Starting /dee2/code/volunteer_pipeline.sh SRR12671414 current disk space = 3052332285952 free memory = 1508655928 SRR12671414 SRAfilesize 1186f6965cec95d2ad94434ed37490e7 SRR12671414.sra SRR12671414.sra file validated SRR12671414 is paired end SRR12671414 is conventional basespace SRR12671414 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671414_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 36.5425 37.0 37.0 37.0 37.0 37.0 2 36.3765 37.0 37.0 37.0 37.0 37.0 3 36.575 37.0 37.0 37.0 37.0 37.0 4 36.6235 37.0 37.0 37.0 37.0 37.0 5 36.5705 37.0 37.0 37.0 37.0 37.0 6 36.6015 37.0 37.0 37.0 37.0 37.0 7 36.5305 37.0 37.0 37.0 37.0 37.0 8 36.684 37.0 37.0 37.0 37.0 37.0 9 36.659 37.0 37.0 37.0 37.0 37.0 10-14 36.6479 37.0 37.0 37.0 37.0 37.0 15-19 36.6144 37.0 37.0 37.0 37.0 37.0 20-24 36.5652 37.0 37.0 37.0 37.0 37.0 25-29 36.563500000000005 37.0 37.0 37.0 37.0 37.0 30-34 36.5313 37.0 37.0 37.0 37.0 37.0 35-39 36.541599999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.499500000000005 37.0 37.0 37.0 37.0 37.0 45-49 36.4988 37.0 37.0 37.0 37.0 37.0 50-54 36.521699999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.4462 37.0 37.0 37.0 37.0 37.0 60-64 36.4441 37.0 37.0 37.0 37.0 37.0 65-69 36.433299999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.3951 37.0 37.0 37.0 37.0 37.0 75-79 36.4745 37.0 37.0 37.0 37.0 37.0 80-84 36.388299999999994 37.0 37.0 37.0 37.0 37.0 85-89 36.3333 37.0 37.0 37.0 37.0 37.0 90-94 36.3365 37.0 37.0 37.0 37.0 37.0 95-99 36.3228 37.0 37.0 37.0 37.0 37.0 100-104 36.2841 37.0 37.0 37.0 37.0 37.0 105-109 36.248000000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.1888 37.0 37.0 37.0 37.0 37.0 115-119 36.260400000000004 37.0 37.0 37.0 37.0 37.0 120-124 36.155699999999996 37.0 37.0 37.0 37.0 37.0 125-129 36.145300000000006 37.0 37.0 37.0 37.0 37.0 130-134 36.0777 37.0 37.0 37.0 37.0 37.0 135-139 36.1227 37.0 37.0 37.0 37.0 37.0 140-144 36.009 37.0 37.0 37.0 37.0 37.0 145-149 35.960699999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.72425 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 0.0 23 1.0 24 0.0 25 2.0 26 1.0 27 3.0 28 10.0 29 15.0 30 24.0 31 33.0 32 37.0 33 51.0 34 106.0 35 242.0 36 3062.0 37 411.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.050000000000004 10.100000000000001 5.75 45.1 2 19.04164576016056 14.024084295032612 37.70697441043653 29.227295534370295 3 17.849999999999998 17.25 26.674999999999997 38.224999999999994 4 23.674999999999997 24.525 22.975 28.825 5 23.125 32.574999999999996 23.674999999999997 20.625 6 20.4 33.300000000000004 24.4 21.9 7 15.7 24.85 43.175000000000004 16.275000000000002 8 16.5 24.65 34.025 24.825 9 17.1 21.975 37.05 23.875 10-14 19.195 29.555 28.199999999999996 23.05 15-19 19.81 28.59 27.415 24.185000000000002 20-24 20.27 28.689999999999998 27.565 23.474999999999998 25-29 19.945 27.900000000000002 28.494999999999997 23.66 30-34 19.43 28.74 28.08 23.75 35-39 19.73 28.535 27.639999999999997 24.095 40-44 19.55 28.425 28.46 23.565 45-49 19.580000000000002 28.449999999999996 27.71 24.26 50-54 19.744999999999997 28.485 27.589999999999996 24.18 55-59 19.525000000000002 28.444999999999997 28.08 23.95 60-64 19.825 28.475 28.105000000000004 23.595 65-69 20.195 28.74 27.065 24.0 70-74 19.415 28.76 27.27 24.555 75-79 20.155 28.005000000000003 28.005000000000003 23.835 80-84 19.905 28.53 27.800000000000004 23.765 85-89 19.2 28.76 28.025 24.015 90-94 20.28 28.24 28.299999999999997 23.18 95-99 19.865 28.199999999999996 28.560000000000002 23.375 100-104 21.029999999999998 27.485 27.595 23.89 105-109 20.325 27.839999999999996 28.095 23.74 110-114 20.62 28.265 27.325 23.79 115-119 20.57 27.500000000000004 28.035 23.895 120-124 20.39 27.595 27.985 24.03 125-129 20.745 27.905 27.495000000000005 23.855 130-134 20.16 28.29 28.21 23.34 135-139 20.565 28.605000000000004 27.07 23.76 140-144 20.849999999999998 28.23 27.61 23.31 145-149 21.55 28.389999999999997 26.029999999999998 24.03 150-151 21.025 27.6625 27.0 24.3125 >>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 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 1.0 18 0.5 19 0.0 20 0.5 21 1.0 22 2.0 23 2.5 24 3.5 25 5.0 26 4.0 27 5.5 28 9.0 29 10.5 30 15.5 31 22.5 32 31.0 33 42.0 34 48.0 35 68.5 36 99.0 37 124.0 38 145.0 39 165.5 40 192.0 41 209.0 42 226.0 43 247.5 44 262.0 45 275.5 46 260.0 47 243.0 48 232.5 49 216.0 50 184.0 51 133.0 52 122.0 53 110.5 54 74.5 55 51.5 56 43.5 57 33.5 58 20.5 59 13.0 60 10.5 61 8.0 62 5.0 63 6.0 64 5.0 65 2.5 66 2.0 67 1.0 68 0.0 69 1.0 70 1.0 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 0.35000000000000003 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 84.65 #Duplication Level Percentage of deduplicated Percentage of total 1 86.08978145304194 72.875 2 10.986414648552865 18.6 3 2.155936207914944 5.475 4 0.47253396337861786 1.6 5 0.1772002362669817 0.75 6 0.05906674542232723 0.3 7 0.029533372711163616 0.17500000000000002 8 0.0 0.0 9 0.029533372711163616 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 GGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGA 9 0.22499999999999998 No Hit GTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACC 7 0.17500000000000002 No Hit CGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAG 6 0.15 No Hit CAGTTGAAGAACTGCTAGCCCAAAATTGATCTGTCGTGGAGTCTGGTGAA 6 0.15 No Hit CCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAA 5 0.125 No Hit CCCAGGTCGGAAATCTCCACGACTTAGATGCTTTCCTTTTCCCCTCTGAA 5 0.125 No Hit GCACGCGCATGGAATGATGAAAAGCCAATAAGAGGCCTGTGAATTCCTTT 5 0.125 No Hit CACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCC 5 0.125 No Hit CACCGTCGTGCTTGCCGTCACCGAGGTCACCCAACCAGGCCTTGAGGCCG 5 0.125 No Hit CTATGAGATATCTTTGTGTAAGATTTTGGCATGTGTTGCATAGCATGCAT 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 0.025 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 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.037500000000000006 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.16249999999999998 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.23750000000000002 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.275 0.0 0.0 0.0 0.0 94-95 0.30000000000000004 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.4375 0.0 0.0 0.0 0.0 100-101 0.5 0.0 0.0 0.0 0.0 102-103 0.6125 0.0 0.0 0.0 0.0 104-105 0.6875 0.0 0.0 0.0 0.0 106-107 0.9125 0.0 0.0 0.0 0.0 108-109 0.975 0.0 0.0 0.0 0.0 110-111 1.0750000000000002 0.0 0.0 0.0 0.0 112-113 1.1749999999999998 0.0 0.0 0.0 0.0 114-115 1.2125 0.0 0.0 0.0 0.0 116-117 1.2999999999999998 0.0 0.0 0.0 0.0 118-119 1.4375 0.0 0.0 0.0 0.0 120-121 1.5625 0.0 0.0 0.0 0.0 122-123 1.7 0.0 0.0 0.0 0.0 124-125 1.7875 0.0 0.0 0.0 0.0 126-127 1.9500000000000002 0.0 0.0 0.0 0.0 128-129 1.9875 0.0 0.0 0.0 0.0 130-131 2.1125 0.0 0.0 0.0 0.0 132-133 2.175 0.0 0.0 0.0 0.0 134-135 2.375 0.0 0.0 0.0 0.0 136-137 2.5875 0.0 0.0 0.0 0.0 138-139 2.7 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTACACA 10 0.006830828 145.0 6 TACACAT 10 0.006830828 145.0 7 ACACATG 10 0.006830828 145.0 8 >>END_MODULE SRR12671414 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671414_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 36.3345 37.0 37.0 37.0 37.0 37.0 2 36.138 37.0 37.0 37.0 37.0 37.0 3 36.244 37.0 37.0 37.0 37.0 37.0 4 36.3235 37.0 37.0 37.0 37.0 37.0 5 36.372 37.0 37.0 37.0 37.0 37.0 6 36.3085 37.0 37.0 37.0 37.0 37.0 7 36.3435 37.0 37.0 37.0 37.0 37.0 8 36.3285 37.0 37.0 37.0 37.0 37.0 9 36.3515 37.0 37.0 37.0 37.0 37.0 10-14 36.3624 37.0 37.0 37.0 37.0 37.0 15-19 36.409 37.0 37.0 37.0 37.0 37.0 20-24 36.3351 37.0 37.0 37.0 37.0 37.0 25-29 36.307599999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.2643 37.0 37.0 37.0 37.0 37.0 35-39 36.305 37.0 37.0 37.0 37.0 37.0 40-44 36.2154 37.0 37.0 37.0 37.0 37.0 45-49 36.2361 37.0 37.0 37.0 37.0 37.0 50-54 36.1982 37.0 37.0 37.0 37.0 37.0 55-59 36.180400000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.1494 37.0 37.0 37.0 37.0 37.0 65-69 36.158100000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.1173 37.0 37.0 37.0 37.0 37.0 75-79 36.093399999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.0709 37.0 37.0 37.0 37.0 37.0 85-89 36.1279 37.0 37.0 37.0 37.0 37.0 90-94 36.022000000000006 37.0 37.0 37.0 37.0 37.0 95-99 36.0462 37.0 37.0 37.0 37.0 37.0 100-104 35.98010000000001 37.0 37.0 37.0 37.0 37.0 105-109 35.886199999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.8088 37.0 37.0 37.0 37.0 37.0 115-119 35.8996 37.0 37.0 37.0 37.0 37.0 120-124 35.8651 37.0 37.0 37.0 37.0 37.0 125-129 35.8223 37.0 37.0 37.0 37.0 37.0 130-134 35.7928 37.0 37.0 37.0 37.0 37.0 135-139 35.6919 37.0 37.0 37.0 37.0 37.0 140-144 35.7592 37.0 37.0 37.0 37.0 37.0 145-149 35.7497 37.0 37.0 37.0 37.0 37.0 150-151 35.50675 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 2.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 1.0 22 1.0 23 2.0 24 2.0 25 5.0 26 5.0 27 8.0 28 11.0 29 20.0 30 30.0 31 41.0 32 47.0 33 93.0 34 174.0 35 481.0 36 2788.0 37 288.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.95 22.125 11.275 28.65 2 24.4 27.175 32.45 15.975 3 19.825 28.9 32.550000000000004 18.725 4 23.549999999999997 36.575 21.975 17.9 5 25.4 37.125 21.5 15.975 6 18.95 41.925000000000004 21.275 17.849999999999998 7 19.25 21.975 40.275 18.5 8 18.875 27.05 29.599999999999998 24.474999999999998 9 22.6 23.775 31.075000000000003 22.55 10-14 21.81 29.759999999999998 27.38 21.05 15-19 22.39 28.544999999999998 27.54 21.525 20-24 22.055 29.13 27.68 21.135 25-29 21.884999999999998 28.455000000000002 29.195 20.465 30-34 22.18 28.585 28.310000000000002 20.925 35-39 21.965 28.565 28.310000000000002 21.16 40-44 22.28 28.395 28.265 21.060000000000002 45-49 22.400000000000002 28.689999999999998 27.785 21.125 50-54 22.650000000000002 28.060000000000002 28.205000000000002 21.085 55-59 23.119999999999997 27.925 28.405 20.549999999999997 60-64 22.66 27.985 27.915 21.44 65-69 22.89 27.450000000000003 27.88 21.78 70-74 22.42 28.194999999999997 28.035 21.349999999999998 75-79 22.689999999999998 27.925 27.85 21.535 80-84 23.105 27.584999999999997 28.03 21.279999999999998 85-89 23.275000000000002 27.215 28.18 21.33 90-94 23.235 28.275 27.77 20.72 95-99 22.945 28.53 27.43 21.095 100-104 23.515 27.85 27.139999999999997 21.495 105-109 23.43 27.985 27.295 21.29 110-114 23.830000000000002 27.965 27.534999999999997 20.669999999999998 115-119 23.655 28.865000000000002 26.924999999999997 20.555 120-124 24.245 28.1 27.089999999999996 20.565 125-129 24.21 28.18 27.055 20.555 130-134 23.94 27.339999999999996 28.16 20.560000000000002 135-139 23.575 27.655 28.110000000000003 20.66 140-144 24.605 27.889999999999997 26.995 20.51 145-149 23.707370737073706 27.53775377537754 27.88278827882788 20.87208720872087 150-151 25.0 28.15 27.237499999999997 19.6125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 4 0.5 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 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 1.5 23 2.5 24 3.5 25 3.5 26 5.5 27 11.0 28 12.0 29 11.0 30 13.0 31 20.0 32 31.0 33 43.5 34 57.5 35 71.5 36 90.5 37 108.5 38 133.5 39 181.0 40 208.0 41 237.0 42 277.0 43 282.5 44 294.0 45 286.0 46 254.5 47 230.0 48 217.5 49 205.5 50 164.5 51 122.5 52 92.0 53 75.5 54 69.0 55 50.5 56 35.5 57 27.5 58 14.0 59 12.0 60 12.0 61 8.5 62 7.5 63 4.5 64 1.5 65 2.0 66 2.0 67 0.5 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 0.5 >>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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.275 #Duplication Level Percentage of deduplicated Percentage of total 1 86.35419756748739 72.775 2 10.88697715811332 18.35 3 2.0172055769801247 5.1 4 0.3263126668644319 1.0999999999999999 5 0.20765351527736575 0.8750000000000001 6 0.08899436369029962 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.11865915158706616 1.35 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 19 0.475 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 13 0.325 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 12 0.3 No Hit CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATC 10 0.25 No Hit GAGGAATCGAGAGAGAAAATTATGGAGCAGGGAAAGGAGGTGTTGAATGT 6 0.15 No Hit CATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAA 6 0.15 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 6 0.15 No Hit GTGAGAATGTTACTTTAACCATGCTCGTCTTCGCTCTTGCGATTCTATTG 5 0.125 No Hit AAGGTGTCTTTTGCAGATTCCTTCATTGACCCTGGTGATGAAATCATGGC 5 0.125 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit GTCCAAGTACTGCATGATGACCACTCGCATTGCCAGCAGTGGACTCCTCG 5 0.125 No Hit ATTCTGAAAATGTGTAGGGGTATTCATCAGGAGAGAAATAACCAAGGCGG 5 0.125 No Hit TATCCTTTGTAGCAGTGCTCAGTCCTGACTCAAGCTTCTTCCAAATTGAA 5 0.125 No Hit GAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCA 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 0.0125 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.037500000000000006 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.0875 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1125 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.2125 0.0 0.0 0.0 0.0 90-91 0.25 0.0 0.0 0.0 0.0 92-93 0.25 0.0 0.0 0.0 0.0 94-95 0.275 0.0 0.0 0.0 0.0 96-97 0.35 0.0 0.0 0.0 0.0 98-99 0.4125 0.0 0.0 0.0 0.0 100-101 0.475 0.0 0.0 0.0 0.0 102-103 0.5874999999999999 0.0 0.0 0.0 0.0 104-105 0.6625000000000001 0.0 0.0 0.0 0.0 106-107 0.8875 0.0 0.0 0.0 0.0 108-109 0.95 0.0 0.0 0.0 0.0 110-111 1.0499999999999998 0.0 0.0 0.0 0.0 112-113 1.15 0.0 0.0 0.0 0.0 114-115 1.2125 0.0 0.0 0.0 0.0 116-117 1.2999999999999998 0.0 0.0 0.0 0.0 118-119 1.4375 0.0 0.0 0.0 0.0 120-121 1.5625 0.0 0.0 0.0 0.0 122-123 1.7 0.0 0.0 0.0 0.0 124-125 1.7875 0.0 0.0 0.0 0.0 126-127 1.9500000000000002 0.0 0.0 0.0 0.0 128-129 2.0125 0.0 0.0 0.0 0.0 130-131 2.1375 0.0 0.0 0.0 0.0 132-133 2.2 0.0 0.0 0.0 0.0 134-135 2.4000000000000004 0.0 0.0 0.0 0.0 136-137 2.6125 0.0 0.0 0.0 0.0 138-139 2.725 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATTTCC 10 0.006830828 145.0 5 CAAAGGA 10 0.006830828 145.0 4 ATATATT 10 0.006830828 145.0 2 >>END_MODULE Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954850 spots for SRR12671414.sra Written 954850 spots for SRR12671414.sra Read 954864 spots for SRR12671414.sra Written 954864 spots for SRR12671414.sra SRR ids: ['SRR12671414.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7n1rmd4f SRR12671414.sra spots: 19097014 blocks: [[1, 954850], [954851, 1909700], [1909701, 2864550], [2864551, 3819400], [3819401, 4774250], [4774251, 5729100], [5729101, 6683950], [6683951, 7638800], [7638801, 8593650], [8593651, 9548500], [9548501, 10503350], [10503351, 11458200], [11458201, 12413050], [12413051, 13367900], [13367901, 14322750], [14322751, 15277600], [15277601, 16232450], [16232451, 17187300], [17187301, 18142150], [18142151, 19097014]] SRR12671414 file size 6468300 SRR12671414 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 SRR12671414 SRR12671414_1.fastq SRR12671414_2.fastq Input file: SRR12671414_1.fastq Paired file: SRR12671414_2.fastq trimmed: SRR12671414-trimmed-pair1.fastq, SRR12671414-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 23:12:00 2025 >> started Tue Feb 11 23:12:23 2025 >> done (23.224s) 19097014 read pairs processed; of these: 52 ( 0.00%) short read pairs filtered out after trimming by size control 966 ( 0.01%) empty read pairs filtered out after trimming by size control 19095996 (99.99%) read pairs available; of these: 818959 ( 4.29%) trimmed read pairs available after processing 18277037 (95.71%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 3 0.00% 20 5 0.00% 21 5 0.00% 22 5 0.00% 23 12 0.00% 24 6 0.00% 25 13 0.00% 26 14 0.00% 27 5 0.00% 28 20 0.00% 29 8 0.00% 30 12 0.00% 31 13 0.00% 32 17 0.00% 33 18 0.00% 34 21 0.00% 35 26 0.00% 36 15 0.00% 37 22 0.00% 38 34 0.00% 39 19 0.00% 40 27 0.00% 41 26 0.00% 42 34 0.00% 43 33 0.00% 44 32 0.00% 45 35 0.00% 46 53 0.00% 47 41 0.00% 48 38 0.00% 49 58 0.00% 50 51 0.00% 51 70 0.00% 52 87 0.00% 53 78 0.00% 54 78 0.00% 55 84 0.00% 56 87 0.00% 57 113 0.00% 58 115 0.00% 59 160 0.00% 60 172 0.00% 61 177 0.00% 62 205 0.00% 63 236 0.00% 64 261 0.00% 65 267 0.00% 66 309 0.00% 67 300 0.00% 68 397 0.00% 69 477 0.00% 70 481 0.00% 71 530 0.00% 72 643 0.00% 73 743 0.00% 74 777 0.00% 75 825 0.00% 76 874 0.00% 77 998 0.01% 78 1113 0.01% 79 1178 0.01% 80 1364 0.01% 81 1534 0.01% 82 1760 0.01% 83 1922 0.01% 84 2113 0.01% 85 2456 0.01% 86 2384 0.01% 87 2666 0.01% 88 2915 0.02% 89 2876 0.02% 90 3301 0.02% 91 3515 0.02% 92 3677 0.02% 93 4097 0.02% 94 4278 0.02% 95 4565 0.02% 96 4938 0.03% 97 5138 0.03% 98 5487 0.03% 99 5650 0.03% 100 6087 0.03% 101 6180 0.03% 102 6534 0.03% 103 6908 0.04% 104 7271 0.04% 105 7309 0.04% 106 7815 0.04% 107 8241 0.04% 108 8345 0.04% 109 8820 0.05% 110 9033 0.05% 111 9110 0.05% 112 9387 0.05% 113 9558 0.05% 114 9954 0.05% 115 10561 0.06% 116 10946 0.06% 117 11503 0.06% 118 11853 0.06% 119 12124 0.06% 120 12352 0.06% 121 12618 0.07% 122 12808 0.07% 123 13266 0.07% 124 13459 0.07% 125 14119 0.07% 126 14427 0.08% 127 14779 0.08% 128 15461 0.08% 129 15652 0.08% 130 16189 0.08% 131 16136 0.08% 132 16455 0.09% 133 16899 0.09% 134 17402 0.09% 135 17238 0.09% 136 17987 0.09% 137 18641 0.10% 138 18847 0.10% 139 20020 0.10% 140 19897 0.10% 141 20475 0.11% 142 21055 0.11% 143 21248 0.11% 144 21703 0.11% 145 22212 0.12% 146 22967 0.12% 147 23391 0.12% 148 24627 0.13% 149 24518 0.13% 150 25377 0.13% 151 18277037 95.71% 19095996 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=23 prefix-density=0.34 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=535.02 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=16.6 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=2.02 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=28 prefix-density=2.00 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=32.35 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=5.6 sequence=AAAGGATGGTAGAGTAGCATCCTTAGCGTTGCTGGTTTACTTTCCTAACAATCCTCAAAACCATTCTTCTTAGACTCTCTATACATTCCAAATAACC SRR12671414 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 23:13:02 Started mapping on | Feb 11 23:13:02 Finished on | Feb 11 23:14:55 Mapping speed, Million of reads per hour | 608.37 Number of input reads | 19095996 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 18074439 Uniquely mapped reads % | 94.65% Average mapped length | 298.57 Number of splices: Total | 18275819 Number of splices: Annotated (sjdb) | 17909725 Number of splices: GT/AG | 17921212 Number of splices: GC/AG | 288037 Number of splices: AT/AC | 11156 Number of splices: Non-canonical | 55414 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.91 Insertion rate per base | 0.02% Insertion average length | 2.22 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 453164 % of reads mapped to multiple loci | 2.37% Number of reads mapped to too many loci | 45772 % of reads mapped to too many loci | 0.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.67% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 568393 568393 568393 N_multimapping 453164 453164 453164 N_noFeature 611099 17685149 703411 N_ambiguous 414647 1119 117020 UnstrandedReadsAssigned:17048693 PositiveStrandReadsAssigned:388171 NegativeStrandReadsAssigned:17254008 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671414 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: SRR12671414-trimmed-pair1.fastq SRR12671414-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,095,996 reads, 16,995,131 reads pseudoaligned [quant] estimated average fragment length: 305.058 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,040 rounds 52401 SRR12671414.ke.tsv 34699 SRR12671414.se.tsv 87100 total ==> SRR12671414.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1713.94 899 23.8635 Potri.005G024800.1.v4.1 1035 730.942 440 27.3867 Potri.004G059700.1.v4.1 961 657.159 1 0.0692308 Potri.007G009000.2.v4.1 1416 1111.94 0 0 Potri.003G141000.2.v4.1 2943 2638.94 1372.56 23.6632 Potri.016G087400.1.v4.1 270 69.9423 984 640.067 Potri.015G069301.1.v4.1 564 280.199 0 0 Potri.010G195200.1.v4.1 1773 1468.94 210 6.50406 Potri.012G127500.1.v4.1 977 673.068 110 7.43539 ==> SRR12671414.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 62 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 212 Potri.001G212900.v4.1 41 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 18 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR12671414 completed mapping pipeline successfully