Starting /dee2/code/volunteer_pipeline.sh SRR12951298 current disk space = 1543393419264 free memory = 1603835620 SRR12951298 SRAfilesize f1653349c14798b6b127cef374c798b6 SRR12951298.sra SRR12951298.sra file validated SRR12951298 is paired end SRR12951298 is conventional basespace SRR12951298 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951298_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5735 37.0 37.0 37.0 37.0 37.0 2 36.251 37.0 37.0 37.0 37.0 37.0 3 36.5295 37.0 37.0 37.0 37.0 37.0 4 36.626 37.0 37.0 37.0 37.0 37.0 5 36.669 37.0 37.0 37.0 37.0 37.0 6 36.6245 37.0 37.0 37.0 37.0 37.0 7 36.473 37.0 37.0 37.0 37.0 37.0 8 36.589 37.0 37.0 37.0 37.0 37.0 9 36.6325 37.0 37.0 37.0 37.0 37.0 10-14 36.576 37.0 37.0 37.0 37.0 37.0 15-19 36.5696 37.0 37.0 37.0 37.0 37.0 20-24 36.5663 37.0 37.0 37.0 37.0 37.0 25-29 36.5098 37.0 37.0 37.0 37.0 37.0 30-34 36.5468 37.0 37.0 37.0 37.0 37.0 35-39 36.5221 37.0 37.0 37.0 37.0 37.0 40-44 36.5129 37.0 37.0 37.0 37.0 37.0 45-49 36.4392 37.0 37.0 37.0 37.0 37.0 50-54 36.453900000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.42 37.0 37.0 37.0 37.0 37.0 60-64 36.341699999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.2993 37.0 37.0 37.0 37.0 37.0 70-74 36.32880000000001 37.0 37.0 37.0 37.0 37.0 75-79 36.302 37.0 37.0 37.0 37.0 37.0 80-84 36.2873 37.0 37.0 37.0 37.0 37.0 85-89 36.259299999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.28920000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.2777 37.0 37.0 37.0 37.0 37.0 100-104 36.288799999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.249700000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.164500000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.1686 37.0 37.0 37.0 37.0 37.0 120-124 36.1053 37.0 37.0 37.0 37.0 37.0 125-129 36.008700000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.959799999999994 37.0 37.0 37.0 37.0 37.0 135-139 35.7741 37.0 37.0 37.0 37.0 37.0 140-144 35.553999999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.3859 37.0 37.0 37.0 37.0 37.0 150-151 35.125 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 3.0 25 4.0 26 2.0 27 5.0 28 11.0 29 18.0 30 27.0 31 23.0 32 61.0 33 97.0 34 138.0 35 299.0 36 2800.0 37 511.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.475 10.5 4.6 38.425 2 20.080321285140563 11.194779116465863 35.21586345381526 33.50903614457831 3 19.75 12.775 26.025 41.449999999999996 4 27.400000000000002 19.900000000000002 21.575 31.125000000000004 5 27.775 26.125 23.575 22.525000000000002 6 25.7 28.625 23.125 22.55 7 19.175 25.775 35.475 19.575 8 19.675 23.925 30.099999999999998 26.3 9 21.025 21.099999999999998 33.7 24.175 10-14 23.54 25.955000000000002 24.82 25.685000000000002 15-19 24.205 24.245 24.955 26.595000000000002 20-24 23.705000000000002 25.005 24.795 26.495 25-29 23.835 25.105 25.095 25.965 30-34 23.39 25.174999999999997 24.695 26.740000000000002 35-39 23.35 24.385 25.419999999999998 26.845000000000002 40-44 23.025000000000002 25.655 25.174999999999997 26.145000000000003 45-49 24.165 24.43 24.975 26.43 50-54 24.215 24.705 24.325 26.755000000000003 55-59 24.060000000000002 25.155 24.43 26.355 60-64 24.18 24.945 24.355 26.52 65-69 24.52 24.485 24.834999999999997 26.16 70-74 25.05 24.365000000000002 24.05 26.534999999999997 75-79 24.654999999999998 24.455 24.36 26.529999999999998 80-84 24.87 24.41 25.03 25.69 85-89 24.605 25.080000000000002 24.654999999999998 25.66 90-94 25.35 24.535 24.605 25.509999999999998 95-99 24.795 24.675 23.935000000000002 26.595000000000002 100-104 25.009999999999998 25.3 23.66 26.029999999999998 105-109 25.045 24.555 23.505000000000003 26.895000000000003 110-114 25.27 24.349999999999998 24.605 25.775 115-119 25.295 25.3 23.39 26.015 120-124 25.345000000000002 24.865000000000002 23.355 26.435 125-129 25.3 24.88 23.085 26.735 130-134 25.169999999999998 25.28 23.135 26.415 135-139 25.285000000000004 25.255 23.325000000000003 26.135 140-144 25.290000000000003 24.68 23.445 26.584999999999997 145-149 25.590000000000003 24.425 23.94 26.045 150-151 26.2875 24.224999999999998 23.400000000000002 26.087500000000002 >>END_MODULE >>Per sequence GC content fail #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 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 1.0 26 1.0 27 2.5 28 2.5 29 1.5 30 5.0 31 7.0 32 10.5 33 14.0 34 16.5 35 35.5 36 52.0 37 59.5 38 71.0 39 87.5 40 110.0 41 131.5 42 143.0 43 157.5 44 170.5 45 179.5 46 177.5 47 183.5 48 195.5 49 177.5 50 173.5 51 158.0 52 134.5 53 125.0 54 106.5 55 101.0 56 98.5 57 84.0 58 77.5 59 84.5 60 79.0 61 72.0 62 67.0 63 65.5 64 67.5 65 55.5 66 50.5 67 59.5 68 61.5 69 56.5 70 50.5 71 45.5 72 35.0 73 21.5 74 18.5 75 17.0 76 15.0 77 12.5 78 6.5 79 2.5 80 3.0 81 1.5 82 0.5 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 0.4 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 82.375 #Duplication Level Percentage of deduplicated Percentage of total 1 83.15629742033383 68.5 2 13.474962063732928 22.2 3 2.488619119878604 6.15 4 0.637329286798179 2.1 5 0.1820940819423369 0.75 6 0.06069802731411229 0.3 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 TATCAACATGTGCTGCGAGGCTGGCAATTCCATGCTCAACTCCTGAATTT 6 0.15 No Hit CCAGTAGAGATACCATGGTGGTTCTGGCGCAGTTGCGTCACAGATATGGC 6 0.15 No Hit AACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCAC 5 0.125 No Hit GTGGGGTTCACTTCGATCTGGAAGCTGGAGCCCTTGAGCGTCTTCACGGA 5 0.125 No Hit GCTGGTTTTCTGTCTGCCTCACTGGAGCCTTGAATCCCTTCTAGGATAGA 5 0.125 No Hit GTCAATCTTTGGTGCCTCCCATTCACCATCTTCCTCATCATCCCAATCTT 5 0.125 No Hit GCCTCTTGGACTTCAGCTCGACGAACCTCAGGTTGCAGTCATCATGCACT 5 0.125 No Hit CGGGGGCGGCACGCGGCGGGCGGAGGGCATCATCGCGTTGGTTGTGGGAG 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 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.0625 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.16249999999999998 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.4 0.0 0.0 0.0 0.0 70-71 0.4125 0.0 0.0 0.0 0.0 72-73 0.4375 0.0 0.0 0.0 0.0 74-75 0.475 0.0 0.0 0.0 0.0 76-77 0.575 0.0 0.0 0.0 0.0 78-79 0.625 0.0 0.0 0.0 0.0 80-81 0.85 0.0 0.0 0.0 0.0 82-83 0.975 0.0 0.0 0.0 0.0 84-85 1.1125 0.0 0.0 0.0 0.0 86-87 1.325 0.0 0.0 0.0 0.0 88-89 1.675 0.0 0.0 0.0 0.0 90-91 2.1 0.0 0.0 0.0 0.0 92-93 2.5375 0.0 0.0 0.0 0.0 94-95 2.7625 0.0 0.0 0.0 0.0 96-97 3.2625 0.0 0.0 0.0 0.0 98-99 3.7750000000000004 0.0 0.0 0.0 0.0 100-101 4.275 0.0 0.0 0.0 0.0 102-103 4.725 0.0 0.0 0.0 0.0 104-105 5.0125 0.0 0.0 0.0 0.0 106-107 5.449999999999999 0.0 0.0 0.0 0.0 108-109 6.3125 0.0 0.0 0.0 0.0 110-111 6.887499999999999 0.0 0.0 0.0 0.0 112-113 7.5 0.0 0.0 0.0 0.0 114-115 8.1625 0.0 0.0 0.0 0.0 116-117 8.8125 0.0 0.0 0.0 0.0 118-119 9.5 0.0 0.0 0.0 0.0 120-121 10.3 0.0 0.0 0.0 0.0 122-123 10.9375 0.0 0.0 0.0 0.0 124-125 11.675 0.0 0.0 0.0 0.0 126-127 12.35 0.0 0.0 0.0 0.0 128-129 13.212499999999999 0.0 0.0 0.0 0.0 130-131 14.1 0.0 0.0 0.0 0.0 132-133 15.100000000000001 0.0 0.0 0.0 0.0 134-135 15.7 0.0 0.0 0.0 0.0 136-137 16.425 0.0 0.0 0.0 0.0 138-139 17.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCTGGT 10 0.006830828 145.0 1 GTCGGGT 10 0.006830828 145.0 1 >>END_MODULE SRR12951298 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951298_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.222 37.0 37.0 37.0 37.0 37.0 2 36.2695 37.0 37.0 37.0 37.0 37.0 3 36.225 37.0 37.0 37.0 37.0 37.0 4 36.3595 37.0 37.0 37.0 37.0 37.0 5 36.4275 37.0 37.0 37.0 37.0 37.0 6 36.3515 37.0 37.0 37.0 37.0 37.0 7 36.33 37.0 37.0 37.0 37.0 37.0 8 36.397 37.0 37.0 37.0 37.0 37.0 9 36.342 37.0 37.0 37.0 37.0 37.0 10-14 36.3692 37.0 37.0 37.0 37.0 37.0 15-19 36.351000000000006 37.0 37.0 37.0 37.0 37.0 20-24 36.308299999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.285 37.0 37.0 37.0 37.0 37.0 30-34 36.2411 37.0 37.0 37.0 37.0 37.0 35-39 36.193200000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.2023 37.0 37.0 37.0 37.0 37.0 45-49 36.242599999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.12329999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.10600000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.129000000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.035199999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.0153 37.0 37.0 37.0 37.0 37.0 75-79 36.0281 37.0 37.0 37.0 37.0 37.0 80-84 36.0128 37.0 37.0 37.0 37.0 37.0 85-89 35.9524 37.0 37.0 37.0 37.0 37.0 90-94 35.9796 37.0 37.0 37.0 37.0 37.0 95-99 35.9241 37.0 37.0 37.0 37.0 37.0 100-104 35.8407 37.0 37.0 37.0 37.0 37.0 105-109 35.88 37.0 37.0 37.0 37.0 37.0 110-114 35.7902 37.0 37.0 37.0 37.0 37.0 115-119 35.8424 37.0 37.0 37.0 37.0 37.0 120-124 35.74980000000001 37.0 37.0 37.0 37.0 37.0 125-129 35.6016 37.0 37.0 37.0 37.0 37.0 130-134 35.446 37.0 37.0 37.0 34.6 37.0 135-139 35.3018 37.0 37.0 37.0 37.0 37.0 140-144 35.1423 37.0 37.0 37.0 34.6 37.0 145-149 34.9864 37.0 37.0 37.0 25.0 37.0 150-151 34.79625 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 3.0 14 5.0 15 2.0 16 0.0 17 2.0 18 0.0 19 1.0 20 2.0 21 7.0 22 5.0 23 6.0 24 7.0 25 8.0 26 9.0 27 12.0 28 10.0 29 19.0 30 28.0 31 25.0 32 44.0 33 90.0 34 194.0 35 473.0 36 2680.0 37 366.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.225 21.45 7.475 31.85 2 30.15 22.725 27.400000000000002 19.725 3 22.175 24.3 30.025000000000002 23.5 4 26.85 29.049999999999997 20.75 23.35 5 29.425 30.5 18.5 21.575 6 24.45 34.35 19.025 22.175 7 22.6 20.0 33.975 23.425 8 24.675 21.725 23.599999999999998 30.0 9 23.474999999999998 23.45 27.0 26.075 10-14 26.674999999999997 25.0 22.259999999999998 26.064999999999998 15-19 26.205000000000002 24.42 23.32 26.055 20-24 25.705 25.515 23.14 25.64 25-29 26.395000000000003 24.365000000000002 23.855 25.385 30-34 25.96 24.85 23.98 25.21 35-39 26.674999999999997 24.54 23.880000000000003 24.905 40-44 25.775 25.305 23.575 25.345000000000002 45-49 26.400000000000002 24.82 23.94 24.84 50-54 26.125 23.72 24.33 25.825 55-59 26.395000000000003 24.154999999999998 23.79 25.66 60-64 26.700000000000003 23.96 23.880000000000003 25.46 65-69 26.345000000000002 24.52 23.79 25.345000000000002 70-74 27.089999999999996 23.919999999999998 23.845 25.145 75-79 27.115000000000002 23.96 24.25 24.675 80-84 27.16 24.675 23.810000000000002 24.355 85-89 27.339999999999996 24.89 23.125 24.645 90-94 27.01 24.805 23.435 24.75 95-99 27.560000000000002 24.805 23.66 23.974999999999998 100-104 27.445000000000004 24.12 24.11 24.325 105-109 27.975 24.610000000000003 23.535 23.880000000000003 110-114 28.64 24.75 22.985 23.625 115-119 28.51 25.2 22.830000000000002 23.46 120-124 29.299999999999997 24.515 22.215 23.97 125-129 28.884999999999998 25.180000000000003 22.825 23.11 130-134 29.75 25.085 22.495 22.67 135-139 30.495 25.455 22.314999999999998 21.735 140-144 31.47 24.93 22.220000000000002 21.38 145-149 31.230000000000004 25.215 22.195 21.36 150-151 32.6625 24.675 22.025 20.6375 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 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 0.5 18 0.5 19 0.0 20 0.5 21 1.0 22 0.5 23 1.5 24 1.5 25 0.5 26 3.0 27 2.5 28 0.5 29 1.5 30 5.0 31 11.5 32 13.0 33 17.0 34 26.5 35 25.0 36 30.0 37 53.5 38 61.5 39 76.0 40 108.0 41 133.0 42 141.0 43 143.0 44 158.5 45 188.5 46 188.5 47 184.5 48 169.0 49 139.5 50 135.5 51 133.5 52 123.5 53 113.5 54 118.0 55 112.0 56 96.5 57 87.5 58 84.5 59 91.0 60 92.5 61 77.5 62 68.0 63 65.0 64 66.5 65 66.0 66 64.0 67 70.5 68 73.5 69 62.5 70 56.0 71 58.5 72 46.5 73 34.0 74 27.0 75 20.5 76 15.5 77 14.5 78 13.5 79 3.0 80 2.0 81 2.5 82 1.0 83 1.0 84 1.0 85 0.5 86 0.5 87 1.0 88 0.5 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 1.5 98 2.5 99 2.0 100 3.0 >>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 82.475 #Duplication Level Percentage of deduplicated Percentage of total 1 83.66171567141558 69.0 2 12.88269172476508 21.25 3 2.5159139133070627 6.225 4 0.6062443164595333 2.0 5 0.2121855107608366 0.8750000000000001 6 0.06062443164595332 0.3 7 0.06062443164595332 0.35000000000000003 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 GCCTCTTCTCGCTTGCTCTACCTGCTGCTTGCAACCATGGCACCCACCGT 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit CTGGCTCATTATGAGTTATACACTGAAGCTCGCCTCTCGCCTCTCTCGCT 6 0.15 No Hit GTCTGACCTGAGCATGGTTAAGACACTAAGTCTCGCTATAGTTCGAACAA 6 0.15 No Hit AAAAGGACTTGCCTACCTTCACAGTGCAGAGGCCAAAGTTATTTATAGGG 5 0.125 No Hit ACCACCTCGCCATGACGACTTCCCCTCCTTCTCCCACAACCAACGCGATG 5 0.125 No Hit AAACTCGCCGCCTCCTTCCCCTCCGCCCTCGTCTCGACCTCGACGCGAAG 5 0.125 No Hit AAGACTGGCAAGTATGTTGAACATCATCTCAAGTTCCCACCATCTGTACC 5 0.125 No Hit ACTTGTTCCGCAGCAACTCTCTCCTCTAGCTAGAACACCACCACAGCATC 5 0.125 No Hit GAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAA 5 0.125 No Hit CAGCATCCTACTGTCAGTTGTCACACACACACACACAGGTGTGTAAGCCA 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 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.0625 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.16249999999999998 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.4 0.0 0.0 0.0 0.0 70-71 0.4125 0.0 0.0 0.0 0.0 72-73 0.4375 0.0 0.0 0.0 0.0 74-75 0.5 0.0 0.0 0.0 0.0 76-77 0.6 0.0 0.0 0.0 0.0 78-79 0.65 0.0 0.0 0.0 0.0 80-81 0.875 0.0 0.0 0.0 0.0 82-83 1.0 0.0 0.0 0.0 0.0 84-85 1.1375 0.0 0.0 0.0 0.0 86-87 1.375 0.0 0.0 0.0 0.0 88-89 1.725 0.0 0.0 0.0 0.0 90-91 2.15 0.0 0.0 0.0 0.0 92-93 2.5875 0.0 0.0 0.0 0.0 94-95 2.8125 0.0 0.0 0.0 0.0 96-97 3.3125 0.0 0.0 0.0 0.0 98-99 3.825 0.0 0.0 0.0 0.0 100-101 4.3375 0.0 0.0 0.0 0.0 102-103 4.800000000000001 0.0 0.0 0.0 0.0 104-105 5.0875 0.0 0.0 0.0 0.0 106-107 5.5125 0.0 0.0 0.0 0.0 108-109 6.3375 0.0 0.0 0.0 0.0 110-111 6.875 0.0 0.0 0.0 0.0 112-113 7.487500000000001 0.0 0.0 0.0 0.0 114-115 8.15 0.0 0.0 0.0 0.0 116-117 8.7875 0.0 0.0 0.0 0.0 118-119 9.475000000000001 0.0 0.0 0.0 0.0 120-121 10.3125 0.0 0.0 0.0 0.0 122-123 10.9625 0.0 0.0 0.0 0.0 124-125 11.6875 0.0 0.0 0.0 0.0 126-127 12.375 0.0 0.0 0.0 0.0 128-129 13.225 0.0 0.0 0.0 0.0 130-131 14.125 0.0 0.0 0.0 0.0 132-133 15.1375 0.0 0.0 0.0 0.0 134-135 15.75 0.0 0.0 0.0 0.0 136-137 16.45 0.0 0.0 0.0 0.0 138-139 17.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCCTCC 10 0.006830828 145.0 9 >>END_MODULE Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449027 spots for SRR12951298.sra Written 1449027 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra Read 1449019 spots for SRR12951298.sra Written 1449019 spots for SRR12951298.sra SRR ids: ['SRR12951298.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4l1jxlr5 SRR12951298.sra spots: 28980388 blocks: [[1, 1449019], [1449020, 2898038], [2898039, 4347057], [4347058, 5796076], [5796077, 7245095], [7245096, 8694114], [8694115, 10143133], [10143134, 11592152], [11592153, 13041171], [13041172, 14490190], [14490191, 15939209], [15939210, 17388228], [17388229, 18837247], [18837248, 20286266], [20286267, 21735285], [21735286, 23184304], [23184305, 24633323], [24633324, 26082342], [26082343, 27531361], [27531362, 28980388]] SRR12951298 file size 9827103 SRR12951298 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 SRR12951298 SRR12951298_1.fastq SRR12951298_2.fastq Input file: SRR12951298_1.fastq Paired file: SRR12951298_2.fastq trimmed: SRR12951298-trimmed-pair1.fastq, SRR12951298-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 Sat Dec 7 11:01:19 2024 >> started Sat Dec 7 11:01:49 2024 >> done (29.954s) 28980388 read pairs processed; of these: 221 ( 0.00%) short read pairs filtered out after trimming by size control 72452 ( 0.25%) empty read pairs filtered out after trimming by size control 28907715 (99.75%) read pairs available; of these: 6310519 (21.83%) trimmed read pairs available after processing 22597196 (78.17%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 11 0.00% 20 11 0.00% 21 22 0.00% 22 32 0.00% 23 29 0.00% 24 30 0.00% 25 37 0.00% 26 33 0.00% 27 50 0.00% 28 50 0.00% 29 54 0.00% 30 49 0.00% 31 78 0.00% 32 71 0.00% 33 74 0.00% 34 68 0.00% 35 87 0.00% 36 99 0.00% 37 84 0.00% 38 105 0.00% 39 88 0.00% 40 134 0.00% 41 124 0.00% 42 130 0.00% 43 134 0.00% 44 142 0.00% 45 174 0.00% 46 159 0.00% 47 193 0.00% 48 258 0.00% 49 302 0.00% 50 372 0.00% 51 416 0.00% 52 459 0.00% 53 467 0.00% 54 520 0.00% 55 624 0.00% 56 639 0.00% 57 805 0.00% 58 958 0.00% 59 1121 0.00% 60 1286 0.00% 61 1570 0.01% 62 1805 0.01% 63 2015 0.01% 64 2295 0.01% 65 2426 0.01% 66 2786 0.01% 67 3033 0.01% 68 3643 0.01% 69 4226 0.01% 70 4992 0.02% 71 5615 0.02% 72 6693 0.02% 73 7722 0.03% 74 8460 0.03% 75 9419 0.03% 76 10530 0.04% 77 11075 0.04% 78 12597 0.04% 79 14007 0.05% 80 15438 0.05% 81 17369 0.06% 82 19467 0.07% 83 21646 0.07% 84 23964 0.08% 85 26522 0.09% 86 28004 0.10% 87 30107 0.10% 88 31849 0.11% 89 33994 0.12% 90 36037 0.12% 91 38978 0.13% 92 41395 0.14% 93 44771 0.15% 94 48086 0.17% 95 50569 0.17% 96 53361 0.18% 97 55913 0.19% 98 56802 0.20% 99 59883 0.21% 100 62115 0.21% 101 64705 0.22% 102 66960 0.23% 103 69961 0.24% 104 73076 0.25% 105 75390 0.26% 106 78173 0.27% 107 80228 0.28% 108 81172 0.28% 109 83202 0.29% 110 84944 0.29% 111 86528 0.30% 112 90288 0.31% 113 91645 0.32% 114 94341 0.33% 115 97899 0.34% 116 98855 0.34% 117 101131 0.35% 118 102761 0.36% 119 103021 0.36% 120 104474 0.36% 121 106194 0.37% 122 106878 0.37% 123 109791 0.38% 124 112565 0.39% 125 113070 0.39% 126 115201 0.40% 127 116686 0.40% 128 116572 0.40% 129 117935 0.41% 130 118888 0.41% 131 117431 0.41% 132 121533 0.42% 133 122096 0.42% 134 121790 0.42% 135 124673 0.43% 136 124842 0.43% 137 124179 0.43% 138 125061 0.43% 139 127620 0.44% 140 127184 0.44% 141 126292 0.44% 142 128825 0.45% 143 127683 0.44% 144 128145 0.44% 145 129608 0.45% 146 129044 0.45% 147 129927 0.45% 148 130001 0.45% 149 130392 0.45% 150 129896 0.45% 151 22597196 78.17% 28907715 reads passed initial QC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=29 prefix-density=0.40 prefix-fanout=2.0 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.05 sequence-density-rank=29 fanout-score=310.17 fanout-score-rank=1 prefix-density=0.74 prefix-fanout=19.1 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=3.87 fanout-score-rank=20 prefix-density=0.39 prefix-fanout=3.5 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=181.84 fanout-score-rank=1 prefix-density=0.21 prefix-fanout=13.0 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR12951298 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:02:29 Started mapping on | Dec 07 11:02:29 Finished on | Dec 07 11:04:59 Mapping speed, Million of reads per hour | 693.79 Number of input reads | 28907715 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 27407318 Uniquely mapped reads % | 94.81% Average mapped length | 288.68 Number of splices: Total | 27145072 Number of splices: Annotated (sjdb) | 25434141 Number of splices: GT/AG | 26774948 Number of splices: GC/AG | 308791 Number of splices: AT/AC | 16323 Number of splices: Non-canonical | 45010 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.01% Deletion average length | 2.67 Insertion rate per base | 0.01% Insertion average length | 2.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 334706 % of reads mapped to multiple loci | 1.16% Number of reads mapped to too many loci | 83413 % of reads mapped to too many loci | 0.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.30% % of reads unmapped: other | 1.45% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1165691 1165691 1165691 N_multimapping 334706 334706 334706 N_noFeature 986358 26706193 1212925 N_ambiguous 564447 3999 91369 UnstrandedReadsAssigned:25856513 PositiveStrandReadsAssigned:697126 NegativeStrandReadsAssigned:26103024 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=145 echo kmer=141 SRR12951298 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12951298-trimmed-pair1.fastq SRR12951298-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,907,715 reads, 26,388,944 reads pseudoaligned [quant] estimated average fragment length: 234.557 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,200 rounds 52973 SRR12951298.ke.tsv 35125 SRR12951298.se.tsv 88098 total ==> SRR12951298.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 702.896 0 0 PNS24247 1044 810.443 79.9274 5.47804 PNS24249 1928 1694.44 262.965 8.6203 PNS24246 1044 810.443 79.9274 5.47804 PNS24248 1044 810.443 79.9274 5.47804 PNS24244 1471 1237.44 86.2529 3.87168 PNS24243 293 114.961 0 0 KQK14069 1603 1369.44 1635.96 66.356 KQK14071 474 260.539 42.4198 9.04371 ==> SRR12951298.se.tsv <== BRADI_1g14170v3 1745 BRADI_1g53295v3 52 BRADI_1g59795v3 560 BRADI_1g07683v3 0 BRADI_1g00485v3 66 BRADI_1g20270v3 3735 BRADI_1g74790v3 265 BRADI_1g09890v3 14 BRADI_1g77505v3 508 BRADI_1g48960v3 0 SRR12951298 completed mapping pipeline successfully