Starting /dee2/code/volunteer_pipeline.sh SRR12670139 current disk space = 3057366622208 free memory = 1350372492 SRR12670139 SRAfilesize cd7c6d544bc4a1b97edc6b09c78282ef SRR12670139.sra SRR12670139.sra file validated SRR12670139 is paired end SRR12670139 is conventional basespace SRR12670139 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670139_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.594 37.0 37.0 37.0 37.0 37.0 2 36.46125 37.0 37.0 37.0 37.0 37.0 3 36.575 37.0 37.0 37.0 37.0 37.0 4 36.632 37.0 37.0 37.0 37.0 37.0 5 36.672 37.0 37.0 37.0 37.0 37.0 6 36.665 37.0 37.0 37.0 37.0 37.0 7 36.5825 37.0 37.0 37.0 37.0 37.0 8 36.6335 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 36.5898 37.0 37.0 37.0 37.0 37.0 15-19 36.5655 37.0 37.0 37.0 37.0 37.0 20-24 36.5235 37.0 37.0 37.0 37.0 37.0 25-29 36.5249 37.0 37.0 37.0 37.0 37.0 30-34 36.5029 37.0 37.0 37.0 37.0 37.0 35-39 36.5115 37.0 37.0 37.0 37.0 37.0 40-44 36.44969999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.442699999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.398 37.0 37.0 37.0 37.0 37.0 55-59 36.4402 37.0 37.0 37.0 37.0 37.0 60-64 36.3798 37.0 37.0 37.0 37.0 37.0 65-69 36.352199999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.334799999999994 37.0 37.0 37.0 37.0 37.0 75-79 36.3376 37.0 37.0 37.0 37.0 37.0 80-84 36.3223 37.0 37.0 37.0 37.0 37.0 85-89 36.2947 37.0 37.0 37.0 37.0 37.0 90-94 36.2453 37.0 37.0 37.0 37.0 37.0 95-99 36.26090000000001 37.0 37.0 37.0 37.0 37.0 100-104 36.2498 37.0 37.0 37.0 37.0 37.0 105-109 36.2399 37.0 37.0 37.0 37.0 37.0 110-114 36.184900000000006 37.0 37.0 37.0 37.0 37.0 115-119 36.2448 37.0 37.0 37.0 37.0 37.0 120-124 36.098 37.0 37.0 37.0 37.0 37.0 125-129 36.072900000000004 37.0 37.0 37.0 37.0 37.0 130-134 36.0015 37.0 37.0 37.0 37.0 37.0 135-139 35.92230000000001 37.0 37.0 37.0 37.0 37.0 140-144 35.77440000000001 37.0 37.0 37.0 37.0 37.0 145-149 35.6295 37.0 37.0 37.0 37.0 37.0 150-151 35.4195 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 0.0 18 1.0 19 1.0 20 0.0 21 0.0 22 0.0 23 0.0 24 1.0 25 1.0 26 3.0 27 4.0 28 10.0 29 16.0 30 26.0 31 41.0 32 44.0 33 55.0 34 111.0 35 314.0 36 3004.0 37 367.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.075 11.425 6.275 46.225 2 18.67334167709637 12.340425531914894 38.34793491864831 30.638297872340424 3 16.75 15.375 27.700000000000003 40.175 4 21.775 24.275 24.5 29.45 5 25.224999999999998 30.525000000000002 23.525 20.724999999999998 6 20.95 34.075 23.825 21.15 7 15.85 26.724999999999998 39.125 18.3 8 17.150000000000002 24.55 33.550000000000004 24.75 9 17.724999999999998 24.224999999999998 35.575 22.475 10-14 19.785 29.220000000000002 28.235 22.759999999999998 15-19 20.43 27.43 27.625 24.515 20-24 20.169999999999998 27.860000000000003 27.97 24.0 25-29 20.21 28.04 27.775 23.974999999999998 30-34 20.01 27.51 28.405 24.075 35-39 20.36 27.68 28.1 23.86 40-44 20.735 27.865000000000002 27.63 23.77 45-49 20.599999999999998 27.71 27.685 24.005000000000003 50-54 20.43 27.42 28.355000000000004 23.794999999999998 55-59 20.365 27.0 27.939999999999998 24.695 60-64 20.185 27.975 27.73 24.11 65-69 20.455000000000002 27.145000000000003 28.235 24.165 70-74 20.555 27.3 28.470000000000002 23.674999999999997 75-79 20.76 28.565 27.195000000000004 23.48 80-84 21.44 27.29 27.810000000000002 23.46 85-89 20.855 28.71 27.055 23.380000000000003 90-94 20.77 28.42 27.24 23.57 95-99 21.475 28.535 26.924999999999997 23.064999999999998 100-104 22.134999999999998 28.13 27.029999999999998 22.705000000000002 105-109 22.41 28.470000000000002 26.195 22.925 110-114 21.959999999999997 28.715000000000003 26.41 22.915 115-119 22.305 28.439999999999998 25.740000000000002 23.515 120-124 21.985 28.525 25.624999999999996 23.865 125-129 21.22 28.345 25.869999999999997 24.565 130-134 21.545 28.57 25.665 24.22 135-139 21.825 27.52 26.045 24.610000000000003 140-144 21.25 27.650000000000002 26.115 24.985 145-149 22.06 27.075 26.755000000000003 24.11 150-151 21.975 27.212500000000002 25.474999999999998 25.337500000000002 >>END_MODULE >>Per sequence GC content warn #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 0.5 19 0.5 20 0.0 21 0.0 22 0.5 23 1.5 24 2.5 25 3.0 26 2.0 27 1.5 28 6.5 29 9.5 30 8.0 31 14.5 32 20.5 33 24.5 34 36.5 35 63.0 36 87.0 37 98.5 38 118.0 39 134.5 40 164.5 41 207.5 42 246.0 43 274.0 44 294.0 45 277.0 46 262.0 47 266.0 48 234.0 49 202.5 50 186.5 51 172.5 52 138.0 53 103.0 54 87.5 55 73.0 56 46.0 57 32.5 58 29.5 59 22.0 60 16.5 61 7.5 62 6.0 63 7.0 64 4.5 65 2.5 66 2.5 67 1.5 68 0.0 69 0.0 70 0.0 71 0.0 72 0.5 73 0.5 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 80.65 #Duplication Level Percentage of deduplicated Percentage of total 1 81.0601363918165 65.375 2 15.189088654680718 24.5 3 2.7588344699318044 6.675000000000001 4 0.7439553626782394 2.4 5 0.21698698078115314 0.8750000000000001 6 0.0 0.0 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 CGTGGATTCTCCTCCTTGTTGTACATGCCGGGAAGTTGCACATTTGTTGG 7 0.17500000000000002 No Hit ATCAACCAGTTCATTCCAGCTCCAGGTGAACTGCTACCACCACTATTGTG 5 0.125 No Hit CGTCCTCTTTGTCACGCCCTAGAAACTTAGAAAGCTGTACAGGGCTGCTA 5 0.125 No Hit CCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCT 5 0.125 No Hit GTTTGTTTTCAGTATCTACAGTGGGTTTAGCAGTTTCAATATGACTACTT 5 0.125 No Hit CATGAAATTCATGAAACCTTCATGGTGATTGTTATGATGAGCACACTTGG 5 0.125 No Hit CAGGTTTTTATTGATGGCACAAAATTGACAGACTTCTTGCTTCCTCGAAG 5 0.125 No Hit GCCCCATTCTCGTCTCTCAAGTTCACATAATCCCCTTTGCTGTTATCATC 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 0.0 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 0.075 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.21250000000000002 0.0 0.0 0.0 0.0 70-71 0.3 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.38749999999999996 0.0 0.0 0.0 0.0 76-77 0.6125 0.0 0.0 0.0 0.0 78-79 0.825 0.0 0.0 0.0 0.0 80-81 1.15 0.0 0.0 0.0 0.0 82-83 1.3 0.0 0.0 0.0 0.0 84-85 1.5375 0.0 0.0 0.0 0.0 86-87 1.775 0.0 0.0 0.0 0.0 88-89 2.3125 0.0 0.0 0.0 0.0 90-91 2.7875 0.0 0.0 0.0 0.0 92-93 3.225 0.0 0.0 0.0 0.0 94-95 3.75 0.0 0.0 0.0 0.0 96-97 4.4125 0.0 0.0 0.0 0.0 98-99 5.125 0.0 0.0 0.0 0.0 100-101 6.1 0.0 0.0 0.0 0.0 102-103 6.9375 0.0 0.0 0.0 0.0 104-105 7.9125 0.0 0.0 0.0 0.0 106-107 8.8125 0.0 0.0 0.0 0.0 108-109 9.8625 0.0 0.0 0.0 0.0 110-111 10.65 0.0 0.0 0.0 0.0 112-113 11.625 0.0 0.0 0.0 0.0 114-115 12.4 0.0 0.0 0.0 0.0 116-117 13.5375 0.0 0.0 0.0 0.0 118-119 14.7375 0.0 0.0 0.0 0.0 120-121 15.6 0.0 0.0 0.0 0.0 122-123 16.8 0.0 0.0 0.0 0.0 124-125 17.987499999999997 0.0 0.0 0.0 0.0 126-127 19.1 0.0 0.0 0.0 0.0 128-129 19.95 0.0 0.0 0.0 0.0 130-131 20.799999999999997 0.0 0.0 0.0 0.0 132-133 21.4625 0.0 0.0 0.0 0.0 134-135 22.3375 0.0 0.0 0.0 0.0 136-137 23.45 0.0 0.0 0.0 0.0 138-139 24.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTT 40 0.0076550315 18.125 35-39 >>END_MODULE SRR12670139 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670139_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 36.326 37.0 37.0 37.0 37.0 37.0 2 36.089 37.0 37.0 37.0 37.0 37.0 3 36.3165 37.0 37.0 37.0 37.0 37.0 4 36.2265 37.0 37.0 37.0 37.0 37.0 5 36.3175 37.0 37.0 37.0 37.0 37.0 6 36.3135 37.0 37.0 37.0 37.0 37.0 7 36.2395 37.0 37.0 37.0 37.0 37.0 8 36.4625 37.0 37.0 37.0 37.0 37.0 9 36.4245 37.0 37.0 37.0 37.0 37.0 10-14 36.379000000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.421099999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.3555 37.0 37.0 37.0 37.0 37.0 25-29 36.317499999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.297799999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.2298 37.0 37.0 37.0 37.0 37.0 40-44 36.27669999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.271499999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.2312 37.0 37.0 37.0 37.0 37.0 55-59 36.1634 37.0 37.0 37.0 37.0 37.0 60-64 36.204800000000006 37.0 37.0 37.0 37.0 37.0 65-69 36.150600000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.104 37.0 37.0 37.0 37.0 37.0 75-79 36.0983 37.0 37.0 37.0 37.0 37.0 80-84 36.049400000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.0139 37.0 37.0 37.0 37.0 37.0 90-94 36.066 37.0 37.0 37.0 37.0 37.0 95-99 35.9908 37.0 37.0 37.0 37.0 37.0 100-104 35.9319 37.0 37.0 37.0 37.0 37.0 105-109 35.8179 37.0 37.0 37.0 37.0 37.0 110-114 35.855399999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.803700000000006 37.0 37.0 37.0 37.0 37.0 120-124 35.66930000000001 37.0 37.0 37.0 37.0 37.0 125-129 35.6237 37.0 37.0 37.0 37.0 37.0 130-134 35.4336 37.0 37.0 37.0 34.6 37.0 135-139 35.2667 37.0 37.0 37.0 37.0 37.0 140-144 34.980399999999996 37.0 37.0 37.0 25.0 37.0 145-149 34.659299999999995 37.0 37.0 37.0 25.0 37.0 150-151 34.399 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 1.0 15 0.0 16 0.0 17 3.0 18 1.0 19 2.0 20 0.0 21 0.0 22 1.0 23 6.0 24 2.0 25 7.0 26 7.0 27 10.0 28 12.0 29 18.0 30 23.0 31 38.0 32 77.0 33 114.0 34 207.0 35 522.0 36 2629.0 37 318.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.074999999999996 22.55 9.75 34.625 2 24.05 28.475 31.825 15.65 3 20.25 27.6 31.225 20.925 4 22.275 32.675 25.525 19.525000000000002 5 24.875 35.449999999999996 21.95 17.724999999999998 6 21.099999999999998 38.975 22.825 17.1 7 19.950000000000003 22.425 37.55 20.075000000000003 8 21.15 25.674999999999997 29.425 23.75 9 21.9 24.925 28.849999999999998 24.325 10-14 22.665 29.085 26.534999999999997 21.715 15-19 23.06 27.87 27.68 21.39 20-24 22.18 28.265 28.07 21.485000000000003 25-29 22.81 27.47 28.15 21.57 30-34 22.38 28.12 28.310000000000002 21.19 35-39 22.384999999999998 28.610000000000003 27.35 21.654999999999998 40-44 22.57 27.529999999999998 28.325 21.575 45-49 23.07 28.215 27.52 21.195 50-54 22.86 28.199999999999996 27.72 21.22 55-59 23.055 28.299999999999997 27.41 21.235 60-64 23.24 27.775 27.965 21.02 65-69 23.24 27.900000000000002 27.634999999999998 21.224999999999998 70-74 23.015 29.095 26.919999999999998 20.97 75-79 22.825 27.57 28.115000000000002 21.490000000000002 80-84 23.515 28.694999999999997 26.695 21.095 85-89 23.98 28.49 26.700000000000003 20.830000000000002 90-94 24.36 28.725 26.38 20.535 95-99 24.085 28.810000000000002 26.825 20.28 100-104 25.224999999999998 28.29 25.895000000000003 20.59 105-109 25.174999999999997 28.035 26.605 20.185 110-114 25.745 28.105000000000004 26.16 19.99 115-119 26.179999999999996 28.48 25.705 19.634999999999998 120-124 26.640000000000004 28.37 25.31 19.68 125-129 26.924999999999997 28.235 25.5 19.34 130-134 28.115000000000002 27.92 25.569999999999997 18.395 135-139 27.965 26.974999999999998 25.825 19.235 140-144 28.854999999999997 26.889999999999997 26.02 18.235 145-149 29.87 27.994999999999997 24.52 17.615 150-151 30.062499999999996 25.825 26.0375 18.075 >>END_MODULE >>Per sequence GC content warn #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 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 1.5 17 1.5 18 1.0 19 0.0 20 0.5 21 1.5 22 2.0 23 1.5 24 2.0 25 3.0 26 4.0 27 4.0 28 5.5 29 5.5 30 9.5 31 20.5 32 24.5 33 37.5 34 49.5 35 62.5 36 85.5 37 97.5 38 131.0 39 165.5 40 195.5 41 248.5 42 269.0 43 266.5 44 259.5 45 264.0 46 259.5 47 241.5 48 221.0 49 192.0 50 181.0 51 150.5 52 118.5 53 99.0 54 74.0 55 59.0 56 53.0 57 36.5 58 24.5 59 24.0 60 14.0 61 5.5 62 4.0 63 6.0 64 5.5 65 1.0 66 0.0 67 0.0 68 0.0 69 1.0 70 1.5 71 0.5 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 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 1.5 100 2.0 >>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 80.65 #Duplication Level Percentage of deduplicated Percentage of total 1 81.27712337259764 65.55 2 14.848109113453193 23.95 3 2.913825170489771 7.049999999999999 4 0.6819590824550528 2.1999999999999997 5 0.15499070055796654 0.625 6 0.09299442033477992 0.44999999999999996 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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 6 0.15 No Hit CCTTGTTGTCTCACAGTACGTATCAATGGAGATCATGAAGCCTCCTCAGA 6 0.15 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit GCCTGGGACATGATGTCTGGGTGCTTGGTTGGTTTGCCTGGATTTTGTTT 5 0.125 No Hit GATCATCGCCTGAAAAACTCTCTCCCTCCTTTATCTCAGAAACCATACAG 5 0.125 No Hit CCAAGACCTGGCCTGAGGATATCTTGCCCCTGCAGCCAGTTGGTCGCTTG 5 0.125 No Hit GTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATG 5 0.125 No Hit GTTTGATGAGCTTAAAAAGACTGCTACAAGAACAATTTCTGCTGCCTCAA 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 0.0 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 0.075 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.21250000000000002 0.0 0.0 0.0 0.0 70-71 0.3 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.38749999999999996 0.0 0.0 0.0 0.0 76-77 0.6125 0.0 0.0 0.0 0.0 78-79 0.825 0.0 0.0 0.0 0.0 80-81 1.125 0.0 0.0 0.0 0.0 82-83 1.275 0.0 0.0 0.0 0.0 84-85 1.5125 0.0 0.0 0.0 0.0 86-87 1.775 0.0 0.0 0.0 0.0 88-89 2.3375 0.0 0.0 0.0 0.0 90-91 2.825 0.0 0.0 0.0 0.0 92-93 3.3125 0.0 0.0 0.0 0.0 94-95 3.85 0.0 0.0 0.0 0.0 96-97 4.5125 0.0 0.0 0.0 0.0 98-99 5.2125 0.0 0.0 0.0 0.0 100-101 6.1625 0.0 0.0 0.0 0.0 102-103 6.9875 0.0 0.0 0.0 0.0 104-105 7.9375 0.0 0.0 0.0 0.0 106-107 8.837499999999999 0.0 0.0 0.0 0.0 108-109 9.8875 0.0 0.0 0.0 0.0 110-111 10.7 0.0 0.0 0.0 0.0 112-113 11.7375 0.0 0.0 0.0 0.0 114-115 12.5 0.0 0.0 0.0 0.0 116-117 13.649999999999999 0.0 0.0 0.0 0.0 118-119 14.8875 0.0 0.0 0.0 0.0 120-121 15.7875 0.0 0.0 0.0 0.0 122-123 17.0 0.0 0.0 0.0 0.0 124-125 18.2 0.0 0.0 0.0 0.0 126-127 19.325000000000003 0.0 0.0 0.0 0.0 128-129 20.175 0.0 0.0 0.0 0.0 130-131 21.025 0.0 0.0 0.0 0.0 132-133 21.762500000000003 0.0 0.0 0.0 0.0 134-135 22.65 0.0 0.0 0.0 0.0 136-137 23.725 0.0 0.0 0.0 0.0 138-139 24.9125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTCAAGT 10 0.006830828 145.0 6 TGTCAAG 10 0.006830828 145.0 5 GTAAAGA 25 8.7132835E-4 87.0 2 AAAAAAA 40 0.0076550315 18.125 95-99 >>END_MODULE Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586236 spots for SRR12670139.sra Written 586236 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra Read 586231 spots for SRR12670139.sra Written 586231 spots for SRR12670139.sra SRR ids: ['SRR12670139.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1_d8fxoy SRR12670139.sra spots: 11724625 blocks: [[1, 586231], [586232, 1172462], [1172463, 1758693], [1758694, 2344924], [2344925, 2931155], [2931156, 3517386], [3517387, 4103617], [4103618, 4689848], [4689849, 5276079], [5276080, 5862310], [5862311, 6448541], [6448542, 7034772], [7034773, 7621003], [7621004, 8207234], [8207235, 8793465], [8793466, 9379696], [9379697, 9965927], [9965928, 10552158], [10552159, 11138389], [11138390, 11724625]] SRR12670139 file size 3962840 SRR12670139 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 SRR12670139 SRR12670139_1.fastq SRR12670139_2.fastq Input file: SRR12670139_1.fastq Paired file: SRR12670139_2.fastq trimmed: SRR12670139-trimmed-pair1.fastq, SRR12670139-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 00:56:16 2025 >> started Tue Feb 11 00:56:35 2025 >> done (19.081s) 11724625 read pairs processed; of these: 42 ( 0.00%) short read pairs filtered out after trimming by size control 3083 ( 0.03%) empty read pairs filtered out after trimming by size control 11721500 (99.97%) read pairs available; of these: 3588864 (30.62%) trimmed read pairs available after processing 8132636 (69.38%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 1 0.00% 20 2 0.00% 21 5 0.00% 22 5 0.00% 23 5 0.00% 24 11 0.00% 25 12 0.00% 26 12 0.00% 27 18 0.00% 28 20 0.00% 29 13 0.00% 30 29 0.00% 31 37 0.00% 32 44 0.00% 33 36 0.00% 34 50 0.00% 35 34 0.00% 36 55 0.00% 37 59 0.00% 38 85 0.00% 39 95 0.00% 40 114 0.00% 41 111 0.00% 42 131 0.00% 43 149 0.00% 44 141 0.00% 45 146 0.00% 46 168 0.00% 47 241 0.00% 48 288 0.00% 49 317 0.00% 50 384 0.00% 51 471 0.00% 52 494 0.00% 53 499 0.00% 54 528 0.00% 55 658 0.01% 56 730 0.01% 57 775 0.01% 58 994 0.01% 59 1151 0.01% 60 1442 0.01% 61 1583 0.01% 62 1859 0.02% 63 2090 0.02% 64 2242 0.02% 65 2385 0.02% 66 2630 0.02% 67 2929 0.02% 68 3479 0.03% 69 3765 0.03% 70 4457 0.04% 71 5115 0.04% 72 5873 0.05% 73 6573 0.06% 74 7343 0.06% 75 8131 0.07% 76 8678 0.07% 77 9390 0.08% 78 10350 0.09% 79 11165 0.10% 80 12351 0.11% 81 13998 0.12% 82 15565 0.13% 83 16789 0.14% 84 18790 0.16% 85 20419 0.17% 86 21991 0.19% 87 22924 0.20% 88 24304 0.21% 89 25387 0.22% 90 27458 0.23% 91 29102 0.25% 92 30613 0.26% 93 33489 0.29% 94 35370 0.30% 95 37119 0.32% 96 38543 0.33% 97 39739 0.34% 98 41064 0.35% 99 41549 0.35% 100 43164 0.37% 101 43915 0.37% 102 45775 0.39% 103 47524 0.41% 104 49025 0.42% 105 50812 0.43% 106 51306 0.44% 107 51963 0.44% 108 52463 0.45% 109 53607 0.46% 110 53809 0.46% 111 53965 0.46% 112 55114 0.47% 113 55508 0.47% 114 57179 0.49% 115 57909 0.49% 116 58822 0.50% 117 59178 0.50% 118 60073 0.51% 119 59517 0.51% 120 59861 0.51% 121 59911 0.51% 122 60187 0.51% 123 60102 0.51% 124 60490 0.52% 125 60679 0.52% 126 61654 0.53% 127 61749 0.53% 128 60822 0.52% 129 60981 0.52% 130 61543 0.53% 131 60606 0.52% 132 59930 0.51% 133 60904 0.52% 134 60154 0.51% 135 60376 0.52% 136 60807 0.52% 137 59948 0.51% 138 60661 0.52% 139 61599 0.53% 140 60618 0.52% 141 60613 0.52% 142 60320 0.51% 143 60006 0.51% 144 59673 0.51% 145 59800 0.51% 146 59810 0.51% 147 58710 0.50% 148 59886 0.51% 149 58932 0.50% 150 59742 0.51% 151 8132636 69.38% 11721500 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.21 fanout-score-rank=34 prefix-density=0.37 prefix-fanout=2.1 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAGCTTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCAT criterion=fanout-score sequence-density=0.03 sequence-density-rank=38 fanout-score=135.28 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=13.6 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.18 fanout-score-rank=28 prefix-density=0.54 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=32 fanout-score=12.04 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=7.3 sequence=CTGAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCA SRR12670139 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:57:18 Started mapping on | Feb 11 00:57:19 Finished on | Feb 11 00:58:35 Mapping speed, Million of reads per hour | 555.23 Number of input reads | 11721500 Average input read length | 282 UNIQUE READS: Uniquely mapped reads number | 11147070 Uniquely mapped reads % | 95.10% Average mapped length | 281.19 Number of splices: Total | 10823276 Number of splices: Annotated (sjdb) | 10584646 Number of splices: GT/AG | 10596781 Number of splices: GC/AG | 185539 Number of splices: AT/AC | 6502 Number of splices: Non-canonical | 34454 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.02% Deletion average length | 2.86 Insertion rate per base | 0.02% Insertion average length | 2.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 262831 % of reads mapped to multiple loci | 2.24% Number of reads mapped to too many loci | 20173 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.41% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 311599 311599 311599 N_multimapping 262831 262831 262831 N_noFeature 379163 10995609 443856 N_ambiguous 149159 584 62025 UnstrandedReadsAssigned:10618748 PositiveStrandReadsAssigned:150877 NegativeStrandReadsAssigned:10641189 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=130 echo kmer=125 SRR12670139 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: SRR12670139-trimmed-pair1.fastq SRR12670139-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,721,500 reads, 10,655,687 reads pseudoaligned [quant] estimated average fragment length: 197.571 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,141 rounds 52401 SRR12670139.ke.tsv 34699 SRR12670139.se.tsv 87100 total ==> SRR12670139.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1821.43 601 31.6201 Potri.005G024800.1.v4.1 1035 838.429 116 13.2584 Potri.004G059700.1.v4.1 961 764.506 3 0.376046 Potri.007G009000.2.v4.1 1416 1219.43 0 0 Potri.003G141000.2.v4.1 2943 2746.43 757 26.4136 Potri.016G087400.1.v4.1 270 112.076 446 381.351 Potri.015G069301.1.v4.1 564 373.952 0 0 Potri.010G195200.1.v4.1 1773 1576.43 63 3.82972 Potri.012G127500.1.v4.1 977 780.475 45 5.52528 ==> SRR12670139.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 60 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 199 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 13 SRR12670139 completed mapping pipeline successfully