Starting /dee2/code/volunteer_pipeline.sh SRR12670119 current disk space = 3057371451392 free memory = 1477453288 SRR12670119 SRAfilesize af0cf6df8fcbbadfb02a3097e9a65a97 SRR12670119.sra SRR12670119.sra file validated SRR12670119 is paired end SRR12670119 is conventional basespace SRR12670119 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670119_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6685 37.0 37.0 37.0 37.0 37.0 2 36.5235 37.0 37.0 37.0 37.0 37.0 3 36.618 37.0 37.0 37.0 37.0 37.0 4 36.689 37.0 37.0 37.0 37.0 37.0 5 36.7185 37.0 37.0 37.0 37.0 37.0 6 36.6845 37.0 37.0 37.0 37.0 37.0 7 36.5985 37.0 37.0 37.0 37.0 37.0 8 36.624 37.0 37.0 37.0 37.0 37.0 9 36.684 37.0 37.0 37.0 37.0 37.0 10-14 36.6126 37.0 37.0 37.0 37.0 37.0 15-19 36.610699999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.608999999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.522299999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.5345 37.0 37.0 37.0 37.0 37.0 35-39 36.5029 37.0 37.0 37.0 37.0 37.0 40-44 36.4511 37.0 37.0 37.0 37.0 37.0 45-49 36.4353 37.0 37.0 37.0 37.0 37.0 50-54 36.4058 37.0 37.0 37.0 37.0 37.0 55-59 36.36749999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.363699999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.338899999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.2707 37.0 37.0 37.0 37.0 37.0 75-79 36.292199999999994 37.0 37.0 37.0 37.0 37.0 80-84 36.3114 37.0 37.0 37.0 37.0 37.0 85-89 36.2787 37.0 37.0 37.0 37.0 37.0 90-94 36.307900000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.253299999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.3174 37.0 37.0 37.0 37.0 37.0 105-109 36.2434 37.0 37.0 37.0 37.0 37.0 110-114 36.1487 37.0 37.0 37.0 37.0 37.0 115-119 36.230599999999995 37.0 37.0 37.0 37.0 37.0 120-124 36.0707 37.0 37.0 37.0 37.0 37.0 125-129 35.9455 37.0 37.0 37.0 37.0 37.0 130-134 35.9099 37.0 37.0 37.0 37.0 37.0 135-139 35.69930000000001 37.0 37.0 37.0 37.0 37.0 140-144 35.504200000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.3572 37.0 37.0 37.0 37.0 37.0 150-151 35.1185 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 7.0 26 4.0 27 10.0 28 9.0 29 16.0 30 30.0 31 22.0 32 54.0 33 62.0 34 143.0 35 326.0 36 2906.0 37 409.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.675 11.675 6.2 41.449999999999996 2 21.13169754631948 12.068102153229844 37.03054581872809 29.769654481722586 3 17.275 15.975 27.725 39.025 4 21.975 24.625 23.875 29.525000000000002 5 24.2 30.125 24.25 21.425 6 22.0 33.85 23.225 20.925 7 16.400000000000002 27.200000000000003 40.325 16.075 8 17.575 25.7 32.425 24.3 9 19.475 23.674999999999997 33.925 22.925 10-14 20.395 29.505 27.67 22.43 15-19 20.53 27.694999999999997 27.83 23.945 20-24 20.244999999999997 27.555000000000003 28.04 24.16 25-29 20.064999999999998 28.83 27.605 23.5 30-34 20.305 28.405 27.665 23.625 35-39 20.87 27.950000000000003 27.775 23.405 40-44 20.474999999999998 28.299999999999997 27.33 23.895 45-49 20.555 27.939999999999998 28.215 23.29 50-54 20.89 27.555000000000003 27.87 23.685000000000002 55-59 21.044999999999998 27.275 27.689999999999998 23.990000000000002 60-64 20.674999999999997 27.49 27.725 24.11 65-69 20.835 27.439999999999998 27.87 23.855 70-74 20.945 27.589999999999996 27.255000000000003 24.21 75-79 21.23 27.72 27.505000000000003 23.544999999999998 80-84 21.15 27.715 27.500000000000004 23.635 85-89 20.485 28.895 27.139999999999997 23.48 90-94 21.72 28.735 26.465 23.080000000000002 95-99 21.575 28.660000000000004 26.35 23.415 100-104 21.455 28.515 26.584999999999997 23.445 105-109 21.59 28.725 25.924999999999997 23.76 110-114 21.5 28.08 26.71 23.71 115-119 21.165 28.84 25.8 24.195 120-124 21.555 28.975 25.474999999999998 23.995 125-129 21.584999999999997 28.93 25.25 24.235 130-134 21.67 28.4 25.569999999999997 24.36 135-139 21.495 28.82 24.98 24.705 140-144 21.645 27.16 26.179999999999996 25.014999999999997 145-149 22.085 27.965 25.145 24.805 150-151 22.45 27.8625 25.05 24.637500000000003 >>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 0.0 13 0.0 14 0.0 15 0.5 16 1.0 17 0.5 18 0.0 19 0.5 20 0.5 21 1.0 22 1.5 23 0.5 24 1.0 25 1.5 26 2.0 27 5.0 28 9.0 29 12.0 30 11.0 31 17.5 32 25.0 33 26.0 34 40.5 35 56.5 36 77.5 37 99.5 38 117.0 39 149.0 40 175.5 41 188.5 42 224.0 43 248.0 44 243.0 45 286.0 46 299.5 47 256.0 48 229.5 49 213.0 50 195.0 51 157.5 52 134.5 53 123.0 54 110.5 55 79.0 56 46.0 57 36.0 58 23.5 59 23.5 60 18.5 61 9.5 62 6.5 63 4.5 64 3.5 65 4.0 66 4.0 67 1.5 68 0.5 69 0.0 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 0.15 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 84.23896727709396 70.15 2 12.518763134193936 20.849999999999998 3 2.701891323926749 6.75 4 0.21014710297208045 0.7000000000000001 5 0.12008405884118883 0.5 6 0.21014710297208045 1.05 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 CAAACACCAGAGAGTTCTTTCTTGAGAGATTGGGGAACCTCTCCTGTAGT 6 0.15 No Hit GCTGTGTTTGCCAAGATCATTCCAAGCCCACCAGCAAGCTTCACTGCAGC 6 0.15 No Hit TCTACGTCGCAGTGAGCCAGTGCCAATGACAGAGGAGCAGGTCCTCGGAC 6 0.15 No Hit CGCCAATTATATAACCCTAATTGCAAAATTACATCTCAAAATCCTCATGT 6 0.15 No Hit CTCTCTTTTCCAAGTAAATGACTCTGGCACAGATACTGCACTAGGCGAAT 6 0.15 No Hit CCGCTGGGTCACTTCAACGGGTTGTGCCATACCTTGACCATCCTTTCCCA 6 0.15 No Hit CGTTGTAGTCCTTTCCCATTTCTTCGCCTCTCCGAGGTGGATAGAGAATA 6 0.15 No Hit CCTTTATGGACTTTAAAACAAGGAGTTCATGAAACACATATACCTCTTCC 5 0.125 No Hit GCCTTTTCGAAGTCTTGGCCGCGGACAGCTTCATCCTTTTCCTTTGTGAT 5 0.125 No Hit GGCAGGTTAAAAAAAATATAAAATTTCCCTTCAGGACCTTAGGAACCTCT 5 0.125 No Hit TGGCCACCAAGCCATGCACCACCTCCAGGGCTAACTGATTGCTCAATTAT 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 0.0 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 0.0125 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 0.025 0.0 0.0 0.0 52-53 0.025 0.05 0.0 0.0 0.0 54-55 0.025 0.05 0.0 0.0 0.0 56-57 0.025 0.05 0.0 0.0 0.0 58-59 0.025 0.05 0.0 0.0 0.0 60-61 0.0875 0.05 0.0 0.0 0.0 62-63 0.15 0.05 0.0 0.0 0.0 64-65 0.175 0.05 0.0 0.0 0.0 66-67 0.25 0.05 0.0 0.0 0.0 68-69 0.2875 0.05 0.0 0.0 0.0 70-71 0.5125 0.05 0.0 0.0 0.0 72-73 0.625 0.05 0.0 0.0 0.0 74-75 0.7875 0.05 0.0 0.0 0.0 76-77 1.025 0.05 0.0 0.0 0.0 78-79 1.275 0.05 0.0 0.0 0.0 80-81 1.55 0.05 0.0 0.0 0.0 82-83 1.85 0.05 0.0 0.0 0.0 84-85 2.3875 0.05 0.0 0.0 0.0 86-87 2.85 0.05 0.0 0.0 0.0 88-89 3.3375 0.05 0.0 0.0 0.0 90-91 3.85 0.05 0.0 0.0 0.0 92-93 4.6 0.05 0.0 0.0 0.0 94-95 5.15 0.05 0.0 0.0 0.0 96-97 5.925 0.05 0.0 0.0 0.0 98-99 6.6625 0.05 0.0 0.0 0.0 100-101 7.5 0.05 0.0 0.0 0.0 102-103 8.4375 0.05 0.0 0.0 0.0 104-105 9.587499999999999 0.05 0.0 0.0 0.0 106-107 10.5375 0.05 0.0 0.0 0.0 108-109 11.775 0.05 0.0 0.0 0.0 110-111 12.6125 0.05 0.0 0.0 0.0 112-113 13.3875 0.05 0.0 0.0 0.0 114-115 14.4375 0.05 0.0 0.0 0.0 116-117 15.75 0.05 0.0 0.0 0.0 118-119 16.612499999999997 0.05 0.0 0.0 0.0 120-121 17.65 0.05 0.0 0.0 0.0 122-123 18.75 0.05 0.0 0.0 0.0 124-125 19.8 0.05 0.0 0.0 0.0 126-127 20.8625 0.05 0.0 0.0 0.0 128-129 21.9 0.05 0.0 0.0 0.0 130-131 22.9625 0.05 0.0 0.0 0.0 132-133 23.9 0.05 0.0 0.0 0.0 134-135 24.875 0.05 0.0 0.0 0.0 136-137 26.0625 0.05 0.0 0.0 0.0 138-139 27.375 0.05 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 35 0.0035366106 20.714287 140-144 >>END_MODULE SRR12670119 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670119_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.192 37.0 37.0 37.0 37.0 37.0 2 36.2305 37.0 37.0 37.0 37.0 37.0 3 36.1625 37.0 37.0 37.0 37.0 37.0 4 36.2545 37.0 37.0 37.0 37.0 37.0 5 36.2225 37.0 37.0 37.0 37.0 37.0 6 36.1365 37.0 37.0 37.0 37.0 37.0 7 36.1205 37.0 37.0 37.0 37.0 37.0 8 36.189 37.0 37.0 37.0 37.0 37.0 9 36.2515 37.0 37.0 37.0 37.0 37.0 10-14 36.250099999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.2432 37.0 37.0 37.0 37.0 37.0 20-24 36.223400000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.112100000000005 37.0 37.0 37.0 37.0 37.0 30-34 36.0723 37.0 37.0 37.0 37.0 37.0 35-39 36.1259 37.0 37.0 37.0 37.0 37.0 40-44 36.0309 37.0 37.0 37.0 37.0 37.0 45-49 36.0597 37.0 37.0 37.0 37.0 37.0 50-54 35.9729 37.0 37.0 37.0 37.0 37.0 55-59 35.992200000000004 37.0 37.0 37.0 37.0 37.0 60-64 35.9409 37.0 37.0 37.0 37.0 37.0 65-69 35.970800000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.914100000000005 37.0 37.0 37.0 37.0 37.0 75-79 35.9005 37.0 37.0 37.0 37.0 37.0 80-84 35.892700000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.8359 37.0 37.0 37.0 37.0 37.0 90-94 35.8952 37.0 37.0 37.0 37.0 37.0 95-99 35.7841 37.0 37.0 37.0 37.0 37.0 100-104 35.701 37.0 37.0 37.0 37.0 37.0 105-109 35.6946 37.0 37.0 37.0 37.0 37.0 110-114 35.6329 37.0 37.0 37.0 37.0 37.0 115-119 35.5813 37.0 37.0 37.0 37.0 37.0 120-124 35.3943 37.0 37.0 37.0 37.0 37.0 125-129 35.2557 37.0 37.0 37.0 34.6 37.0 130-134 35.0207 37.0 37.0 37.0 25.0 37.0 135-139 34.799299999999995 37.0 37.0 37.0 25.0 37.0 140-144 34.5548 37.0 37.0 37.0 25.0 37.0 145-149 34.173899999999996 37.0 37.0 37.0 25.0 37.0 150-151 33.907 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 3.0 15 3.0 16 1.0 17 6.0 18 3.0 19 3.0 20 2.0 21 2.0 22 3.0 23 2.0 24 6.0 25 9.0 26 9.0 27 12.0 28 17.0 29 17.0 30 28.0 31 44.0 32 84.0 33 119.0 34 264.0 35 650.0 36 2492.0 37 217.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.275000000000006 22.5 10.549999999999999 29.675 2 26.1 26.75 30.875000000000004 16.275000000000002 3 21.3 28.325 31.7 18.675 4 23.5 33.975 24.15 18.375 5 25.025 37.574999999999996 20.724999999999998 16.675 6 20.65 37.974999999999994 22.975 18.4 7 20.9 22.625 37.25 19.225 8 20.75 26.1 29.825000000000003 23.325000000000003 9 22.425 24.875 29.799999999999997 22.900000000000002 10-14 23.775 29.65 25.185000000000002 21.39 15-19 23.84 27.775 27.634999999999998 20.75 20-24 23.48 28.51 27.425 20.585 25-29 23.185 27.47 27.644999999999996 21.7 30-34 23.175 28.105000000000004 27.935 20.785 35-39 23.395 28.775000000000002 26.615 21.215 40-44 23.34 28.285 27.284999999999997 21.09 45-49 23.990000000000002 27.615000000000002 27.24 21.154999999999998 50-54 23.31 27.339999999999996 27.450000000000003 21.9 55-59 23.21 27.265 27.72 21.805 60-64 23.155 27.400000000000002 27.834999999999997 21.61 65-69 23.235 28.000000000000004 27.215 21.55 70-74 23.535 27.889999999999997 27.755000000000003 20.82 75-79 23.96 27.165 27.77 21.105 80-84 23.87 28.315 27.0 20.815 85-89 24.169999999999998 28.555000000000003 26.525 20.75 90-94 24.33 27.894999999999996 26.895000000000003 20.880000000000003 95-99 24.98 28.01 26.515 20.495 100-104 25.605 28.665000000000003 25.724999999999998 20.005 105-109 25.740000000000002 28.265 25.615 20.380000000000003 110-114 26.229999999999997 28.57 25.395 19.805 115-119 26.169999999999998 28.345 25.655 19.830000000000002 120-124 27.32 28.410000000000004 25.124999999999996 19.145 125-129 28.08 28.375 25.014999999999997 18.529999999999998 130-134 28.82 27.800000000000004 24.865000000000002 18.515 135-139 30.395 27.189999999999998 24.435000000000002 17.98 140-144 31.175000000000004 26.825 24.64 17.36 145-149 33.055 25.645 24.075 17.224999999999998 150-151 33.5 26.0625 23.35 17.0875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 1.0 5 1.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 0.5 14 0.5 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 1.0 24 1.5 25 1.5 26 2.0 27 2.0 28 2.5 29 5.0 30 11.5 31 22.5 32 29.5 33 35.5 34 45.5 35 55.0 36 71.0 37 94.0 38 110.5 39 138.5 40 185.5 41 215.5 42 235.0 43 259.0 44 286.0 45 292.0 46 296.5 47 282.0 48 235.0 49 217.0 50 183.0 51 123.0 52 99.0 53 99.0 54 85.5 55 68.0 56 57.0 57 43.5 58 23.5 59 15.5 60 14.0 61 8.5 62 7.0 63 5.5 64 2.5 65 2.5 66 2.5 67 2.0 68 2.0 69 1.0 70 0.5 71 0.5 72 0.5 73 0.0 74 0.5 75 1.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.5 85 1.0 86 0.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.5 94 1.0 95 1.0 96 1.0 97 1.0 98 0.5 99 0.0 100 2.5 >>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 84.0 #Duplication Level Percentage of deduplicated Percentage of total 1 85.14880952380952 71.525 2 11.875 19.950000000000003 3 2.3511904761904763 5.925 4 0.26785714285714285 0.8999999999999999 5 0.1488095238095238 0.625 6 0.17857142857142858 0.8999999999999999 7 0.029761904761904764 0.17500000000000002 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit GCTTCGATTAACAGCTGGTGTCTCACCTCTGTCTCTGCCTCTAAGAGATC 6 0.15 No Hit AAAGATAGAGTTCTTGCAACTTATGGAATTAATGCAGTCTGCACACACCT 6 0.15 No Hit GCTTCTGCTGCCAGTGCTTTTGAAGCTGCAAAGGAGATAATGGAGGCTCT 6 0.15 No Hit GAGGGCTAAAATCACATTTGCTTCTGAGAGGAGAGCAGCCTGAAATTCTG 6 0.15 No Hit GGTGACGTTGGGAGCAGGTATTGCTATATGGGGAGTATAAGTCCATCAAA 6 0.15 No Hit ATAACAGTGGATTCTCGAGAGATAAACGAAACTGGTGAAAAAAAGGATGC 6 0.15 No Hit ACAGACATGGTTACTTATGCAGACACTGATGTTGTCATTGTTGGTGCTGG 5 0.125 No Hit CTAAGAATAACCCTTGTCTCATTGGAGAACCTGGGGTTGGGAAAACTGCA 5 0.125 No Hit TGAGAATTGGGGTCGTGTACCTGCTCTGGGTTGCACTTCATCCTTCATCA 5 0.125 No Hit CAGGACCTATTGAATGAGTTCTGTAGTCTTGGGACAAAGCAAGGTGATGC 5 0.125 No Hit ATTTTCATAAACAATTAAACTCACAGCAGTACATAGGAACTTTACATGGT 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 0.0 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 0.0125 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 0.025 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 0.0875 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.3 0.0 0.0 0.0 0.0 70-71 0.5375 0.0 0.0 0.0 0.0 72-73 0.65 0.0 0.0 0.0 0.0 74-75 0.8125 0.0 0.0 0.0 0.0 76-77 1.05 0.0 0.0 0.0 0.0 78-79 1.3 0.0 0.0 0.0 0.0 80-81 1.575 0.0 0.0 0.0 0.0 82-83 1.875 0.0 0.0 0.0 0.0 84-85 2.4125 0.0 0.0 0.0 0.0 86-87 2.8625 0.0 0.0 0.0 0.0 88-89 3.3875 0.0 0.0 0.0 0.0 90-91 3.85 0.0 0.0 0.0 0.0 92-93 4.574999999999999 0.0 0.0 0.0 0.0 94-95 5.125 0.0 0.0 0.0 0.0 96-97 5.8875 0.0 0.0 0.0 0.0 98-99 6.625 0.0 0.0 0.0 0.0 100-101 7.475 0.0 0.0 0.0 0.0 102-103 8.4 0.0 0.0 0.0 0.0 104-105 9.537500000000001 0.0 0.0 0.0 0.0 106-107 10.4875 0.0 0.0 0.0 0.0 108-109 11.725 0.0 0.0 0.0 0.0 110-111 12.5625 0.0 0.0 0.0 0.0 112-113 13.337499999999999 0.0 0.0 0.0 0.0 114-115 14.375 0.0 0.0 0.0 0.0 116-117 15.65 0.0 0.0 0.0 0.0 118-119 16.512500000000003 0.0 0.0 0.0 0.0 120-121 17.5 0.0 0.0 0.0 0.0 122-123 18.575000000000003 0.0 0.0 0.0 0.0 124-125 19.625 0.0 0.0 0.0 0.0 126-127 20.725 0.0 0.0 0.0 0.0 128-129 21.775 0.0 0.0 0.0 0.0 130-131 22.8875 0.0 0.0 0.0 0.0 132-133 23.825000000000003 0.0 0.0 0.0 0.0 134-135 24.825000000000003 0.0 0.0 0.0 0.0 136-137 26.05 0.0 0.0 0.0 0.0 138-139 27.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATGTTGC 10 0.006830828 145.0 7 >>END_MODULE Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434080 spots for SRR12670119.sra Written 434080 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra Read 434064 spots for SRR12670119.sra Written 434064 spots for SRR12670119.sra SRR ids: ['SRR12670119.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fgjvvd51 SRR12670119.sra spots: 8681296 blocks: [[1, 434064], [434065, 868128], [868129, 1302192], [1302193, 1736256], [1736257, 2170320], [2170321, 2604384], [2604385, 3038448], [3038449, 3472512], [3472513, 3906576], [3906577, 4340640], [4340641, 4774704], [4774705, 5208768], [5208769, 5642832], [5642833, 6076896], [6076897, 6510960], [6510961, 6945024], [6945025, 7379088], [7379089, 7813152], [7813153, 8247216], [8247217, 8681296]] SRR12670119 file size 2931159 SRR12670119 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 SRR12670119 SRR12670119_1.fastq SRR12670119_2.fastq Input file: SRR12670119_1.fastq Paired file: SRR12670119_2.fastq trimmed: SRR12670119-trimmed-pair1.fastq, SRR12670119-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 00:19:40 2025 >> started Tue Feb 11 00:19:49 2025 >> done (9.415s) 8681296 read pairs processed; of these: 26 ( 0.00%) short read pairs filtered out after trimming by size control 6349 ( 0.07%) empty read pairs filtered out after trimming by size control 8674921 (99.93%) read pairs available; of these: 2710875 (31.25%) trimmed read pairs available after processing 5964046 (68.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 1 0.00% 20 3 0.00% 21 5 0.00% 22 5 0.00% 23 15 0.00% 24 23 0.00% 25 27 0.00% 26 25 0.00% 27 25 0.00% 28 36 0.00% 29 34 0.00% 30 37 0.00% 31 51 0.00% 32 37 0.00% 33 46 0.00% 34 52 0.00% 35 81 0.00% 36 90 0.00% 37 69 0.00% 38 92 0.00% 39 109 0.00% 40 148 0.00% 41 152 0.00% 42 162 0.00% 43 160 0.00% 44 175 0.00% 45 216 0.00% 46 234 0.00% 47 253 0.00% 48 269 0.00% 49 340 0.00% 50 428 0.00% 51 507 0.01% 52 591 0.01% 53 563 0.01% 54 628 0.01% 55 678 0.01% 56 720 0.01% 57 932 0.01% 58 1026 0.01% 59 1218 0.01% 60 1455 0.02% 61 1701 0.02% 62 1911 0.02% 63 2181 0.03% 64 2446 0.03% 65 2321 0.03% 66 2722 0.03% 67 2974 0.03% 68 3240 0.04% 69 3807 0.04% 70 4371 0.05% 71 4912 0.06% 72 5623 0.06% 73 6391 0.07% 74 7095 0.08% 75 7540 0.09% 76 8269 0.10% 77 8957 0.10% 78 9585 0.11% 79 10323 0.12% 80 11236 0.13% 81 12578 0.14% 82 14194 0.16% 83 15283 0.18% 84 17060 0.20% 85 18128 0.21% 86 19007 0.22% 87 19554 0.23% 88 20402 0.24% 89 21142 0.24% 90 22093 0.25% 91 23950 0.28% 92 25452 0.29% 93 27374 0.32% 94 28739 0.33% 95 30381 0.35% 96 31469 0.36% 97 31760 0.37% 98 32218 0.37% 99 32274 0.37% 100 33353 0.38% 101 33660 0.39% 102 35156 0.41% 103 36843 0.42% 104 37717 0.43% 105 38768 0.45% 106 39614 0.46% 107 39891 0.46% 108 39365 0.45% 109 40247 0.46% 110 39097 0.45% 111 40098 0.46% 112 40817 0.47% 113 40711 0.47% 114 42386 0.49% 115 42993 0.50% 116 43270 0.50% 117 44155 0.51% 118 43933 0.51% 119 42895 0.49% 120 43196 0.50% 121 43819 0.51% 122 43342 0.50% 123 43050 0.50% 124 44400 0.51% 125 44151 0.51% 126 45185 0.52% 127 44833 0.52% 128 44600 0.51% 129 44764 0.52% 130 44284 0.51% 131 43555 0.50% 132 43920 0.51% 133 43567 0.50% 134 43327 0.50% 135 44097 0.51% 136 43965 0.51% 137 43885 0.51% 138 43587 0.50% 139 44862 0.52% 140 44038 0.51% 141 43218 0.50% 142 43355 0.50% 143 42616 0.49% 144 43273 0.50% 145 42926 0.49% 146 42604 0.49% 147 43027 0.50% 148 43319 0.50% 149 42350 0.49% 150 42405 0.49% 151 5964046 68.75% 8674921 reads passed initial QC criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=17 prefix-density=0.49 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=152.20 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=13.6 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=24 prefix-density=0.51 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.14 sequence-density-rank=23 fanout-score=34.25 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=12.7 sequence=AAAGAAAAGAAAA SRR12670119 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:20:30 Started mapping on | Feb 11 00:20:31 Finished on | Feb 11 00:21:26 Mapping speed, Million of reads per hour | 567.81 Number of input reads | 8674921 Average input read length | 281 UNIQUE READS: Uniquely mapped reads number | 8162007 Uniquely mapped reads % | 94.09% Average mapped length | 279.93 Number of splices: Total | 7732441 Number of splices: Annotated (sjdb) | 7557581 Number of splices: GT/AG | 7570774 Number of splices: GC/AG | 131748 Number of splices: AT/AC | 4907 Number of splices: Non-canonical | 25012 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.79 Insertion rate per base | 0.02% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 198624 % of reads mapped to multiple loci | 2.29% Number of reads mapped to too many loci | 38223 % of reads mapped to too many loci | 0.44% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.03% % of reads unmapped: other | 0.15% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 314290 314290 314290 N_multimapping 198624 198624 198624 N_noFeature 287838 8050587 339264 N_ambiguous 108602 431 48396 UnstrandedReadsAssigned:7765567 PositiveStrandReadsAssigned:110989 NegativeStrandReadsAssigned:7774347 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=128 echo kmer=123 SRR12670119 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: SRR12670119-trimmed-pair1.fastq SRR12670119-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,674,921 reads, 7,832,044 reads pseudoaligned [quant] estimated average fragment length: 198.421 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,122 rounds 52401 SRR12670119.ke.tsv 34699 SRR12670119.se.tsv 87100 total ==> SRR12670119.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.58 328 24.327 Potri.005G024800.1.v4.1 1035 837.579 66 10.64 Potri.004G059700.1.v4.1 961 763.63 1 0.176824 Potri.007G009000.2.v4.1 1416 1218.58 0 0 Potri.003G141000.2.v4.1 2943 2745.58 372.154 18.3026 Potri.016G087400.1.v4.1 270 113.426 291 346.421 Potri.015G069301.1.v4.1 564 373.435 0 0 Potri.010G195200.1.v4.1 1773 1575.58 12 1.02841 Potri.012G127500.1.v4.1 977 779.605 40 6.92804 ==> SRR12670119.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 139 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 116 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 7 SRR12670119 completed mapping pipeline successfully