Starting /dee2/code/volunteer_pipeline.sh SRR12951327 current disk space = 1543106535424 free memory = 1603082104 SRR12951327 SRAfilesize 41456437ffe51bb79bddb14c07853f91 SRR12951327.sra SRR12951327.sra file validated SRR12951327 is paired end SRR12951327 is conventional basespace SRR12951327 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951327_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 36.494 37.0 37.0 37.0 37.0 37.0 2 36.21275 37.0 37.0 37.0 37.0 37.0 3 36.5115 37.0 37.0 37.0 37.0 37.0 4 36.5585 37.0 37.0 37.0 37.0 37.0 5 36.6395 37.0 37.0 37.0 37.0 37.0 6 36.5855 37.0 37.0 37.0 37.0 37.0 7 36.5565 37.0 37.0 37.0 37.0 37.0 8 36.5285 37.0 37.0 37.0 37.0 37.0 9 36.621 37.0 37.0 37.0 37.0 37.0 10-14 36.5674 37.0 37.0 37.0 37.0 37.0 15-19 36.5512 37.0 37.0 37.0 37.0 37.0 20-24 36.5132 37.0 37.0 37.0 37.0 37.0 25-29 36.4853 37.0 37.0 37.0 37.0 37.0 30-34 36.4968 37.0 37.0 37.0 37.0 37.0 35-39 36.502500000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.4773 37.0 37.0 37.0 37.0 37.0 45-49 36.4066 37.0 37.0 37.0 37.0 37.0 50-54 36.3988 37.0 37.0 37.0 37.0 37.0 55-59 36.336200000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.31869999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.3138 37.0 37.0 37.0 37.0 37.0 70-74 36.30329999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.3063 37.0 37.0 37.0 37.0 37.0 80-84 36.311 37.0 37.0 37.0 37.0 37.0 85-89 36.2718 37.0 37.0 37.0 37.0 37.0 90-94 36.242200000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.204699999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.226800000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.1973 37.0 37.0 37.0 37.0 37.0 110-114 36.1456 37.0 37.0 37.0 37.0 37.0 115-119 36.146 37.0 37.0 37.0 37.0 37.0 120-124 36.080200000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.9711 37.0 37.0 37.0 37.0 37.0 130-134 35.8783 37.0 37.0 37.0 37.0 37.0 135-139 35.6255 37.0 37.0 37.0 37.0 37.0 140-144 35.3814 37.0 37.0 37.0 37.0 37.0 145-149 35.134100000000004 37.0 37.0 37.0 34.6 37.0 150-151 34.8395 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 0.0 23 0.0 24 3.0 25 5.0 26 1.0 27 4.0 28 11.0 29 19.0 30 25.0 31 36.0 32 75.0 33 111.0 34 148.0 35 325.0 36 2722.0 37 514.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 54.2 10.424999999999999 4.9750000000000005 30.4 2 22.25295448830777 9.454362584862961 34.121196882071914 34.17148604475735 3 20.724999999999998 18.5 26.25 34.525 4 25.025 22.35 23.525 29.099999999999998 5 27.85 29.2 22.1 20.849999999999998 6 25.224999999999998 31.0 22.175 21.6 7 18.625 24.025 38.550000000000004 18.8 8 19.900000000000002 21.625 30.85 27.625 9 23.0 20.5 30.675 25.825 10-14 24.455 25.985000000000003 24.755 24.805 15-19 23.990000000000002 24.47 25.480000000000004 26.06 20-24 24.224999999999998 24.77 24.834999999999997 26.169999999999998 25-29 24.05 24.490000000000002 24.77 26.69 30-34 24.795 24.715 24.175 26.314999999999998 35-39 24.86 24.905 23.865 26.369999999999997 40-44 23.855 25.119999999999997 24.995 26.029999999999998 45-49 24.765 25.064999999999998 23.78 26.39 50-54 24.145 24.955 24.14 26.76 55-59 24.349999999999998 24.79 24.27 26.590000000000003 60-64 24.445 24.345 24.625 26.584999999999997 65-69 24.86 25.34 23.615 26.185000000000002 70-74 25.490000000000002 23.845 24.16 26.505000000000003 75-79 24.785 24.375 24.104999999999997 26.735 80-84 25.61 24.91 23.580000000000002 25.900000000000002 85-89 25.1 24.825 23.745 26.33 90-94 25.095 24.235 24.125 26.545 95-99 24.82 24.795 24.115000000000002 26.27 100-104 25.5 24.64 23.7 26.16 105-109 25.28 25.22 23.400000000000002 26.1 110-114 25.28 25.335 23.155 26.229999999999997 115-119 26.229999999999997 24.715 23.13 25.924999999999997 120-124 25.31 25.169999999999998 22.925 26.595000000000002 125-129 25.369999999999997 24.95 22.935 26.745 130-134 25.224999999999998 25.14 22.7 26.935 135-139 25.6 24.455 23.155 26.790000000000003 140-144 24.825 24.66 23.419999999999998 27.095000000000002 145-149 25.19 24.404999999999998 23.22 27.185 150-151 25.362499999999997 24.975 22.7 26.9625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 1.0 27 2.5 28 8.5 29 11.0 30 7.0 31 7.0 32 10.0 33 12.5 34 21.0 35 30.0 36 36.5 37 54.0 38 73.0 39 83.5 40 96.0 41 117.0 42 132.0 43 155.5 44 173.0 45 181.5 46 205.0 47 200.5 48 172.0 49 159.5 50 145.0 51 142.5 52 131.0 53 112.0 54 117.0 55 110.5 56 111.5 57 109.0 58 94.0 59 82.5 60 69.5 61 64.5 62 62.5 63 71.0 64 82.5 65 67.0 66 56.5 67 61.5 68 52.5 69 45.0 70 43.0 71 42.0 72 45.0 73 35.0 74 27.5 75 24.5 76 16.5 77 11.5 78 7.0 79 3.5 80 2.0 81 1.0 82 0.5 83 1.5 84 1.0 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 0.575 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 81.675 #Duplication Level Percentage of deduplicated Percentage of total 1 82.7670645852464 67.60000000000001 2 13.559840832568105 22.15 3 2.6629935720844813 6.525 4 0.7346189164370982 2.4 5 0.12243648607284971 0.5 6 0.09182736455463728 0.44999999999999996 7 0.030609121518212427 0.17500000000000002 8 0.030609121518212427 0.2 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGACACAATCTCGGTT 8 0.2 TruSeq Adapter, Index 7 (97% over 37bp) GCTTTCTTGAAGAGTTAGTCCGACTCTTGGCCCTAATGCAGTAGTTATCA 7 0.17500000000000002 No Hit GGGGCAGGTACGAGAGGGTCTCGAACTTCTTGATGCCCTCGATCGGCCAC 6 0.15 No Hit GTGTCCACGGGAGGCGGGGAAGGCTCCATTGGGATGCGGCGGCGGCCGGA 6 0.15 No Hit CCTGGATCTTGGCCTTCACGTTGTCGATCGTGTCCGAGGACTCGACCTCG 6 0.15 No Hit GCAAGAATGGACAGCACAGTGTTTGCAGTGATCAGTGGAGGCTCTTTCAA 5 0.125 No Hit GCCTGCATGATCACACCAGCTACAGCAACTGCACACTGTGCAGCTTCAGC 5 0.125 No Hit GGGGGAGGTCGAAGTTGATCCCCTTGATGGCCGGGTGGCGTGCCACGATG 5 0.125 No Hit CCCTGAGATCGGTGGCGACCTTCTCCAGATCCTCGGCGCTGCTCTTGCCA 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 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 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.0625 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.175 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.275 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.30000000000000004 0.0 0.0 0.0 0.0 74-75 0.4 0.0 0.0 0.0 0.0 76-77 0.5125 0.0 0.0 0.0 0.0 78-79 0.6375 0.0 0.0 0.0 0.0 80-81 0.7125 0.0 0.0 0.0 0.0 82-83 0.8999999999999999 0.0 0.0 0.0 0.0 84-85 1.25 0.0 0.0 0.0 0.0 86-87 1.5625 0.0 0.0 0.0 0.0 88-89 1.8375 0.0 0.0 0.0 0.0 90-91 2.275 0.0 0.0 0.0 0.0 92-93 2.6875 0.0 0.0 0.0 0.0 94-95 3.1125 0.0 0.0 0.0 0.0 96-97 3.475 0.0 0.0 0.0 0.0 98-99 4.05 0.0 0.0 0.0 0.0 100-101 4.575 0.0 0.0 0.0 0.0 102-103 5.112500000000001 0.0 0.0 0.0 0.0 104-105 5.675 0.0 0.0 0.0 0.0 106-107 6.387499999999999 0.0 0.0 0.0 0.0 108-109 7.1375 0.0 0.0 0.0 0.0 110-111 7.875 0.0 0.0 0.0 0.0 112-113 8.85 0.0 0.0 0.0 0.0 114-115 9.7 0.0 0.0 0.0 0.0 116-117 10.65 0.0 0.0 0.0 0.0 118-119 11.675 0.0 0.0 0.0 0.0 120-121 12.375 0.0 0.0 0.0 0.0 122-123 13.2625 0.0 0.0 0.0 0.0 124-125 14.2 0.0 0.0 0.0 0.0 126-127 15.2375 0.0 0.0 0.0 0.0 128-129 16.200000000000003 0.0 0.0 0.0 0.0 130-131 16.9375 0.0 0.0 0.0 0.0 132-133 17.9125 0.0 0.0 0.0 0.0 134-135 19.0 0.0 0.0 0.0 0.0 136-137 19.8125 0.0 0.0 0.0 0.0 138-139 20.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATAGCTC 10 0.006830828 145.0 9 >>END_MODULE SRR12951327 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951327_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 36.202 37.0 37.0 37.0 37.0 37.0 2 36.016 37.0 37.0 37.0 37.0 37.0 3 36.013 37.0 37.0 37.0 37.0 37.0 4 36.1635 37.0 37.0 37.0 37.0 37.0 5 36.1355 37.0 37.0 37.0 37.0 37.0 6 36.1665 37.0 37.0 37.0 37.0 37.0 7 36.2375 37.0 37.0 37.0 37.0 37.0 8 36.2525 37.0 37.0 37.0 37.0 37.0 9 36.2245 37.0 37.0 37.0 37.0 37.0 10-14 36.18990000000001 37.0 37.0 37.0 37.0 37.0 15-19 36.1444 37.0 37.0 37.0 37.0 37.0 20-24 36.0852 37.0 37.0 37.0 37.0 37.0 25-29 36.0184 37.0 37.0 37.0 37.0 37.0 30-34 35.9434 37.0 37.0 37.0 37.0 37.0 35-39 35.924400000000006 37.0 37.0 37.0 37.0 37.0 40-44 35.919 37.0 37.0 37.0 37.0 37.0 45-49 35.93899999999999 37.0 37.0 37.0 37.0 37.0 50-54 35.9567 37.0 37.0 37.0 37.0 37.0 55-59 35.8952 37.0 37.0 37.0 37.0 37.0 60-64 35.8402 37.0 37.0 37.0 37.0 37.0 65-69 35.871500000000005 37.0 37.0 37.0 37.0 37.0 70-74 35.7786 37.0 37.0 37.0 37.0 37.0 75-79 35.7941 37.0 37.0 37.0 37.0 37.0 80-84 35.7064 37.0 37.0 37.0 37.0 37.0 85-89 35.67399999999999 37.0 37.0 37.0 37.0 37.0 90-94 35.7243 37.0 37.0 37.0 37.0 37.0 95-99 35.7384 37.0 37.0 37.0 37.0 37.0 100-104 35.6505 37.0 37.0 37.0 37.0 37.0 105-109 35.5964 37.0 37.0 37.0 37.0 37.0 110-114 35.6014 37.0 37.0 37.0 37.0 37.0 115-119 35.627 37.0 37.0 37.0 37.0 37.0 120-124 35.5312 37.0 37.0 37.0 37.0 37.0 125-129 35.4404 37.0 37.0 37.0 37.0 37.0 130-134 35.261700000000005 37.0 37.0 37.0 34.6 37.0 135-139 35.1901 37.0 37.0 37.0 34.6 37.0 140-144 35.1158 37.0 37.0 37.0 27.4 37.0 145-149 34.864599999999996 37.0 37.0 37.0 27.4 37.0 150-151 34.5505 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 3.0 13 5.0 14 12.0 15 6.0 16 1.0 17 2.0 18 3.0 19 5.0 20 1.0 21 4.0 22 11.0 23 5.0 24 11.0 25 8.0 26 7.0 27 16.0 28 15.0 29 22.0 30 20.0 31 38.0 32 64.0 33 109.0 34 184.0 35 541.0 36 2579.0 37 328.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.24999999999999 19.75 5.975 24.025 2 31.275 20.225 25.724999999999998 22.775000000000002 3 23.9 22.75 30.95 22.400000000000002 4 27.474999999999998 29.75 18.9 23.875 5 27.85 32.525 18.775 20.849999999999998 6 25.374999999999996 31.924999999999997 19.925 22.775000000000002 7 23.075000000000003 19.175 33.125 24.625 8 23.925 21.725 24.775 29.575000000000003 9 25.474999999999998 20.075000000000003 25.224999999999998 29.225 10-14 27.075 23.45 23.13 26.345000000000002 15-19 27.105 23.72 23.415 25.759999999999998 20-24 27.49 23.62 23.16 25.729999999999997 25-29 26.779999999999998 23.56 23.494999999999997 26.165 30-34 26.36 23.655 23.705000000000002 26.279999999999998 35-39 26.195 24.46 23.395 25.95 40-44 27.21 24.415 22.925 25.45 45-49 26.25 22.770000000000003 24.175 26.805 50-54 26.365 23.655 23.885 26.095000000000002 55-59 26.395000000000003 24.4 24.13 25.074999999999996 60-64 26.275 23.885 24.2 25.64 65-69 26.57 23.845 23.525 26.06 70-74 26.840000000000003 24.11 23.585 25.465 75-79 27.07 24.19 23.785 24.955 80-84 26.765 24.385 23.885 24.965 85-89 28.084999999999997 23.69 23.57 24.654999999999998 90-94 27.060000000000002 24.47 23.494999999999997 24.975 95-99 27.200000000000003 25.805 22.52 24.474999999999998 100-104 27.98 24.545 22.85 24.625 105-109 28.22 24.23 23.485 24.065 110-114 27.88 25.025 23.385 23.71 115-119 28.46 24.52 23.105 23.915 120-124 28.599999999999998 24.425 22.52 24.455 125-129 28.335 25.635 23.11 22.919999999999998 130-134 29.035 25.509999999999998 21.82 23.635 135-139 29.599999999999998 25.34 22.795 22.264999999999997 140-144 30.214999999999996 25.195 22.7 21.89 145-149 30.97 24.545 22.455 22.03 150-151 29.65 25.5 21.8 23.05 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 1.0 12 0.5 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 0.5 21 0.5 22 0.5 23 1.5 24 1.5 25 0.0 26 0.0 27 1.0 28 6.5 29 8.0 30 5.0 31 6.0 32 6.5 33 8.0 34 14.5 35 24.0 36 33.5 37 50.5 38 66.0 39 73.5 40 92.0 41 110.5 42 127.5 43 151.5 44 153.5 45 157.5 46 173.5 47 172.0 48 165.5 49 158.5 50 143.5 51 131.5 52 132.5 53 125.5 54 104.0 55 104.5 56 118.0 57 108.5 58 94.0 59 86.0 60 80.0 61 68.5 62 72.0 63 90.0 64 85.5 65 69.5 66 63.5 67 74.0 68 70.0 69 58.0 70 64.5 71 58.5 72 41.5 73 32.0 74 26.5 75 26.0 76 24.5 77 16.5 78 10.0 79 5.5 80 4.0 81 4.5 82 2.5 83 0.5 84 0.5 85 0.5 86 0.5 87 1.0 88 1.0 89 1.5 90 2.0 91 1.5 92 1.5 93 2.0 94 1.5 95 1.0 96 1.0 97 1.0 98 2.0 99 2.5 100 5.0 >>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 82.075 #Duplication Level Percentage of deduplicated Percentage of total 1 83.24703015534573 68.325 2 13.25007614986293 21.75 3 2.497715504112093 6.15 4 0.7614986293024673 2.5 5 0.09137983551629607 0.375 6 0.06091989034419738 0.3 7 0.03045994517209869 0.17500000000000002 8 0.03045994517209869 0.2 9 0.03045994517209869 0.22499999999999998 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 9 0.22499999999999998 No Hit GCCTCTTCTCGCTTGCTCTACCTGCTGCTTGCAACCATGGCACCCACCGT 8 0.2 No Hit ATTAGGTGCTTTTCTGGCCGGGGCCCTCCTTGCAGAAACAAACTTTCGTA 7 0.17500000000000002 No Hit TCTCAATCGCACCGAGAAAAATCTCCTAGCGATCGAAGCGAAGCCTCTCC 6 0.15 No Hit GCCCATTCCAAACTCCAAAGCACGCTCCTCCTCCGCTGCCGCCGCCGCCT 6 0.15 No Hit GGGAAAATGGAAAGCTGTCGCGGCGATACGCCGCCGCCCCCGTCTGCAAG 5 0.125 No Hit GAGGGTTTCTATAAGCTAGCATTGGCCTATGCACCTGTTCCCGATCTTCA 5 0.125 No Hit TATCAATCGAGAGACCTATGTTGATAGGCTGATTGCACGATATGGAGACG 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 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 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.0625 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.175 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.275 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.30000000000000004 0.0 0.0 0.0 0.0 74-75 0.4 0.0 0.0 0.0 0.0 76-77 0.5125 0.0 0.0 0.0 0.0 78-79 0.6375 0.0 0.0 0.0 0.0 80-81 0.7125 0.0 0.0 0.0 0.0 82-83 0.8999999999999999 0.0 0.0 0.0 0.0 84-85 1.25 0.0 0.0 0.0 0.0 86-87 1.5625 0.0 0.0 0.0 0.0 88-89 1.7875 0.0 0.0 0.0 0.0 90-91 2.1875 0.0 0.0 0.0 0.0 92-93 2.6125 0.0 0.0 0.0 0.0 94-95 3.0 0.0 0.0 0.0 0.0 96-97 3.35 0.0 0.0 0.0 0.0 98-99 3.925 0.0 0.0 0.0 0.0 100-101 4.45 0.0 0.0 0.0 0.0 102-103 4.9625 0.0 0.0 0.0 0.0 104-105 5.5375 0.0 0.0 0.0 0.0 106-107 6.275 0.0 0.0 0.0 0.0 108-109 7.0375 0.0 0.0 0.0 0.0 110-111 7.800000000000001 0.0 0.0 0.0 0.0 112-113 8.787500000000001 0.0 0.0 0.0 0.0 114-115 9.625 0.0 0.0 0.0 0.0 116-117 10.575 0.0 0.0 0.0 0.0 118-119 11.625 0.0 0.0 0.0 0.0 120-121 12.35 0.0 0.0 0.0 0.0 122-123 13.2625 0.0 0.0 0.0 0.0 124-125 14.2 0.0 0.0 0.0 0.0 126-127 15.2375 0.0 0.0 0.0 0.0 128-129 16.2 0.0 0.0 0.0 0.0 130-131 16.950000000000003 0.0 0.0 0.0 0.0 132-133 17.9375 0.0 0.0 0.0 0.0 134-135 19.0625 0.0 0.0 0.0 0.0 136-137 19.8875 0.0 0.0 0.0 0.0 138-139 20.512500000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGTGGC 10 0.006830828 145.0 5 >>END_MODULE Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606300 spots for SRR12951327.sra Written 1606300 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra Read 1606286 spots for SRR12951327.sra Written 1606286 spots for SRR12951327.sra SRR ids: ['SRR12951327.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_021pduac SRR12951327.sra spots: 32125734 blocks: [[1, 1606286], [1606287, 3212572], [3212573, 4818858], [4818859, 6425144], [6425145, 8031430], [8031431, 9637716], [9637717, 11244002], [11244003, 12850288], [12850289, 14456574], [14456575, 16062860], [16062861, 17669146], [17669147, 19275432], [19275433, 20881718], [20881719, 22488004], [22488005, 24094290], [24094291, 25700576], [25700577, 27306862], [27306863, 28913148], [28913149, 30519434], [30519435, 32125734]] SRR12951327 file size 10896029 SRR12951327 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 SRR12951327 SRR12951327_1.fastq SRR12951327_2.fastq Input file: SRR12951327_1.fastq Paired file: SRR12951327_2.fastq trimmed: SRR12951327-trimmed-pair1.fastq, SRR12951327-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 12:03:20 2024 >> started Sat Dec 7 12:04:03 2024 >> done (42.680s) 32125734 read pairs processed; of these: 686 ( 0.00%) short read pairs filtered out after trimming by size control 52329 ( 0.16%) empty read pairs filtered out after trimming by size control 32072719 (99.83%) read pairs available; of these: 7286650 (22.72%) trimmed read pairs available after processing 24786069 (77.28%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 34 0.00% 19 25 0.00% 20 57 0.00% 21 69 0.00% 22 102 0.00% 23 116 0.00% 24 126 0.00% 25 127 0.00% 26 163 0.00% 27 174 0.00% 28 162 0.00% 29 153 0.00% 30 149 0.00% 31 172 0.00% 32 136 0.00% 33 169 0.00% 34 164 0.00% 35 171 0.00% 36 192 0.00% 37 206 0.00% 38 240 0.00% 39 237 0.00% 40 222 0.00% 41 277 0.00% 42 277 0.00% 43 304 0.00% 44 362 0.00% 45 405 0.00% 46 458 0.00% 47 495 0.00% 48 568 0.00% 49 609 0.00% 50 712 0.00% 51 872 0.00% 52 1038 0.00% 53 1024 0.00% 54 1196 0.00% 55 1313 0.00% 56 1465 0.00% 57 1657 0.01% 58 1978 0.01% 59 2329 0.01% 60 2751 0.01% 61 3175 0.01% 62 3519 0.01% 63 3802 0.01% 64 4282 0.01% 65 4691 0.01% 66 5286 0.02% 67 5971 0.02% 68 6811 0.02% 69 7758 0.02% 70 8870 0.03% 71 10340 0.03% 72 12034 0.04% 73 13358 0.04% 74 14653 0.05% 75 15702 0.05% 76 16955 0.05% 77 18359 0.06% 78 20283 0.06% 79 22925 0.07% 80 24834 0.08% 81 27991 0.09% 82 31487 0.10% 83 33779 0.11% 84 37495 0.12% 85 39368 0.12% 86 41471 0.13% 87 43312 0.14% 88 45737 0.14% 89 47784 0.15% 90 51592 0.16% 91 55452 0.17% 92 59402 0.19% 93 63577 0.20% 94 66577 0.21% 95 68849 0.21% 96 71496 0.22% 97 72713 0.23% 98 73676 0.23% 99 76488 0.24% 100 79929 0.25% 101 82699 0.26% 102 85836 0.27% 103 89500 0.28% 104 92404 0.29% 105 94824 0.30% 106 96873 0.30% 107 97060 0.30% 108 98226 0.31% 109 100060 0.31% 110 100508 0.31% 111 103340 0.32% 112 107312 0.33% 113 109714 0.34% 114 113843 0.35% 115 115013 0.36% 116 116060 0.36% 117 117037 0.36% 118 116404 0.36% 119 116273 0.36% 120 117393 0.37% 121 119229 0.37% 122 120922 0.38% 123 123006 0.38% 124 126180 0.39% 125 126678 0.39% 126 128123 0.40% 127 126336 0.39% 128 127005 0.40% 129 127141 0.40% 130 126601 0.39% 131 125961 0.39% 132 129057 0.40% 133 130108 0.41% 134 130992 0.41% 135 133419 0.42% 136 133141 0.42% 137 131418 0.41% 138 131963 0.41% 139 131809 0.41% 140 129633 0.40% 141 130191 0.41% 142 131635 0.41% 143 130313 0.41% 144 132694 0.41% 145 134421 0.42% 146 134945 0.42% 147 135377 0.42% 148 131418 0.41% 149 130324 0.41% 150 130992 0.41% 151 24786069 77.28% 32072719 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=35 prefix-density=0.23 prefix-fanout=1.9 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=539.95 fanout-score-rank=1 prefix-density=0.74 prefix-fanout=21.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=2.40 fanout-score-rank=32 prefix-density=0.20 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=1477.60 fanout-score-rank=1 prefix-density=1.00 prefix-fanout=21.3 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGA SRR12951327 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 12:04:39 Started mapping on | Dec 07 12:04:40 Finished on | Dec 07 12:07:34 Mapping speed, Million of reads per hour | 663.57 Number of input reads | 32072719 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 29792785 Uniquely mapped reads % | 92.89% Average mapped length | 286.23 Number of splices: Total | 29049734 Number of splices: Annotated (sjdb) | 27167521 Number of splices: GT/AG | 28649281 Number of splices: GC/AG | 327949 Number of splices: AT/AC | 19357 Number of splices: Non-canonical | 53147 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.73 Insertion rate per base | 0.01% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 339275 % of reads mapped to multiple loci | 1.06% Number of reads mapped to too many loci | 52267 % of reads mapped to too many loci | 0.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.20% % of reads unmapped: other | 0.69% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1940659 1940659 1940659 N_multimapping 339275 339275 339275 N_noFeature 1042562 29049173 1294708 N_ambiguous 577311 4609 86368 UnstrandedReadsAssigned:28172912 PositiveStrandReadsAssigned:739003 NegativeStrandReadsAssigned:28411709 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=142 echo kmer=137 SRR12951327 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: SRR12951327-trimmed-pair1.fastq SRR12951327-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,072,719 reads, 28,850,038 reads pseudoaligned [quant] estimated average fragment length: 237.53 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,293 rounds 52973 SRR12951327.ke.tsv 35125 SRR12951327.se.tsv 88098 total ==> SRR12951327.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 700.139 0 0 PNS24247 1044 807.47 85.5751 5.63254 PNS24249 1928 1691.47 321.402 10.0988 PNS24246 1044 807.47 85.5751 5.63254 PNS24248 1044 807.47 85.5751 5.63254 PNS24244 1471 1234.47 102.872 4.42895 PNS24243 293 119.155 0 0 KQK14069 1603 1366.47 2890.94 112.44 KQK14071 474 262.512 56.6401 11.4672 ==> SRR12951327.se.tsv <== BRADI_1g14170v3 3078 BRADI_1g53295v3 70 BRADI_1g59795v3 695 BRADI_1g07683v3 0 BRADI_1g00485v3 74 BRADI_1g20270v3 3568 BRADI_1g74790v3 339 BRADI_1g09890v3 41 BRADI_1g77505v3 493 BRADI_1g48960v3 11 SRR12951327 completed mapping pipeline successfully