.01% 70 920 0.01% 71 1059 0.01% 72 1176 0.01% 73 1304 0.01% 74 1454 0.01% 75 1623 0.01% 76 1785 0.01% 77 1916 0.01% 78 1936 0.01% 79 2196 0.01% 80 2352 0.01% 81 2698 0.02% 82 2942 0.02% 83 3217 0.02% 84 3476 0.02% 85 3708 0.02% 86 4083 0.03% 87 4170 0.03% 88 4407 0.03% 89 4427 0.03% 90 4874 0.03% 91 4957 0.03% 92 5368 0.03% 93 5797 0.04% 94 6115 0.04% 95 6275 0.04% 96 6696 0.04% 97 6859 0.04% 98 6814 0.04% 99 7576 0.05% 100 7484 0.05% 101 7671 0.05% 102 8014 0.05% 103 8354 0.05% 104 8581 0.05% 105 8959 0.06% 106 9197 0.06% 107 9548 0.06% 108 9722 0.06% 109 10081 0.06% 110 10069 0.06% 111 10547 0.07% 112 10619 0.07% 113 10934 0.07% 114 11242 0.07% 115 11604 0.07% 116 12219 0.08% 117 12422 0.08% 118 12954 0.08% 119 12953 0.08% 120 13399 0.09% 121 13732 0.09% 122 13608 0.09% 123 13847 0.09% 124 14276 0.09% 125 14416 0.09% 126 15205 0.10% 127 15567 0.10% 128 15785 0.10% 129 16194 0.10% 130 16859 0.11% 131 16706 0.11% 132 16407 0.10% 133 17250 0.11% 134 17264 0.11% 135 17976 0.11% 136 18021 0.11% 137 18604 0.12% 138 19089 0.12% 139 19746 0.13% 140 19634 0.12% 141 20102 0.13% 142 20969 0.13% 143 20290 0.13% 144 21159 0.13% 145 21426 0.14% 146 21964 0.14% 147 22309 0.14% 148 23210 0.15% 149 23046 0.15% 150 24045 0.15% 151 14850654 94.37% 15735952 reads passed initial QC criterion=sequence-density sequence-density=0.69 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=19 prefix-density=0.70 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=23 fanout-score=89.06 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=3.2 sequence=ATCAAGCTTCCGATTAAAGATACATAATTCCATGGAATGGAACCAACAAAGCAGCAGGAAATACAAGACACTTACAGATTACTAGCCATCAAATGAGATCCTGTAGAAAGGATTTGAGGAGGCCATGGCTAGCTAACTGTACTTTAATTTACAGCAAATACTATATTAGACAAACATGGAGTGACCAGACTTCTTCTTTTTATTTATTATAGTTCCATAAAACTGCTTGGTTGGAGCCATGCGGCGACGTTTTCTCATTTGCAGGAGCATGGATCACAGGTGCAGTTTGATCCACATTTGCAGCCATTCTCAGCACCAAAGTTCATCTCAGAGCTCTCGTAGAACATCCTAACTGGAGCTACACCAGCAATGATTGTCTGACTTGTGGTGGTCTCGGAGAAACTCAAGTCTGGGTACATGCTGCATCCATTGCAGCCACTGCCGCACTTGCA criterion=sequence-density sequence-density=0.80 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=24 prefix-density=0.80 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.15 sequence-density-rank=22 fanout-score=30.42 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=11.8 sequence=AAAGAAAAGAAAA SRR12671350 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 17:34:50 Started mapping on | Feb 11 17:34:51 Finished on | Feb 11 17:36:32 Mapping speed, Million of reads per hour | 560.89 Number of input reads | 15735952 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 14776565 Uniquely mapped reads % | 93.90% Average mapped length | 297.53 Number of splices: Total | 14991820 Number of splices: Annotated (sjdb) | 14698271 Number of splices: GT/AG | 14700074 Number of splices: GC/AG | 246254 Number of splices: AT/AC | 8606 Number of splices: Non-canonical | 36886 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.83 Insertion rate per base | 0.02% Insertion average length | 2.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 359346 % of reads mapped to multiple loci | 2.28% Number of reads mapped to too many loci | 26074 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.57% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 600041 600041 600041 N_multimapping 359346 359346 359346 N_noFeature 518207 14578001 593269 N_ambiguous 209859 871 85882 UnstrandedReadsAssigned:14048499 PositiveStrandReadsAssigned:197693 NegativeStrandReadsAssigned:14097414 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671350 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: SRR12671350-trimmed-pair1.fastq SRR12671350-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,735,952 reads, 14,080,380 reads pseudoaligned [quant] estimated average fragment length: 294.19 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,189 rounds 52401 SRR12671350.ke.tsv 34699 SRR12671350.se.tsv 87100 total ==> SRR12671350.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1724.81 413 16.251 Potri.005G024800.1.v4.1 1035 741.81 146 13.3577 Potri.004G059700.1.v4.1 961 668.031 16 1.62553 Potri.007G009000.2.v4.1 1416 1122.81 0 0 Potri.003G141000.2.v4.1 2943 2649.81 675.738 17.3076 Potri.016G087400.1.v4.1 270 73.5573 546 503.778 Potri.015G069301.1.v4.1 564 288.124 0 0 Potri.010G195200.1.v4.1 1773 1479.81 40 1.83454 Potri.012G127500.1.v4.1 977 683.921 78 7.74035 ==> SRR12671350.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 605 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 182 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 20 SRR12671350 completed mapping pipeline successfully