Starting /dee2/code/volunteer_pipeline.sh SRR12670148 current disk space = 3056979357696 free memory = 1269842592 SRR12670148 SRAfilesize 776514b9a73148ddf73051f4bc9d30ce SRR12670148.sra SRR12670148.sra file validated SRR12670148 is paired end SRR12670148 is conventional basespace SRR12670148 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670148_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 36.627 37.0 37.0 37.0 37.0 37.0 2 36.47125 37.0 37.0 37.0 37.0 37.0 3 36.6345 37.0 37.0 37.0 37.0 37.0 4 36.69 37.0 37.0 37.0 37.0 37.0 5 36.6715 37.0 37.0 37.0 37.0 37.0 6 36.6555 37.0 37.0 37.0 37.0 37.0 7 36.596 37.0 37.0 37.0 37.0 37.0 8 36.683 37.0 37.0 37.0 37.0 37.0 9 36.607 37.0 37.0 37.0 37.0 37.0 10-14 36.6185 37.0 37.0 37.0 37.0 37.0 15-19 36.62820000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.5745 37.0 37.0 37.0 37.0 37.0 25-29 36.529199999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.4824 37.0 37.0 37.0 37.0 37.0 35-39 36.5233 37.0 37.0 37.0 37.0 37.0 40-44 36.4882 37.0 37.0 37.0 37.0 37.0 45-49 36.468999999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.4276 37.0 37.0 37.0 37.0 37.0 55-59 36.4491 37.0 37.0 37.0 37.0 37.0 60-64 36.415299999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.3747 37.0 37.0 37.0 37.0 37.0 70-74 36.339800000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.3078 37.0 37.0 37.0 37.0 37.0 80-84 36.2732 37.0 37.0 37.0 37.0 37.0 85-89 36.2706 37.0 37.0 37.0 37.0 37.0 90-94 36.3037 37.0 37.0 37.0 37.0 37.0 95-99 36.227199999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.2752 37.0 37.0 37.0 37.0 37.0 105-109 36.2342 37.0 37.0 37.0 37.0 37.0 110-114 36.1668 37.0 37.0 37.0 37.0 37.0 115-119 36.218399999999995 37.0 37.0 37.0 37.0 37.0 120-124 36.0315 37.0 37.0 37.0 37.0 37.0 125-129 35.99679999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.93429999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.8208 37.0 37.0 37.0 37.0 37.0 140-144 35.668 37.0 37.0 37.0 37.0 37.0 145-149 35.5922 37.0 37.0 37.0 37.0 37.0 150-151 35.39275000000001 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 1.0 22 0.0 23 1.0 24 1.0 25 4.0 26 5.0 27 4.0 28 8.0 29 10.0 30 28.0 31 23.0 32 50.0 33 77.0 34 114.0 35 331.0 36 2953.0 37 389.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.825 11.799999999999999 6.0249999999999995 40.35 2 18.097622027534417 12.841051314142678 37.12140175219024 31.939924906132667 3 16.3 17.0 28.349999999999998 38.35 4 22.400000000000002 23.674999999999997 23.724999999999998 30.2 5 21.5 30.675 25.85 21.975 6 19.175 34.925 23.9 22.0 7 14.2 25.55 43.175000000000004 17.075000000000003 8 16.875 25.674999999999997 33.475 23.974999999999998 9 16.025 25.124999999999996 35.175 23.674999999999997 10-14 19.189999999999998 29.485 28.255000000000003 23.07 15-19 20.32 27.445000000000004 28.315 23.919999999999998 20-24 18.985 28.83 27.975 24.21 25-29 19.615 29.520000000000003 27.205000000000002 23.66 30-34 19.945 28.51 27.775 23.77 35-39 20.330000000000002 28.02 27.875 23.775 40-44 19.650000000000002 29.315 28.125 22.91 45-49 19.66 28.715000000000003 27.91 23.715 50-54 19.7 28.325 28.22 23.755000000000003 55-59 20.82 28.115000000000002 28.139999999999997 22.925 60-64 20.075000000000003 28.15 28.03 23.745 65-69 20.65 28.275 27.85 23.225 70-74 20.73 28.49 27.565 23.215 75-79 20.294999999999998 28.310000000000002 27.57 23.825 80-84 20.95 28.549999999999997 27.495000000000005 23.005 85-89 20.925 28.884999999999998 27.125 23.064999999999998 90-94 20.265 28.365000000000002 27.834999999999997 23.535 95-99 20.175 28.449999999999996 27.495000000000005 23.880000000000003 100-104 20.715 28.904999999999998 26.884999999999998 23.494999999999997 105-109 20.715 28.96 26.46 23.865 110-114 21.64 28.410000000000004 26.224999999999998 23.724999999999998 115-119 21.25 28.03 26.855 23.865 120-124 20.035 28.884999999999998 26.46 24.62 125-129 20.875 28.21 26.450000000000003 24.465 130-134 20.72 28.444999999999997 26.045 24.79 135-139 21.165 28.115000000000002 26.025 24.695 140-144 20.405 27.845 26.58 25.169999999999998 145-149 20.97 27.355 26.58 25.095 150-151 20.849999999999998 27.0125 26.4125 25.724999999999998 >>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 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 1.0 22 1.5 23 1.0 24 1.0 25 2.5 26 4.5 27 5.5 28 8.0 29 17.0 30 25.5 31 32.5 32 33.5 33 33.0 34 44.5 35 74.0 36 93.5 37 106.5 38 128.0 39 152.5 40 183.5 41 221.5 42 254.5 43 262.0 44 272.0 45 264.0 46 247.5 47 258.0 48 251.5 49 225.5 50 175.0 51 137.0 52 115.0 53 81.5 54 69.0 55 54.0 56 45.0 57 38.0 58 20.5 59 16.0 60 13.5 61 10.5 62 9.0 63 4.0 64 1.5 65 1.0 66 1.0 67 0.5 68 0.0 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 0.125 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.625 #Duplication Level Percentage of deduplicated Percentage of total 1 79.42766295707472 62.45 2 15.707472178060414 24.7 3 3.4976152623211445 8.25 4 1.0174880763116056 3.2 5 0.3179650238473768 1.25 6 0.03179650238473768 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 CACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGAC 6 0.15 No Hit CTGACCTTGAAGATCTCCTGCGACTTAATGATTCGTCTTTTTTCCTTTGA 5 0.125 No Hit CCATCATCAACCACATTGTTCACTGCATTGGCTTTTTTATGATCTACTAC 5 0.125 No Hit GTCTTCTTAAAATCCGCTGCCCCTCCATTGTACGTAGCCACGGCAATCCC 5 0.125 No Hit TTCGCAATTTAGGACTTTCTGAACCAGGCGCTTATATTCATTCACGTTTG 5 0.125 No Hit CTTCAATCAAGTTCTGATCCAGCAGAACCTTGTTGCTCCCACTAGAATCC 5 0.125 No Hit ATCGTCACCAGAATTTCTCCTCTTATTTGCCCCAATATCATAATCTGACT 5 0.125 No Hit GCACTTTGTAGGTGATTTTCCTGGAGCGGTCGTCAACGGATTCAACTACA 5 0.125 No Hit GCCTCATCAGCACAACAAATCACTGTGGCTGGTGCTTTCTCACACACATC 5 0.125 No Hit GCCCTTTTTAACCCCTTCCAGCCCTTGAAGGAAGCTGCTAAAAGATTGCC 5 0.125 No Hit CAACTGTGTATCTCCCAAGTCCCACCCAAAATATTTTCTCAGGGAGAAGA 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 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2625 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.5125 0.0 0.0 0.0 0.0 74-75 0.675 0.0 0.0 0.0 0.0 76-77 1.0 0.0 0.0 0.0 0.0 78-79 1.1375000000000002 0.0 0.0 0.0 0.0 80-81 1.325 0.0 0.0 0.0 0.0 82-83 1.65 0.0 0.0 0.0 0.0 84-85 2.0125 0.0 0.0 0.0 0.0 86-87 2.4000000000000004 0.0 0.0 0.0 0.0 88-89 2.75 0.0 0.0 0.0 0.0 90-91 3.1875 0.0 0.0 0.0 0.0 92-93 3.7375 0.0 0.0 0.0 0.0 94-95 4.449999999999999 0.0 0.0 0.0 0.0 96-97 4.9875 0.0 0.0 0.0 0.0 98-99 5.7 0.0 0.0 0.0 0.0 100-101 6.25 0.0 0.0 0.0 0.0 102-103 7.0625 0.0 0.0 0.0 0.0 104-105 8.05 0.0 0.0 0.0 0.0 106-107 8.9375 0.0 0.0 0.0 0.0 108-109 10.2 0.0 0.0 0.0 0.0 110-111 11.05 0.0 0.0 0.0 0.0 112-113 11.8375 0.0 0.0 0.0 0.0 114-115 12.5625 0.0 0.0 0.0 0.0 116-117 13.5 0.0 0.0 0.0 0.0 118-119 14.4375 0.0 0.0 0.0 0.0 120-121 15.2875 0.0 0.0 0.0 0.0 122-123 16.125 0.0 0.0 0.0 0.0 124-125 16.875 0.0 0.0 0.0 0.0 126-127 18.0375 0.0 0.0 0.0 0.0 128-129 19.1375 0.0 0.0 0.0 0.0 130-131 20.0875 0.0 0.0 0.0 0.0 132-133 20.6625 0.0 0.0 0.0 0.0 134-135 21.5125 0.0 0.0 0.0 0.0 136-137 22.3125 0.0 0.0 0.0 0.0 138-139 23.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCTATT 10 0.006830828 145.0 145 TACCAAT 10 0.006830828 145.0 7 CCTAGGA 10 0.006830828 145.0 1 AAAAAAA 35 0.0035366106 20.714287 135-139 >>END_MODULE SRR12670148 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670148_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 36.281 37.0 37.0 37.0 37.0 37.0 2 36.169 37.0 37.0 37.0 37.0 37.0 3 36.266 37.0 37.0 37.0 37.0 37.0 4 36.195 37.0 37.0 37.0 37.0 37.0 5 36.2665 37.0 37.0 37.0 37.0 37.0 6 36.366 37.0 37.0 37.0 37.0 37.0 7 36.4335 37.0 37.0 37.0 37.0 37.0 8 36.2975 37.0 37.0 37.0 37.0 37.0 9 36.322 37.0 37.0 37.0 37.0 37.0 10-14 36.3986 37.0 37.0 37.0 37.0 37.0 15-19 36.42229999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.287099999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.291799999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.285500000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.2226 37.0 37.0 37.0 37.0 37.0 40-44 36.2044 37.0 37.0 37.0 37.0 37.0 45-49 36.1783 37.0 37.0 37.0 37.0 37.0 50-54 36.199799999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.1103 37.0 37.0 37.0 37.0 37.0 60-64 36.1248 37.0 37.0 37.0 37.0 37.0 65-69 36.1012 37.0 37.0 37.0 37.0 37.0 70-74 36.1125 37.0 37.0 37.0 37.0 37.0 75-79 36.0452 37.0 37.0 37.0 37.0 37.0 80-84 35.9863 37.0 37.0 37.0 37.0 37.0 85-89 35.984500000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.984700000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.923899999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.870999999999995 37.0 37.0 37.0 37.0 37.0 105-109 35.8249 37.0 37.0 37.0 37.0 37.0 110-114 35.690200000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.852000000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.5968 37.0 37.0 37.0 37.0 37.0 125-129 35.4807 37.0 37.0 37.0 37.0 37.0 130-134 35.3334 37.0 37.0 37.0 34.6 37.0 135-139 35.185199999999995 37.0 37.0 37.0 29.8 37.0 140-144 34.993 37.0 37.0 37.0 25.0 37.0 145-149 34.6705 37.0 37.0 37.0 25.0 37.0 150-151 34.527249999999995 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 5.0 15 0.0 16 0.0 17 1.0 18 2.0 19 0.0 20 1.0 21 2.0 22 1.0 23 5.0 24 4.0 25 4.0 26 7.0 27 10.0 28 12.0 29 16.0 30 24.0 31 43.0 32 72.0 33 103.0 34 213.0 35 614.0 36 2601.0 37 259.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.2 24.224999999999998 10.775 25.8 2 26.900000000000002 26.974999999999998 32.025 14.099999999999998 3 19.900000000000002 28.275 32.6 19.225 4 23.35 34.125 23.5 19.025 5 24.85 37.724999999999994 22.15 15.275 6 20.225 40.2 23.400000000000002 16.175 7 20.175 23.075000000000003 37.824999999999996 18.925 8 19.925 27.425 28.225 24.425 9 21.675 24.099999999999998 30.55 23.674999999999997 10-14 22.509999999999998 29.575000000000003 27.284999999999997 20.630000000000003 15-19 22.975 27.74 28.21 21.075 20-24 22.35 28.58 28.67 20.4 25-29 22.175 28.355000000000004 28.810000000000002 20.66 30-34 22.62 28.565 28.349999999999998 20.465 35-39 22.205 28.53 28.299999999999997 20.965 40-44 23.494999999999997 29.025000000000002 27.35 20.13 45-49 22.3 28.165000000000003 29.005 20.53 50-54 22.645 27.925 28.4 21.029999999999998 55-59 22.255 28.465 28.349999999999998 20.93 60-64 22.185 28.105000000000004 28.775000000000002 20.935000000000002 65-69 22.689999999999998 27.560000000000002 28.994999999999997 20.755000000000003 70-74 22.945 28.22 27.450000000000003 21.385 75-79 23.135 27.689999999999998 28.1 21.075 80-84 23.28 27.965 27.92 20.835 85-89 24.154999999999998 27.694999999999997 27.500000000000004 20.65 90-94 23.849999999999998 28.53 27.495000000000005 20.125 95-99 24.505 28.595 26.965 19.935 100-104 24.66 27.91 27.555000000000003 19.875 105-109 25.490000000000002 28.470000000000002 26.36 19.68 110-114 25.3 28.99 26.72 18.990000000000002 115-119 26.215 29.07 25.945 18.77 120-124 26.665 28.065 25.895000000000003 19.375 125-129 27.655 27.955000000000002 25.619999999999997 18.77 130-134 28.52 27.62 25.55 18.310000000000002 135-139 29.475 26.82 25.335 18.37 140-144 30.130000000000003 26.529999999999998 24.9 18.44 145-149 31.81 26.27 24.715 17.205000000000002 150-151 33.7875 27.1 22.662499999999998 16.45 >>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 0.5 8 0.5 9 0.0 10 0.5 11 1.0 12 0.5 13 0.0 14 0.5 15 0.5 16 0.5 17 1.0 18 1.0 19 2.0 20 2.0 21 1.0 22 1.0 23 2.0 24 3.5 25 3.5 26 4.0 27 4.0 28 13.0 29 24.0 30 24.0 31 24.0 32 29.0 33 44.0 34 64.0 35 86.0 36 86.0 37 108.0 38 150.0 39 188.5 40 221.0 41 217.5 42 227.0 43 260.0 44 282.5 45 275.5 46 269.0 47 248.5 48 210.0 49 188.0 50 162.0 51 130.0 52 99.5 53 84.0 54 72.5 55 48.5 56 32.0 57 24.0 58 15.0 59 10.0 60 15.0 61 12.0 62 10.0 63 9.0 64 2.0 65 1.0 66 0.5 67 0.5 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 0.5 94 0.5 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 78.725 #Duplication Level Percentage of deduplicated Percentage of total 1 79.96189266433788 62.949999999999996 2 15.147665925690696 23.849999999999998 3 3.429660209590346 8.1 4 1.079707843759924 3.4000000000000004 5 0.31756113051762463 1.25 6 0.0 0.0 7 0.0 0.0 8 0.031756113051762465 0.2 9 0.0 0.0 >10 0.031756113051762465 0.25 >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 10 0.25 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 8 0.2 No Hit AGTGTAAAAGCATCTAGAAGTAGGTTCTTGTAATGTCTCCACCACTTTCT 5 0.125 No Hit GTTCATTTTAAAAGCATTAGAATCTGGTTCAAAAACAATTTCTTCTTCAG 5 0.125 No Hit CGTGTCTAATTTTTTTTCGCTTTACATACAGGATAATAAACCTGTCATGT 5 0.125 No Hit TATGGCTCGCCTTTGCAGAAAAGTCGTGGAAACACCAATTCAATGCTCTA 5 0.125 No Hit AAACAACATAATATATGGCTCCTAATCTTTCCCATCTTTTATCAGCAATC 5 0.125 No Hit GTGTTGGTGCCATTTTATTTCAACTTGTGACAGGAAAAACCCCATTCACT 5 0.125 No Hit GGGAAAGAAACGAAGATGGATGTTCTAGTTATGGAAAACCTTCTATTTAG 5 0.125 No Hit AAGAAACTAGAGAAGGTGAACTAACAAGGGATCTGCTAAAAGAGAGGTGG 5 0.125 No Hit TGGATGGCAGAGCAATTCGGGTCTCAGTTGCAGAAGCTAAGCCAAGGCGT 5 0.125 No Hit GTGGTGATGAAAATGTTAATGGTGAAGTTAAAAATGTTAGCACAAGTGTT 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 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.23750000000000002 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.4875 0.0 0.0 0.0 0.0 74-75 0.6625 0.0 0.0 0.0 0.0 76-77 1.0 0.0 0.0 0.0 0.0 78-79 1.1375000000000002 0.0 0.0 0.0 0.0 80-81 1.325 0.0 0.0 0.0 0.0 82-83 1.6749999999999998 0.0 0.0 0.0 0.0 84-85 2.05 0.0 0.0 0.0 0.0 86-87 2.425 0.0 0.0 0.0 0.0 88-89 2.7750000000000004 0.0 0.0 0.0 0.0 90-91 3.2125000000000004 0.0 0.0 0.0 0.0 92-93 3.775 0.0 0.0 0.0 0.0 94-95 4.5 0.0 0.0 0.0 0.0 96-97 5.0375 0.0 0.0 0.0 0.0 98-99 5.75 0.0 0.0 0.0 0.0 100-101 6.3 0.0 0.0 0.0 0.0 102-103 7.112500000000001 0.0 0.0 0.0 0.0 104-105 8.15 0.0 0.0 0.0 0.0 106-107 9.0625 0.0 0.0 0.0 0.0 108-109 10.325 0.0 0.0 0.0 0.0 110-111 11.175 0.0 0.0 0.0 0.0 112-113 11.9625 0.0 0.0 0.0 0.0 114-115 12.7 0.0 0.0 0.0 0.0 116-117 13.675 0.0 0.0 0.0 0.0 118-119 14.6125 0.0 0.0 0.0 0.0 120-121 15.4625 0.0 0.0 0.0 0.0 122-123 16.2875 0.0 0.0 0.0 0.0 124-125 17.025 0.0 0.0 0.0 0.0 126-127 18.1875 0.0 0.0 0.0 0.0 128-129 19.2875 0.0 0.0 0.0 0.0 130-131 20.237499999999997 0.0 0.0 0.0 0.0 132-133 20.825 0.0 0.0 0.0 0.0 134-135 21.6875 0.0 0.0 0.0 0.0 136-137 22.4875 0.0 0.0 0.0 0.0 138-139 23.1625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTAAGT 10 0.006830828 145.0 1 ACTTTGC 10 0.006830828 145.0 145 >>END_MODULE Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555759 spots for SRR12670148.sra Written 555759 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra Read 555754 spots for SRR12670148.sra Written 555754 spots for SRR12670148.sra SRR ids: ['SRR12670148.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t9xr831e SRR12670148.sra spots: 11115085 blocks: [[1, 555754], [555755, 1111508], [1111509, 1667262], [1667263, 2223016], [2223017, 2778770], [2778771, 3334524], [3334525, 3890278], [3890279, 4446032], [4446033, 5001786], [5001787, 5557540], [5557541, 6113294], [6113295, 6669048], [6669049, 7224802], [7224803, 7780556], [7780557, 8336310], [8336311, 8892064], [8892065, 9447818], [9447819, 10003572], [10003573, 10559326], [10559327, 11115085]] SRR12670148 file size 3755691 SRR12670148 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 SRR12670148 SRR12670148_1.fastq SRR12670148_2.fastq Input file: SRR12670148_1.fastq Paired file: SRR12670148_2.fastq trimmed: SRR12670148-trimmed-pair1.fastq, SRR12670148-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 02:24:08 2025 >> started Tue Feb 11 02:30:06 2025 >> done (357.614s) 11115085 read pairs processed; of these: 74 ( 0.00%) short read pairs filtered out after trimming by size control 6193 ( 0.06%) empty read pairs filtered out after trimming by size control 11108818 (99.94%) read pairs available; of these: 3098610 (27.89%) trimmed read pairs available after processing 8010208 (72.11%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 6 0.00% 20 14 0.00% 21 9 0.00% 22 19 0.00% 23 33 0.00% 24 22 0.00% 25 40 0.00% 26 51 0.00% 27 61 0.00% 28 52 0.00% 29 52 0.00% 30 72 0.00% 31 101 0.00% 32 75 0.00% 33 89 0.00% 34 107 0.00% 35 72 0.00% 36 111 0.00% 37 134 0.00% 38 138 0.00% 39 148 0.00% 40 209 0.00% 41 173 0.00% 42 249 0.00% 43 257 0.00% 44 253 0.00% 45 255 0.00% 46 281 0.00% 47 343 0.00% 48 480 0.00% 49 515 0.00% 50 582 0.01% 51 723 0.01% 52 719 0.01% 53 800 0.01% 54 787 0.01% 55 918 0.01% 56 1059 0.01% 57 1285 0.01% 58 1483 0.01% 59 1718 0.02% 60 1958 0.02% 61 2275 0.02% 62 2482 0.02% 63 2827 0.03% 64 3115 0.03% 65 3305 0.03% 66 3555 0.03% 67 3934 0.04% 68 4459 0.04% 69 5198 0.05% 70 5975 0.05% 71 6601 0.06% 72 7685 0.07% 73 8513 0.08% 74 9289 0.08% 75 9889 0.09% 76 10629 0.10% 77 11393 0.10% 78 12214 0.11% 79 13629 0.12% 80 14543 0.13% 81 16771 0.15% 82 18106 0.16% 83 19634 0.18% 84 21446 0.19% 85 22478 0.20% 86 23610 0.21% 87 24263 0.22% 88 25574 0.23% 89 25792 0.23% 90 28143 0.25% 91 29943 0.27% 92 30597 0.28% 93 33121 0.30% 94 34569 0.31% 95 36079 0.32% 96 36281 0.33% 97 37825 0.34% 98 37629 0.34% 99 38039 0.34% 100 39846 0.36% 101 39989 0.36% 102 41771 0.38% 103 42693 0.38% 104 44013 0.40% 105 44544 0.40% 106 44988 0.40% 107 44922 0.40% 108 45204 0.41% 109 44687 0.40% 110 44935 0.40% 111 45404 0.41% 112 46220 0.42% 113 47064 0.42% 114 48078 0.43% 115 48320 0.43% 116 48728 0.44% 117 49159 0.44% 118 49173 0.44% 119 47931 0.43% 120 49341 0.44% 121 48644 0.44% 122 48185 0.43% 123 49135 0.44% 124 49655 0.45% 125 49223 0.44% 126 50179 0.45% 127 49527 0.45% 128 49320 0.44% 129 48680 0.44% 130 48891 0.44% 131 47564 0.43% 132 47761 0.43% 133 47994 0.43% 134 47801 0.43% 135 47892 0.43% 136 48184 0.43% 137 48557 0.44% 138 48296 0.43% 139 48911 0.44% 140 47510 0.43% 141 47755 0.43% 142 47360 0.43% 143 47391 0.43% 144 47773 0.43% 145 46857 0.42% 146 47182 0.42% 147 46894 0.42% 148 47145 0.42% 149 46566 0.42% 150 46898 0.42% 151 8010208 72.11% 11108818 reads passed initial QC criterion=sequence-density sequence-density=0.74 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=26 prefix-density=0.74 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTAGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=43.27 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=7.1 sequence=ACCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=1.45 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=35 prefix-density=1.45 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.07 sequence-density-rank=30 fanout-score=37.04 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=11.4 sequence=AAGGCCAAGATCCAGGACAAGGA SRR12670148 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 03:48:14 Started mapping on | Feb 11 03:48:36 Finished on | Feb 11 06:18:17 Mapping speed, Million of reads per hour | 4.45 Number of input reads | 11108818 Average input read length | 282 UNIQUE READS: Uniquely mapped reads number | 10379430 Uniquely mapped reads % | 93.43% Average mapped length | 281.08 Number of splices: Total | 9855234 Number of splices: Annotated (sjdb) | 9574212 Number of splices: GT/AG | 9651732 Number of splices: GC/AG | 145893 Number of splices: AT/AC | 7357 Number of splices: Non-canonical | 50252 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 289284 % of reads mapped to multiple loci | 2.60% Number of reads mapped to too many loci | 23915 % of reads mapped to too many loci | 0.22% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.56% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 440104 440104 440104 N_multimapping 289284 289284 289284 N_noFeature 479427 10199402 555840 N_ambiguous 178954 703 74986 UnstrandedReadsAssigned:9721049 PositiveStrandReadsAssigned:179325 NegativeStrandReadsAssigned:9748604 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=132 echo kmer=127 SRR12670148 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: SRR12670148-trimmed-pair1.fastq SRR12670148-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,108,818 reads, 9,720,960 reads pseudoaligned [quant] estimated average fragment length: 208.408 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,031 rounds 52401 SRR12670148.ke.tsv 34699 SRR12670148.se.tsv 87100 total ==> SRR12670148.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1810.59 601 32.4254 Potri.005G024800.1.v4.1 1035 827.592 213 25.1417 Potri.004G059700.1.v4.1 961 753.619 1 0.129622 Potri.007G009000.2.v4.1 1416 1208.59 0 0 Potri.003G141000.2.v4.1 2943 2735.59 697.892 24.9211 Potri.016G087400.1.v4.1 270 113.593 631 542.637 Potri.015G069301.1.v4.1 564 366.034 0 0 Potri.010G195200.1.v4.1 1773 1565.59 164 10.2328 Potri.012G127500.1.v4.1 977 769.606 22 2.79245 ==> SRR12670148.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 94 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 154 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 17 SRR12670148 completed mapping pipeline successfully