Starting /dee2/code/volunteer_pipeline.sh SRR12919360 current disk space = 3050876633088 free memory = 1581612704 SRR12919360 SRAfilesize bacccd44b1bf1671f2434a297f816446 SRR12919360.sra SRR12919360.sra file validated SRR12919360 is paired end SRR12919360 is conventional basespace SRR12919360 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919360_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 36.598 37.0 37.0 37.0 37.0 37.0 2 36.39075 37.0 37.0 37.0 37.0 37.0 3 36.641 37.0 37.0 37.0 37.0 37.0 4 36.683 37.0 37.0 37.0 37.0 37.0 5 36.7265 37.0 37.0 37.0 37.0 37.0 6 36.692 37.0 37.0 37.0 37.0 37.0 7 36.578 37.0 37.0 37.0 37.0 37.0 8 36.6725 37.0 37.0 37.0 37.0 37.0 9 36.6655 37.0 37.0 37.0 37.0 37.0 10-14 36.6726 37.0 37.0 37.0 37.0 37.0 15-19 36.64309999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.6139 37.0 37.0 37.0 37.0 37.0 25-29 36.5677 37.0 37.0 37.0 37.0 37.0 30-34 36.51 37.0 37.0 37.0 37.0 37.0 35-39 36.522 37.0 37.0 37.0 37.0 37.0 40-44 36.556799999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.502300000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.48010000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.45139999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.4243 37.0 37.0 37.0 37.0 37.0 65-69 36.4045 37.0 37.0 37.0 37.0 37.0 70-74 36.3725 37.0 37.0 37.0 37.0 37.0 75-79 36.3218 37.0 37.0 37.0 37.0 37.0 80-84 36.329699999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.2642 37.0 37.0 37.0 37.0 37.0 90-94 36.206 37.0 37.0 37.0 37.0 37.0 95-99 36.2385 37.0 37.0 37.0 37.0 37.0 100-104 36.216899999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.1844 37.0 37.0 37.0 37.0 37.0 110-114 36.1194 37.0 37.0 37.0 37.0 37.0 115-119 36.1358 37.0 37.0 37.0 37.0 37.0 120-124 36.1272 37.0 37.0 37.0 37.0 37.0 125-129 36.0498 37.0 37.0 37.0 37.0 37.0 130-134 35.938599999999994 37.0 37.0 37.0 37.0 37.0 135-139 35.780100000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.6554 37.0 37.0 37.0 37.0 37.0 145-149 35.5562 37.0 37.0 37.0 37.0 37.0 150-151 35.4215 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 2.0 24 2.0 25 2.0 26 8.0 27 5.0 28 16.0 29 18.0 30 25.0 31 29.0 32 39.0 33 71.0 34 103.0 35 280.0 36 2993.0 37 407.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.225 12.3 6.9750000000000005 39.5 2 20.160682902334923 13.482299774039669 36.1787597288476 30.178257594777808 3 17.150000000000002 18.55 29.349999999999998 34.949999999999996 4 22.3 25.45 24.05 28.199999999999996 5 23.575 31.025000000000002 25.1 20.3 6 19.975 35.3 22.325 22.400000000000002 7 15.55 26.224999999999998 41.9 16.325 8 17.05 26.150000000000002 31.775 25.025 9 16.950000000000003 26.174999999999997 32.824999999999996 24.05 10-14 19.759999999999998 29.98 27.345000000000002 22.915 15-19 20.025000000000002 28.095 28.305000000000003 23.575 20-24 19.98 28.09 27.815 24.115000000000002 25-29 19.695 28.915000000000003 27.889999999999997 23.5 30-34 20.05 28.89 27.305 23.755000000000003 35-39 20.355 29.060000000000002 26.810000000000002 23.775 40-44 19.64 29.025000000000002 27.495000000000005 23.84 45-49 19.46 29.189999999999998 27.474999999999998 23.875 50-54 19.775000000000002 28.565 27.345000000000002 24.315 55-59 20.195 28.415000000000003 27.650000000000002 23.74 60-64 19.455 29.515 27.279999999999998 23.75 65-69 19.845 28.465 27.41 24.279999999999998 70-74 19.985 28.32 28.095 23.599999999999998 75-79 19.869999999999997 28.945 27.66 23.525 80-84 20.14 28.28 28.62 22.96 85-89 19.955000000000002 29.015 27.48 23.549999999999997 90-94 20.29 29.220000000000002 26.935 23.555 95-99 20.925 28.4 27.345000000000002 23.330000000000002 100-104 20.630000000000003 28.595 27.975 22.8 105-109 20.385 27.6 28.155 23.86 110-114 21.235 28.405 27.1 23.26 115-119 20.445 28.265 27.37 23.919999999999998 120-124 20.645 28.854999999999997 26.655 23.845 125-129 20.685000000000002 29.189999999999998 26.640000000000004 23.485 130-134 20.965 28.310000000000002 26.945000000000004 23.78 135-139 21.315 28.665000000000003 26.305 23.715 140-144 21.525 28.225 26.979999999999997 23.27 145-149 21.495 28.515 25.935000000000002 24.055 150-151 21.075 29.275000000000002 25.9875 23.6625 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.5 24 4.0 25 4.5 26 3.0 27 6.0 28 8.5 29 11.5 30 18.5 31 29.0 32 40.5 33 51.5 34 58.5 35 67.5 36 91.0 37 115.0 38 134.0 39 168.0 40 199.5 41 208.0 42 227.5 43 263.5 44 274.0 45 255.5 46 262.0 47 262.5 48 230.0 49 197.5 50 169.5 51 140.0 52 111.0 53 91.0 54 65.5 55 50.5 56 43.5 57 32.5 58 24.0 59 17.5 60 14.0 61 12.0 62 12.0 63 6.5 64 4.5 65 3.5 66 1.5 67 2.0 68 0.5 69 1.0 70 1.0 71 0.0 72 0.5 73 0.5 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 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.42500000000000004 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 91.5 #Duplication Level Percentage of deduplicated Percentage of total 1 91.99453551912569 84.175 2 6.967213114754098 12.75 3 0.819672131147541 2.25 4 0.1912568306010929 0.7000000000000001 5 0.0273224043715847 0.125 6 0.0 0.0 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 CCAGCATCCAATTGTCTGTCGAACAAAGCCATGAGACTACTGAAGGTAAG 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 0.075 0.0 8 0.0 0.0 0.0 0.075 0.0 9 0.0 0.0 0.0 0.075 0.0 10-11 0.0 0.0 0.0 0.075 0.0 12-13 0.0 0.0 0.0 0.075 0.0 14-15 0.0 0.0 0.0 0.075 0.0 16-17 0.0 0.0 0.0 0.075 0.0 18-19 0.0 0.0 0.0 0.075 0.0 20-21 0.0 0.0 0.0 0.075 0.0 22-23 0.0 0.0 0.0 0.075 0.0 24-25 0.0 0.0 0.0 0.075 0.0 26-27 0.0 0.0 0.0 0.075 0.0 28-29 0.0 0.0 0.0 0.075 0.0 30-31 0.0 0.0 0.0 0.075 0.0 32-33 0.0 0.0 0.0 0.075 0.0 34-35 0.0 0.0 0.0 0.075 0.0 36-37 0.0 0.0 0.0 0.075 0.0 38-39 0.0 0.0 0.0 0.075 0.0 40-41 0.0 0.0 0.0 0.075 0.0 42-43 0.0 0.0 0.0 0.075 0.0 44-45 0.0 0.0 0.0 0.075 0.0 46-47 0.0 0.0 0.0 0.075 0.0 48-49 0.0 0.0 0.0 0.075 0.0 50-51 0.0 0.0 0.0 0.075 0.0 52-53 0.0 0.0 0.0 0.075 0.0 54-55 0.0 0.0 0.0 0.075 0.0 56-57 0.0 0.0 0.0 0.075 0.0 58-59 0.0 0.0 0.0 0.075 0.0 60-61 0.0 0.0 0.0 0.075 0.0 62-63 0.0 0.0 0.0 0.075 0.0 64-65 0.0 0.0 0.0 0.075 0.0 66-67 0.0 0.0 0.0 0.075 0.0 68-69 0.0 0.0 0.0 0.075 0.0 70-71 0.025 0.0 0.0 0.075 0.0 72-73 0.05 0.0 0.0 0.075 0.0 74-75 0.05 0.025 0.0 0.075 0.0 76-77 0.1 0.025 0.0 0.075 0.0 78-79 0.1125 0.025 0.0 0.075 0.0 80-81 0.1625 0.025 0.0 0.075 0.0 82-83 0.3875 0.025 0.0 0.075 0.0 84-85 0.425 0.025 0.0 0.075 0.0 86-87 0.5 0.025 0.0 0.075 0.0 88-89 0.6 0.025 0.0 0.075 0.0 90-91 0.7250000000000001 0.025 0.0 0.075 0.0 92-93 0.8875 0.025 0.0 0.075 0.0 94-95 1.125 0.025 0.0 0.075 0.0 96-97 1.35 0.025 0.0 0.075 0.0 98-99 1.5625 0.025 0.0 0.075 0.0 100-101 1.675 0.025 0.0 0.075 0.0 102-103 1.7875 0.025 0.0 0.075 0.0 104-105 2.3125 0.025 0.0 0.075 0.0 106-107 2.5375 0.025 0.0 0.075 0.0 108-109 2.775 0.025 0.0 0.075 0.0 110-111 3.0250000000000004 0.025 0.0 0.075 0.0 112-113 3.4375 0.025 0.0 0.075 0.0 114-115 3.9 0.025 0.0 0.075 0.0 116-117 4.425 0.025 0.0 0.075 0.0 118-119 4.975 0.025 0.0 0.075 0.0 120-121 5.475 0.025 0.0 0.075 0.0 122-123 6.0125 0.025 0.0 0.075 0.0 124-125 6.5375 0.025 0.0 0.075 0.0 126-127 7.175 0.025 0.0 0.075 0.0 128-129 7.862500000000001 0.025 0.0 0.075 0.0 130-131 8.337499999999999 0.025 0.0 0.075 0.0 132-133 8.912500000000001 0.025 0.0 0.075 0.0 134-135 9.5375 0.025 0.0 0.075 0.0 136-137 10.1375 0.025 0.0 0.075 0.0 138-139 10.975000000000001 0.025 0.0 0.075 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCTCTG 10 0.006830828 145.0 7 GTGAGAT 10 0.006830828 145.0 1 TCTCGGT 10 0.006830828 145.0 5 TGAGATT 10 0.006830828 145.0 2 >>END_MODULE SRR12919360 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919360_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 36.3245 37.0 37.0 37.0 37.0 37.0 2 36.284 37.0 37.0 37.0 37.0 37.0 3 36.382 37.0 37.0 37.0 37.0 37.0 4 36.302 37.0 37.0 37.0 37.0 37.0 5 36.41 37.0 37.0 37.0 37.0 37.0 6 36.409 37.0 37.0 37.0 37.0 37.0 7 36.432 37.0 37.0 37.0 37.0 37.0 8 36.414 37.0 37.0 37.0 37.0 37.0 9 36.438 37.0 37.0 37.0 37.0 37.0 10-14 36.4202 37.0 37.0 37.0 37.0 37.0 15-19 36.3627 37.0 37.0 37.0 37.0 37.0 20-24 36.3729 37.0 37.0 37.0 37.0 37.0 25-29 36.3004 37.0 37.0 37.0 37.0 37.0 30-34 36.2607 37.0 37.0 37.0 37.0 37.0 35-39 36.262 37.0 37.0 37.0 37.0 37.0 40-44 36.2453 37.0 37.0 37.0 37.0 37.0 45-49 36.1853 37.0 37.0 37.0 37.0 37.0 50-54 36.186600000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.1673 37.0 37.0 37.0 37.0 37.0 60-64 36.1442 37.0 37.0 37.0 37.0 37.0 65-69 36.117900000000006 37.0 37.0 37.0 37.0 37.0 70-74 36.0897 37.0 37.0 37.0 37.0 37.0 75-79 36.0234 37.0 37.0 37.0 37.0 37.0 80-84 36.0125 37.0 37.0 37.0 37.0 37.0 85-89 35.984899999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.8974 37.0 37.0 37.0 37.0 37.0 95-99 35.996 37.0 37.0 37.0 37.0 37.0 100-104 35.896300000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.86899999999999 37.0 37.0 37.0 37.0 37.0 110-114 35.906 37.0 37.0 37.0 37.0 37.0 115-119 35.7893 37.0 37.0 37.0 37.0 37.0 120-124 35.745999999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.7379 37.0 37.0 37.0 37.0 37.0 130-134 35.5718 37.0 37.0 37.0 37.0 37.0 135-139 35.535199999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.331300000000006 37.0 37.0 37.0 37.0 37.0 145-149 35.2738 37.0 37.0 37.0 34.6 37.0 150-151 35.07225 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 5.0 15 2.0 16 3.0 17 2.0 18 0.0 19 2.0 20 1.0 21 1.0 22 4.0 23 1.0 24 5.0 25 9.0 26 3.0 27 10.0 28 13.0 29 25.0 30 28.0 31 37.0 32 51.0 33 68.0 34 136.0 35 491.0 36 2737.0 37 362.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.0 23.35 10.8 25.85 2 29.175 25.324999999999996 30.075000000000003 15.425 3 20.175 28.249999999999996 33.15 18.425 4 23.525 33.25 24.575 18.65 5 22.5 36.925000000000004 22.775000000000002 17.8 6 21.525 37.55 23.25 17.675 7 21.025 21.625 38.800000000000004 18.55 8 21.0 25.324999999999996 28.075 25.6 9 21.025 23.375 33.074999999999996 22.525000000000002 10-14 23.215 29.04 27.155 20.59 15-19 23.335 27.98 28.294999999999998 20.39 20-24 22.235 28.115000000000002 28.925 20.724999999999998 25-29 22.745 28.470000000000002 28.035 20.75 30-34 22.89 28.310000000000002 28.335 20.465 35-39 23.035 27.675 28.43 20.86 40-44 23.015 28.525 27.91 20.549999999999997 45-49 23.29 27.97 28.325 20.415 50-54 22.675 28.610000000000003 27.744999999999997 20.97 55-59 23.195 28.88 27.839999999999996 20.085 60-64 22.735 28.705000000000002 28.005000000000003 20.555 65-69 23.599999999999998 28.139999999999997 27.584999999999997 20.674999999999997 70-74 22.895 28.060000000000002 28.075 20.97 75-79 22.939999999999998 27.63 28.845 20.585 80-84 23.474999999999998 27.279999999999998 28.96 20.285 85-89 23.44 28.48 27.675 20.405 90-94 23.465 28.105000000000004 27.82 20.61 95-99 23.515 28.449999999999996 27.63 20.405 100-104 23.69 28.144999999999996 28.449999999999996 19.715 105-109 23.44 28.035 27.950000000000003 20.575 110-114 24.135 27.58 27.650000000000002 20.635 115-119 24.585 28.595 27.07 19.75 120-124 24.990000000000002 28.249999999999996 27.200000000000003 19.56 125-129 24.84 28.03 26.88 20.25 130-134 24.654999999999998 27.675 27.77 19.900000000000002 135-139 25.174999999999997 27.96 27.505000000000003 19.36 140-144 25.264999999999997 27.310000000000002 26.86 20.565 145-149 26.064999999999998 27.685 27.339999999999996 18.91 150-151 26.924999999999997 28.125 26.125 18.825 >>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 0.5 6 0.5 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 0.5 17 1.0 18 0.5 19 0.5 20 0.5 21 1.5 22 2.0 23 2.0 24 3.5 25 3.5 26 5.5 27 9.5 28 11.0 29 11.0 30 18.5 31 25.0 32 30.5 33 38.5 34 53.5 35 77.5 36 85.0 37 110.0 38 159.5 39 176.5 40 199.0 41 247.0 42 293.5 43 294.0 44 266.0 45 261.0 46 252.5 47 234.5 48 200.5 49 174.0 50 157.0 51 129.0 52 103.5 53 82.5 54 68.5 55 58.0 56 40.5 57 27.5 58 22.0 59 16.5 60 10.0 61 6.5 62 5.0 63 4.5 64 5.5 65 3.0 66 1.5 67 2.0 68 1.0 69 0.0 70 1.0 71 1.0 72 0.0 73 0.0 74 0.5 75 0.5 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.5 96 0.5 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 0.0 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 91.55 #Duplication Level Percentage of deduplicated Percentage of total 1 92.10813762971054 84.325 2 6.963407973784817 12.75 3 0.7373020207536866 2.025 4 0.1365374112506827 0.5 5 0.027307482250136534 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.027307482250136534 0.27499999999999997 >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 GTTGCATTTATCTAAAGTATTGTCACTTTACTTAACACTTGAGCTGCATA 11 0.27499999999999997 No Hit GAAGTGGGGCACATTGGGAGCACTATAACGTGAGCGAGGACCCTTCCTTC 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 0.0 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 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.1625 0.0 0.0 0.0 0.0 82-83 0.3875 0.0 0.0 0.0 0.0 84-85 0.425 0.0 0.0 0.0 0.0 86-87 0.5 0.0 0.0 0.0 0.0 88-89 0.6 0.0 0.0 0.0 0.0 90-91 0.7375 0.0 0.0 0.0 0.0 92-93 0.9125 0.0 0.0 0.0 0.0 94-95 1.15 0.0 0.0 0.0 0.0 96-97 1.375 0.0 0.0 0.0 0.0 98-99 1.5875 0.0 0.0 0.0 0.0 100-101 1.7 0.0 0.0 0.0 0.0 102-103 1.8375 0.0 0.0 0.0 0.0 104-105 2.3625 0.0 0.0 0.0 0.0 106-107 2.575 0.0 0.0 0.0 0.0 108-109 2.8 0.0 0.0 0.0 0.0 110-111 3.05 0.0 0.0 0.0 0.0 112-113 3.4625000000000004 0.0 0.0 0.0 0.0 114-115 3.9375 0.0 0.0 0.0 0.0 116-117 4.475 0.0 0.0 0.0 0.0 118-119 5.025 0.0 0.0 0.0 0.0 120-121 5.525 0.0 0.0 0.0 0.0 122-123 6.050000000000001 0.0 0.0 0.0 0.0 124-125 6.5875 0.0 0.0 0.0 0.0 126-127 7.225 0.0 0.0 0.0 0.0 128-129 7.9 0.0 0.0 0.0 0.0 130-131 8.3875 0.0 0.0 0.0 0.0 132-133 8.9875 0.0 0.0 0.0 0.0 134-135 9.625 0.0 0.0 0.0 0.0 136-137 10.2375 0.0 0.0 0.0 0.0 138-139 11.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTAAGT 10 0.006830828 145.0 9 >>END_MODULE Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705935 spots for SRR12919360.sra Written 705935 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra Read 705927 spots for SRR12919360.sra Written 705927 spots for SRR12919360.sra SRR ids: ['SRR12919360.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_quci36ug SRR12919360.sra spots: 14118548 blocks: [[1, 705927], [705928, 1411854], [1411855, 2117781], [2117782, 2823708], [2823709, 3529635], [3529636, 4235562], [4235563, 4941489], [4941490, 5647416], [5647417, 6353343], [6353344, 7059270], [7059271, 7765197], [7765198, 8471124], [8471125, 9177051], [9177052, 9882978], [9882979, 10588905], [10588906, 11294832], [11294833, 12000759], [12000760, 12706686], [12706687, 13412613], [13412614, 14118548]] SRR12919360 file size 4776399 SRR12919360 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 SRR12919360 SRR12919360_1.fastq SRR12919360_2.fastq Input file: SRR12919360_1.fastq Paired file: SRR12919360_2.fastq trimmed: SRR12919360-trimmed-pair1.fastq, SRR12919360-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 Wed Feb 12 20:36:39 2025 >> started Wed Feb 12 20:36:55 2025 >> done (15.796s) 14118548 read pairs processed; of these: 18 ( 0.00%) short read pairs filtered out after trimming by size control 201 ( 0.00%) empty read pairs filtered out after trimming by size control 14118329 (100.00%) read pairs available; of these: 2293939 (16.25%) trimmed read pairs available after processing 11824390 (83.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 3 0.00% 20 7 0.00% 21 2 0.00% 22 2 0.00% 23 6 0.00% 24 5 0.00% 25 5 0.00% 26 9 0.00% 27 7 0.00% 28 7 0.00% 29 7 0.00% 30 7 0.00% 31 14 0.00% 32 8 0.00% 33 14 0.00% 34 12 0.00% 35 18 0.00% 36 10 0.00% 37 11 0.00% 38 10 0.00% 39 23 0.00% 40 13 0.00% 41 18 0.00% 42 28 0.00% 43 23 0.00% 44 24 0.00% 45 31 0.00% 46 23 0.00% 47 34 0.00% 48 46 0.00% 49 58 0.00% 50 64 0.00% 51 64 0.00% 52 83 0.00% 53 77 0.00% 54 94 0.00% 55 78 0.00% 56 115 0.00% 57 153 0.00% 58 154 0.00% 59 169 0.00% 60 244 0.00% 61 339 0.00% 62 331 0.00% 63 394 0.00% 64 356 0.00% 65 504 0.00% 66 474 0.00% 67 618 0.00% 68 706 0.01% 69 785 0.01% 70 945 0.01% 71 1133 0.01% 72 1343 0.01% 73 1573 0.01% 74 1713 0.01% 75 1901 0.01% 76 2131 0.02% 77 2321 0.02% 78 2537 0.02% 79 3100 0.02% 80 3456 0.02% 81 4214 0.03% 82 4768 0.03% 83 5263 0.04% 84 5856 0.04% 85 6397 0.05% 86 6691 0.05% 87 7228 0.05% 88 7672 0.05% 89 8544 0.06% 90 9536 0.07% 91 10556 0.07% 92 11612 0.08% 93 12833 0.09% 94 14096 0.10% 95 14693 0.10% 96 15725 0.11% 97 16355 0.12% 98 16688 0.12% 99 17959 0.13% 100 19027 0.13% 101 19944 0.14% 102 21804 0.15% 103 23274 0.16% 104 24802 0.18% 105 25986 0.18% 106 26516 0.19% 107 26694 0.19% 108 27751 0.20% 109 28442 0.20% 110 29039 0.21% 111 30216 0.21% 112 31838 0.23% 113 32970 0.23% 114 34664 0.25% 115 35846 0.25% 116 36181 0.26% 117 36815 0.26% 118 37099 0.26% 119 37265 0.26% 120 37956 0.27% 121 38773 0.27% 122 39653 0.28% 123 41502 0.29% 124 43188 0.31% 125 43847 0.31% 126 44512 0.32% 127 44314 0.31% 128 44499 0.32% 129 44663 0.32% 130 45107 0.32% 131 44986 0.32% 132 46314 0.33% 133 47670 0.34% 134 48052 0.34% 135 49406 0.35% 136 50138 0.36% 137 50728 0.36% 138 50358 0.36% 139 49942 0.35% 140 49849 0.35% 141 50355 0.36% 142 51601 0.37% 143 50958 0.36% 144 52904 0.37% 145 53517 0.38% 146 54017 0.38% 147 54054 0.38% 148 52898 0.37% 149 53544 0.38% 150 53334 0.38% 151 11824390 83.75% 14118329 reads passed initial QC criterion=sequence-density sequence-density=0.82 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=33 prefix-density=0.82 prefix-fanout=2.0 sequence=GGAATTGAATTAATGAACTTGGTGGCAGCAAGGAAGGCGTTGTAGGAGGCTAAATAGCTAACTCCAGAGTCTGAACT criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=146.63 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=13.9 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTG criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=36 prefix-density=0.54 prefix-fanout=2.0 sequence=TGTCAAATGAAAAGCTCTTCGTGGTGTTCCAAGGTGTTTCAAATGTAGCTGGTGAAACAAGTTCAGACTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=29 fanout-score=27.82 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=9.9 sequence=AAGGCCAAGATCCAGGACAAGGA SRR12919360 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 20:37:54 Started mapping on | Feb 12 20:37:55 Finished on | Feb 12 20:39:51 Mapping speed, Million of reads per hour | 438.16 Number of input reads | 14118329 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 12848872 Uniquely mapped reads % | 91.01% Average mapped length | 292.17 Number of splices: Total | 11881369 Number of splices: Annotated (sjdb) | 11578047 Number of splices: GT/AG | 11665574 Number of splices: GC/AG | 167194 Number of splices: AT/AC | 11210 Number of splices: Non-canonical | 37391 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.85 Insertion rate per base | 0.03% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 375088 % of reads mapped to multiple loci | 2.66% Number of reads mapped to too many loci | 158025 % of reads mapped to too many loci | 1.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.96% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 894369 894369 894369 N_multimapping 375088 375088 375088 N_noFeature 524981 12703686 590231 N_ambiguous 175232 651 94985 UnstrandedReadsAssigned:12148659 PositiveStrandReadsAssigned:144535 NegativeStrandReadsAssigned:12163656 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12919360 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: SRR12919360-trimmed-pair1.fastq SRR12919360-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,118,329 reads, 12,182,565 reads pseudoaligned [quant] estimated average fragment length: 244.977 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,081 rounds 52401 SRR12919360.ke.tsv 34699 SRR12919360.se.tsv 87100 total ==> SRR12919360.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1774.02 405 21.0375 Potri.005G024800.1.v4.1 1035 791.023 205 23.8816 Potri.004G059700.1.v4.1 961 717.198 16 2.05579 Potri.007G009000.2.v4.1 1416 1172.02 0 0 Potri.003G141000.2.v4.1 2943 2699.02 506.899 17.3066 Potri.016G087400.1.v4.1 270 95.5178 815.046 786.314 Potri.015G069301.1.v4.1 564 333.849 0 0 Potri.010G195200.1.v4.1 1773 1529.02 131 7.89506 Potri.012G127500.1.v4.1 977 733.12 3206 402.983 ==> SRR12919360.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 129 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 158 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 2 SRR12919360 completed mapping pipeline successfully