Starting /dee2/code/volunteer_pipeline.sh SRR12670180 current disk space = 3055561351168 free memory = 1262292964 SRR12670180 SRAfilesize 70aaeb0a6832d0fd70f71dd23dc2d3a3 SRR12670180.sra SRR12670180.sra file validated SRR12670180 is paired end SRR12670180 is conventional basespace SRR12670180 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670180_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 36.61 37.0 37.0 37.0 37.0 37.0 2 36.489 37.0 37.0 37.0 37.0 37.0 3 36.697 37.0 37.0 37.0 37.0 37.0 4 36.691 37.0 37.0 37.0 37.0 37.0 5 36.659 37.0 37.0 37.0 37.0 37.0 6 36.6675 37.0 37.0 37.0 37.0 37.0 7 36.597 37.0 37.0 37.0 37.0 37.0 8 36.634 37.0 37.0 37.0 37.0 37.0 9 36.6505 37.0 37.0 37.0 37.0 37.0 10-14 36.6557 37.0 37.0 37.0 37.0 37.0 15-19 36.654 37.0 37.0 37.0 37.0 37.0 20-24 36.618700000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.560700000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5772 37.0 37.0 37.0 37.0 37.0 35-39 36.5327 37.0 37.0 37.0 37.0 37.0 40-44 36.5178 37.0 37.0 37.0 37.0 37.0 45-49 36.514599999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.437599999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.4313 37.0 37.0 37.0 37.0 37.0 60-64 36.4352 37.0 37.0 37.0 37.0 37.0 65-69 36.3427 37.0 37.0 37.0 37.0 37.0 70-74 36.3514 37.0 37.0 37.0 37.0 37.0 75-79 36.3155 37.0 37.0 37.0 37.0 37.0 80-84 36.3486 37.0 37.0 37.0 37.0 37.0 85-89 36.2926 37.0 37.0 37.0 37.0 37.0 90-94 36.29619999999999 37.0 37.0 37.0 37.0 37.0 95-99 36.257 37.0 37.0 37.0 37.0 37.0 100-104 36.28830000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.2656 37.0 37.0 37.0 37.0 37.0 110-114 36.2291 37.0 37.0 37.0 37.0 37.0 115-119 36.233399999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.1335 37.0 37.0 37.0 37.0 37.0 125-129 36.065999999999995 37.0 37.0 37.0 37.0 37.0 130-134 36.0616 37.0 37.0 37.0 37.0 37.0 135-139 35.998900000000006 37.0 37.0 37.0 37.0 37.0 140-144 35.8129 37.0 37.0 37.0 37.0 37.0 145-149 35.8332 37.0 37.0 37.0 37.0 37.0 150-151 35.61425 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 0.0 25 5.0 26 5.0 27 10.0 28 14.0 29 10.0 30 15.0 31 29.0 32 42.0 33 49.0 34 92.0 35 308.0 36 3020.0 37 400.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.975 10.625 6.225 42.175000000000004 2 18.145363408521302 13.05764411027569 38.471177944862156 30.32581453634085 3 18.25 16.125 27.750000000000004 37.875 4 23.925 24.7 23.125 28.249999999999996 5 22.425 31.6 24.775 21.2 6 20.625 34.225 25.900000000000002 19.25 7 15.950000000000001 25.874999999999996 40.300000000000004 17.875 8 17.175 26.5 32.324999999999996 24.0 9 18.75 22.775000000000002 34.375 24.099999999999998 10-14 19.794999999999998 28.875 27.544999999999998 23.785 15-19 20.175 28.015 27.815 23.995 20-24 20.27 28.060000000000002 27.665 24.005000000000003 25-29 20.385 28.23 27.98 23.405 30-34 20.02 28.09 28.03 23.86 35-39 20.1 27.72 28.51 23.669999999999998 40-44 20.72 28.360000000000003 27.38 23.54 45-49 20.505000000000003 27.700000000000003 28.315 23.48 50-54 20.22 28.29 28.134999999999998 23.355 55-59 20.5 28.605000000000004 27.450000000000003 23.445 60-64 20.315 28.444999999999997 27.794999999999998 23.445 65-69 20.044999999999998 28.34 28.305000000000003 23.31 70-74 20.385 27.97 27.735 23.91 75-79 21.065 28.395 27.169999999999998 23.369999999999997 80-84 21.0 27.71 27.66 23.630000000000003 85-89 20.76 28.444999999999997 27.47 23.325000000000003 90-94 20.915 28.04 27.525 23.52 95-99 21.23 28.28 27.54 22.95 100-104 20.815 29.2 26.05 23.935000000000002 105-109 21.584999999999997 28.18 26.779999999999998 23.455000000000002 110-114 21.48 28.98 26.634999999999998 22.905 115-119 21.905 28.04 26.119999999999997 23.935000000000002 120-124 22.009999999999998 28.189999999999998 25.89 23.91 125-129 21.7 28.76 25.1 24.44 130-134 21.52 28.975 25.395 24.11 135-139 21.34 28.225 25.745 24.69 140-144 21.099999999999998 28.08 25.605 25.215 145-149 22.095000000000002 27.58 26.075 24.25 150-151 22.900000000000002 27.224999999999998 24.712500000000002 25.162499999999998 >>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 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.0 22 1.0 23 2.0 24 2.5 25 3.5 26 3.0 27 3.0 28 8.0 29 10.5 30 12.5 31 21.0 32 23.0 33 30.5 34 44.5 35 59.0 36 91.0 37 117.0 38 139.0 39 157.5 40 181.0 41 209.5 42 226.5 43 242.5 44 264.0 45 270.5 46 265.0 47 253.0 48 242.5 49 231.0 50 197.5 51 154.5 52 112.0 53 96.5 54 83.0 55 54.5 56 45.5 57 42.5 58 29.5 59 24.0 60 17.0 61 8.5 62 8.0 63 4.5 64 0.5 65 1.5 66 2.5 67 2.0 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 0.25 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 80.675 #Duplication Level Percentage of deduplicated Percentage of total 1 81.90269600247908 66.07499999999999 2 13.72792066935234 22.15 3 3.2537960954446854 7.875 4 0.7747133560582584 2.5 5 0.30988534242330334 1.25 6 0.030988534242330338 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 CTGGTTTCGATCCCAGCATAGACTCGAACTTCTCCAGTGCTTCCTCATAT 6 0.15 No Hit GCTCCACCTGGTTTTACCTTTAGCAGCGAAAGCTAAAGCCCGATCAGCAA 5 0.125 No Hit CCTGATAATCTGCGAGGCCGGGGGTGTTCTGGTATTGGGTGTGCTTCCAC 5 0.125 No Hit GCCGCTAATACGATCTCTATCTCGGTCTTTCTCACGGTCCCGGTCCCGGT 5 0.125 No Hit CCAGCTAGAAAGAGGAGATCAGAAGGGCTACCGCCTTCCGAGGGTAAAGC 5 0.125 No Hit CAAGCTAAGTAGTACAGTTCTCAATTACGGTACACTCACAGAGCCCCATT 5 0.125 No Hit GTATCTCGAATCTCAAACCCACTTGGATGAGATCTTCTCAAGGAAAGATC 5 0.125 No Hit TAGCAAATGCAGAGTTTTGGCCTTTGAGGTGCGAAGTGAGGGACTTATAG 5 0.125 No Hit GTCCAACTCACGCAAATTCGTAGCAGATAAGTTTGAAGCACTGTAAGCAA 5 0.125 No Hit CTCGAAATTCAGGATCAATGTATCCGGGCGTGCCTGCAGGTACAGTTATG 5 0.125 No Hit GCCTCACGGTACCTTTGCCTGATAAGCTTTGCGGGTTCACCAGCGTTCCC 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 0.075 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 0.0875 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.2875 0.0 0.0 0.0 0.0 68-69 0.375 0.0 0.0 0.0 0.0 70-71 0.425 0.0 0.0 0.0 0.0 72-73 0.675 0.0 0.0 0.0 0.0 74-75 0.85 0.0 0.0 0.0 0.0 76-77 0.9875 0.0 0.0 0.0 0.0 78-79 1.225 0.0 0.0 0.0 0.0 80-81 1.45 0.0 0.0 0.0 0.0 82-83 1.725 0.0 0.0 0.0 0.0 84-85 2.05 0.0 0.0 0.0 0.0 86-87 2.5250000000000004 0.0 0.0 0.0 0.0 88-89 2.9000000000000004 0.0 0.0 0.0 0.0 90-91 3.525 0.0 0.0 0.0 0.0 92-93 4.0375 0.0 0.0 0.0 0.0 94-95 4.4875 0.0 0.0 0.0 0.0 96-97 5.3625 0.0 0.0 0.0 0.0 98-99 5.949999999999999 0.0 0.0 0.0 0.0 100-101 6.612500000000001 0.0 0.0 0.0 0.0 102-103 7.15 0.0 0.0 0.0 0.0 104-105 8.1125 0.0 0.0 0.0 0.0 106-107 8.65 0.0 0.0 0.0 0.0 108-109 9.4 0.0 0.0 0.0 0.0 110-111 10.3625 0.0 0.0 0.0 0.0 112-113 11.575 0.0 0.0 0.0 0.0 114-115 12.712499999999999 0.0 0.0 0.0 0.0 116-117 13.8625 0.0 0.0 0.0 0.0 118-119 14.75 0.0 0.0 0.0 0.0 120-121 15.7 0.0 0.0 0.0 0.0 122-123 16.675 0.0 0.0 0.0 0.0 124-125 17.950000000000003 0.0 0.0 0.0 0.0 126-127 19.1375 0.0 0.0 0.0 0.0 128-129 20.025 0.0 0.0 0.0 0.0 130-131 20.9625 0.0 0.0 0.0 0.0 132-133 22.1125 0.0 0.0 0.0 0.0 134-135 23.0 0.0 0.0 0.0 0.0 136-137 23.987499999999997 0.0 0.0 0.0 0.0 138-139 25.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGATTT 10 0.006830828 145.0 3 GTCGATT 10 0.006830828 145.0 2 GATTTGG 10 0.006830828 145.0 5 ATTTGGC 10 0.006830828 145.0 6 TTTGGCT 10 0.006830828 145.0 7 TGTCGAT 10 0.006830828 145.0 1 CGATTTG 10 0.006830828 145.0 4 >>END_MODULE SRR12670180 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670180_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 36.352 37.0 37.0 37.0 37.0 37.0 2 36.261 37.0 37.0 37.0 37.0 37.0 3 36.2175 37.0 37.0 37.0 37.0 37.0 4 36.365 37.0 37.0 37.0 37.0 37.0 5 36.4525 37.0 37.0 37.0 37.0 37.0 6 36.2955 37.0 37.0 37.0 37.0 37.0 7 36.4005 37.0 37.0 37.0 37.0 37.0 8 36.441 37.0 37.0 37.0 37.0 37.0 9 36.383 37.0 37.0 37.0 37.0 37.0 10-14 36.419399999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.4085 37.0 37.0 37.0 37.0 37.0 20-24 36.345299999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.3209 37.0 37.0 37.0 37.0 37.0 30-34 36.303700000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.2547 37.0 37.0 37.0 37.0 37.0 40-44 36.2176 37.0 37.0 37.0 37.0 37.0 45-49 36.199400000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.2332 37.0 37.0 37.0 37.0 37.0 55-59 36.1887 37.0 37.0 37.0 37.0 37.0 60-64 36.1082 37.0 37.0 37.0 37.0 37.0 65-69 36.144999999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.119699999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.1491 37.0 37.0 37.0 37.0 37.0 80-84 36.094300000000004 37.0 37.0 37.0 37.0 37.0 85-89 36.0293 37.0 37.0 37.0 37.0 37.0 90-94 36.0126 37.0 37.0 37.0 37.0 37.0 95-99 35.9221 37.0 37.0 37.0 37.0 37.0 100-104 35.9019 37.0 37.0 37.0 37.0 37.0 105-109 35.8921 37.0 37.0 37.0 37.0 37.0 110-114 35.7755 37.0 37.0 37.0 37.0 37.0 115-119 35.8351 37.0 37.0 37.0 37.0 37.0 120-124 35.7442 37.0 37.0 37.0 37.0 37.0 125-129 35.668 37.0 37.0 37.0 37.0 37.0 130-134 35.3774 37.0 37.0 37.0 34.6 37.0 135-139 35.3504 37.0 37.0 37.0 32.2 37.0 140-144 35.117399999999996 37.0 37.0 37.0 27.4 37.0 145-149 34.942099999999996 37.0 37.0 37.0 25.0 37.0 150-151 34.65175 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 1.0 15 0.0 16 2.0 17 0.0 18 3.0 19 1.0 20 3.0 21 3.0 22 2.0 23 4.0 24 6.0 25 4.0 26 8.0 27 8.0 28 14.0 29 13.0 30 21.0 31 28.0 32 60.0 33 94.0 34 187.0 35 598.0 36 2654.0 37 285.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.2 21.075 11.025 28.7 2 26.924999999999997 25.825 31.874999999999996 15.375 3 19.675 28.425 31.775 20.125 4 24.474999999999998 33.4 24.3 17.825 5 23.875 38.074999999999996 21.224999999999998 16.825000000000003 6 19.45 40.150000000000006 22.225 18.175 7 20.724999999999998 21.25 38.5 19.525000000000002 8 20.7 24.9 28.525 25.874999999999996 9 20.25 24.875 31.3 23.575 10-14 22.8 29.360000000000003 26.57 21.27 15-19 23.095 28.444999999999997 27.62 20.84 20-24 22.755 28.305000000000003 28.415000000000003 20.525 25-29 23.225 28.349999999999998 27.575 20.849999999999998 30-34 23.150000000000002 28.57 27.205000000000002 21.075 35-39 22.345000000000002 27.755000000000003 28.205000000000002 21.695 40-44 23.48 28.13 28.27 20.119999999999997 45-49 23.425 27.395000000000003 27.725 21.455 50-54 23.01 27.794999999999998 28.535 20.66 55-59 23.369999999999997 27.16 28.13 21.34 60-64 22.63 27.935 28.52 20.915 65-69 23.155 27.445000000000004 28.685 20.715 70-74 23.685000000000002 28.134999999999998 27.77 20.41 75-79 23.875 27.975 27.845 20.305 80-84 23.77 28.225 27.215 20.79 85-89 23.98 28.065 27.395000000000003 20.560000000000002 90-94 24.435000000000002 27.67 26.985 20.91 95-99 24.625 28.144999999999996 27.229999999999997 20.0 100-104 24.6 27.805000000000003 26.765 20.830000000000002 105-109 25.4 27.900000000000002 27.02 19.68 110-114 25.525 28.110000000000003 26.915 19.45 115-119 26.590000000000003 27.975 25.805 19.63 120-124 27.1 28.835 24.93 19.134999999999998 125-129 27.694999999999997 27.400000000000002 25.52 19.384999999999998 130-134 28.62 27.725 25.14 18.515 135-139 29.849999999999998 28.165000000000003 24.58 17.405 140-144 30.54 26.775 24.925 17.76 145-149 32.019999999999996 26.87 23.705000000000002 17.405 150-151 32.0625 27.250000000000004 23.7875 16.900000000000002 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.5 11 1.0 12 1.0 13 0.5 14 0.0 15 0.0 16 1.0 17 1.5 18 1.0 19 1.0 20 1.0 21 1.0 22 2.5 23 2.5 24 2.0 25 2.5 26 4.0 27 6.0 28 5.5 29 7.0 30 18.5 31 27.5 32 29.5 33 35.5 34 52.5 35 67.0 36 87.5 37 112.0 38 125.5 39 178.0 40 202.5 41 208.0 42 245.5 43 255.5 44 261.5 45 260.0 46 249.5 47 250.0 48 232.0 49 198.5 50 183.0 51 159.5 52 127.5 53 98.5 54 72.0 55 55.5 56 40.5 57 33.5 58 28.0 59 16.5 60 11.0 61 10.5 62 4.5 63 3.5 64 3.0 65 0.5 66 1.5 67 1.0 68 0.0 69 0.5 70 0.5 71 0.0 72 0.0 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 0.0 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 0.5 92 0.5 93 0.0 94 0.0 95 0.0 96 0.5 97 0.5 98 0.5 99 2.0 100 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 80.65 #Duplication Level Percentage of deduplicated Percentage of total 1 82.26906385616863 66.35 2 13.32920024798512 21.5 3 3.0688158710477373 7.425 4 0.9299442033477991 3.0 5 0.3099814011159331 1.25 6 0.06199628022318661 0.3 7 0.030998140111593304 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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 7 0.17500000000000002 No Hit GCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCACACT 6 0.15 No Hit TGGGAACATGGATTATACCGGTGAACTCACAGAAAAGGAAATTATCAGAG 6 0.15 No Hit GTGACACACAAAGGTGACATAAAAAAATTTCAACTAGCCACAAGAAACAG 5 0.125 No Hit CCTTGATGCTCTTCTCCAAGACTATGCTTATAGAGCATTTGTTCGTCCTA 5 0.125 No Hit AGACTCTCCAGAAGATGATGGACCAGTGGAGTTGCAAGAAACAACGAAGC 5 0.125 No Hit GTAAAGAGCACCTCAAACTCAAATTGCTAAACCCTCCAGAGGAACTCAAG 5 0.125 No Hit TGTGTCTCTGTTTTTGTGGGATATAGAGCAGCAACTAGATCCAGGAATGA 5 0.125 No Hit GGAAAATCCTTCCAGTGTGAACTTGTCTTTGCCAAGATGGGAATTAACCC 5 0.125 No Hit CAACCGAAGCAGACTCGCATGTCATAACTGTACCTGCAGGCACGCCCGGA 5 0.125 No Hit GAAGAGGCACAAGGTAGAGAGCAGATAAGATAGCAGCAAAATCCCAGCAC 5 0.125 No Hit GCAGCCACATGGAAAATATGCAGGAATTTTTGCAGCCTGTACGGAGCATA 5 0.125 No Hit GTAGACTGGCCAGCGAATAGAGTACGCGATACCTTCATCAAGTTCTTCGA 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 0.075 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 0.0875 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.2875 0.0 0.0 0.0 0.0 68-69 0.375 0.0 0.0 0.0 0.0 70-71 0.425 0.0 0.0 0.0 0.0 72-73 0.675 0.0 0.0 0.0 0.0 74-75 0.85 0.0 0.0 0.0 0.0 76-77 0.9875 0.0 0.0 0.0 0.0 78-79 1.2374999999999998 0.0 0.0 0.0 0.0 80-81 1.475 0.0 0.0 0.0 0.0 82-83 1.75 0.0 0.0 0.0 0.0 84-85 2.075 0.0 0.0 0.0 0.0 86-87 2.5250000000000004 0.0 0.0 0.0 0.0 88-89 2.9000000000000004 0.0 0.0 0.0 0.0 90-91 3.525 0.0 0.0 0.0 0.0 92-93 4.0375 0.0 0.0 0.0 0.0 94-95 4.4875 0.0 0.0 0.0 0.0 96-97 5.3625 0.0 0.0 0.0 0.0 98-99 5.949999999999999 0.0 0.0 0.0 0.0 100-101 6.5875 0.0 0.0 0.0 0.0 102-103 7.125 0.0 0.0 0.0 0.0 104-105 8.0875 0.0 0.0 0.0 0.0 106-107 8.65 0.0 0.0 0.0 0.0 108-109 9.425 0.0 0.0 0.0 0.0 110-111 10.4125 0.0 0.0 0.0 0.0 112-113 11.649999999999999 0.0 0.0 0.0 0.0 114-115 12.787500000000001 0.0 0.0 0.0 0.0 116-117 13.9375 0.0 0.0 0.0 0.0 118-119 14.825 0.0 0.0 0.0 0.0 120-121 15.7625 0.0 0.0 0.0 0.0 122-123 16.75 0.0 0.0 0.0 0.0 124-125 18.0375 0.0 0.0 0.0 0.0 126-127 19.25 0.0 0.0 0.0 0.0 128-129 20.112499999999997 0.0 0.0 0.0 0.0 130-131 21.05 0.0 0.0 0.0 0.0 132-133 22.1875 0.0 0.0 0.0 0.0 134-135 23.075 0.0 0.0 0.0 0.0 136-137 24.075000000000003 0.0 0.0 0.0 0.0 138-139 25.137500000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGACTGA 10 0.006830828 145.0 7 ATGGACT 10 0.006830828 145.0 5 AATGGAC 10 0.006830828 145.0 4 >>END_MODULE Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678445 spots for SRR12670180.sra Written 678445 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra Read 678438 spots for SRR12670180.sra Written 678438 spots for SRR12670180.sra SRR ids: ['SRR12670180.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a60ka2y2 SRR12670180.sra spots: 13568767 blocks: [[1, 678438], [678439, 1356876], [1356877, 2035314], [2035315, 2713752], [2713753, 3392190], [3392191, 4070628], [4070629, 4749066], [4749067, 5427504], [5427505, 6105942], [6105943, 6784380], [6784381, 7462818], [7462819, 8141256], [8141257, 8819694], [8819695, 9498132], [9498133, 10176570], [10176571, 10855008], [10855009, 11533446], [11533447, 12211884], [12211885, 12890322], [12890323, 13568767]] SRR12670180 file size 4589560 SRR12670180 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 SRR12670180 SRR12670180_1.fastq SRR12670180_2.fastq Input file: SRR12670180_1.fastq Paired file: SRR12670180_2.fastq trimmed: SRR12670180-trimmed-pair1.fastq, SRR12670180-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 08:58:51 2025 >> started Tue Feb 11 08:59:12 2025 >> done (21.615s) 13568767 read pairs processed; of these: 50 ( 0.00%) short read pairs filtered out after trimming by size control 2152 ( 0.02%) empty read pairs filtered out after trimming by size control 13566565 (99.98%) read pairs available; of these: 3807159 (28.06%) trimmed read pairs available after processing 9759406 (71.94%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 6 0.00% 20 8 0.00% 21 8 0.00% 22 7 0.00% 23 6 0.00% 24 10 0.00% 25 19 0.00% 26 16 0.00% 27 22 0.00% 28 30 0.00% 29 27 0.00% 30 35 0.00% 31 45 0.00% 32 41 0.00% 33 42 0.00% 34 69 0.00% 35 59 0.00% 36 66 0.00% 37 100 0.00% 38 101 0.00% 39 126 0.00% 40 129 0.00% 41 139 0.00% 42 167 0.00% 43 143 0.00% 44 186 0.00% 45 186 0.00% 46 232 0.00% 47 312 0.00% 48 299 0.00% 49 338 0.00% 50 436 0.00% 51 483 0.00% 52 605 0.00% 53 583 0.00% 54 654 0.00% 55 691 0.01% 56 752 0.01% 57 901 0.01% 58 1080 0.01% 59 1256 0.01% 60 1528 0.01% 61 1787 0.01% 62 1881 0.01% 63 2183 0.02% 64 2443 0.02% 65 2471 0.02% 66 2721 0.02% 67 3273 0.02% 68 3750 0.03% 69 4085 0.03% 70 4899 0.04% 71 5404 0.04% 72 6338 0.05% 73 6911 0.05% 74 7610 0.06% 75 8316 0.06% 76 9127 0.07% 77 9972 0.07% 78 10716 0.08% 79 11762 0.09% 80 13291 0.10% 81 14685 0.11% 82 16622 0.12% 83 17931 0.13% 84 19825 0.15% 85 21315 0.16% 86 22629 0.17% 87 23673 0.17% 88 25124 0.19% 89 26342 0.19% 90 28673 0.21% 91 30404 0.22% 92 32119 0.24% 93 34921 0.26% 94 37230 0.27% 95 38846 0.29% 96 40310 0.30% 97 41459 0.31% 98 42049 0.31% 99 43451 0.32% 100 45769 0.34% 101 46132 0.34% 102 48656 0.36% 103 50691 0.37% 104 52363 0.39% 105 53516 0.39% 106 54595 0.40% 107 54591 0.40% 108 55202 0.41% 109 55838 0.41% 110 55787 0.41% 111 57066 0.42% 112 58881 0.43% 113 59297 0.44% 114 60540 0.45% 115 61367 0.45% 116 61985 0.46% 117 62400 0.46% 118 62877 0.46% 119 61454 0.45% 120 62476 0.46% 121 62988 0.46% 122 63420 0.47% 123 64658 0.48% 124 65114 0.48% 125 64733 0.48% 126 66567 0.49% 127 65943 0.49% 128 64927 0.48% 129 64458 0.48% 130 64648 0.48% 131 64538 0.48% 132 63982 0.47% 133 65118 0.48% 134 64246 0.47% 135 66270 0.49% 136 65873 0.49% 137 65140 0.48% 138 64693 0.48% 139 65641 0.48% 140 64167 0.47% 141 63751 0.47% 142 63835 0.47% 143 63318 0.47% 144 64598 0.48% 145 64385 0.47% 146 64182 0.47% 147 64227 0.47% 148 64875 0.48% 149 62822 0.46% 150 64064 0.47% 151 9759406 71.94% 13566565 reads passed initial QC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=2.19 fanout-score-rank=19 prefix-density=0.43 prefix-fanout=2.1 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=179.19 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=15.2 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGT criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=22 prefix-density=0.61 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=25 fanout-score=9.19 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=5.1 sequence=TTATCCATGGCAGCTCGAGAATTGGTCGACTATGGAAAAGATAGCGTTACCGTCAATATCCCATCAACTGGCGATGTATCATCTAGAAGCCAGCCTCCTACCTATGCCCCACGAACTGGCAGTGGAT SRR12670180 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 09:00:17 Started mapping on | Feb 11 09:00:17 Finished on | Feb 11 09:01:29 Mapping speed, Million of reads per hour | 678.33 Number of input reads | 13566565 Average input read length | 280 UNIQUE READS: Uniquely mapped reads number | 10346958 Uniquely mapped reads % | 76.27% Average mapped length | 285.33 Number of splices: Total | 10492195 Number of splices: Annotated (sjdb) | 10268019 Number of splices: GT/AG | 10274341 Number of splices: GC/AG | 175619 Number of splices: AT/AC | 5970 Number of splices: Non-canonical | 36265 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.80 Insertion rate per base | 0.02% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 262604 % of reads mapped to multiple loci | 1.94% Number of reads mapped to too many loci | 56762 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 21.28% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2957003 2957003 2957003 N_multimapping 262604 262604 262604 N_noFeature 375731 10221489 421696 N_ambiguous 227239 1598 146715 UnstrandedReadsAssigned:9743988 PositiveStrandReadsAssigned:123871 NegativeStrandReadsAssigned:9778547 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=134 echo kmer=129 SRR12670180 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: SRR12670180-trimmed-pair1.fastq SRR12670180-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,566,565 reads, 12,177,446 reads pseudoaligned [quant] estimated average fragment length: 199.083 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,128 rounds 52401 SRR12670180.ke.tsv 34699 SRR12670180.se.tsv 87100 total ==> SRR12670180.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1819.92 423 20.1793 Potri.005G024800.1.v4.1 1035 836.917 313 32.4698 Potri.004G059700.1.v4.1 961 762.977 0 0 Potri.007G009000.2.v4.1 1416 1217.92 0 0 Potri.003G141000.2.v4.1 2943 2744.92 761.972 24.1006 Potri.016G087400.1.v4.1 270 113.398 548 419.557 Potri.015G069301.1.v4.1 564 372.004 0 0 Potri.010G195200.1.v4.1 1773 1574.92 44 2.42556 Potri.012G127500.1.v4.1 977 778.961 108 12.0372 ==> SRR12670180.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 102 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 149 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 14 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 6 SRR12670180 completed mapping pipeline successfully