Starting /dee2/code/volunteer_pipeline.sh SRR6958458 current disk space = 1547640016896 free memory = 1593045416 SRR6958458 SRAfilesize 4fb0ad1be76ab0b40a07284a7ecf1ff4 SRR6958458.sra SRR6958458.sra file validated SRR6958458 is paired end SRR6958458 is conventional basespace SRR6958458 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958458_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.11975 33.0 31.0 33.0 18.0 33.0 2 31.41875 33.0 31.0 33.0 27.0 34.0 3 30.689 33.0 29.0 33.0 27.0 33.0 4 31.76525 33.0 32.0 33.0 30.0 34.0 5 32.241 33.0 32.0 33.0 31.0 34.0 6 36.2215 38.0 37.0 38.0 33.0 38.0 7 36.50775 38.0 38.0 38.0 34.0 38.0 8 37.05175 38.0 38.0 38.0 35.0 38.0 9 37.22075 38.0 38.0 38.0 36.0 38.0 10-14 37.31695 38.0 38.0 38.0 36.6 38.0 15-19 37.4268 38.0 38.0 38.0 37.0 38.0 20-24 37.41275 38.0 38.0 38.0 37.0 38.0 25-29 37.24115 38.0 38.0 38.0 36.6 38.0 30-34 37.1088 38.0 38.0 38.0 36.2 38.0 35-39 37.0212 38.0 38.0 38.0 36.0 38.0 40-44 37.09185 38.0 38.0 38.0 35.8 38.0 45-49 36.90815 38.0 38.0 38.0 35.4 38.0 50-54 36.7209 38.0 38.0 38.0 34.6 38.0 55-59 36.62705 38.0 38.0 38.0 34.2 38.0 60-64 36.8765 38.0 38.0 38.0 35.2 38.0 65-69 36.878499999999995 38.0 38.0 38.0 35.0 38.0 70-74 36.43415 38.0 37.8 38.0 33.8 38.0 75-79 36.2471 38.0 37.2 38.0 33.2 38.0 80-84 36.2038 38.0 37.4 38.0 33.2 38.0 85-89 36.47115 38.0 37.8 38.0 34.0 38.0 90-94 36.247350000000004 38.0 37.6 38.0 33.2 38.0 95-99 35.94195 38.0 36.8 38.0 32.0 38.0 100-104 35.371050000000004 38.0 36.2 38.0 29.4 38.0 105-109 34.98115 38.0 35.2 38.0 27.6 38.0 110-114 35.10080000000001 38.0 35.6 38.0 28.2 38.0 115-119 35.19895 38.0 35.2 38.0 28.4 38.0 120-124 34.985749999999996 38.0 35.0 38.0 27.8 38.0 125-129 34.814499999999995 38.0 35.0 38.0 27.6 38.0 130-134 34.40185 38.0 34.4 38.0 25.0 38.0 135-139 33.93635 38.0 34.0 38.0 23.2 38.0 140-144 33.00195 37.2 33.2 38.0 18.6 38.0 145-149 31.59905 36.6 31.2 38.0 11.4 38.0 150-151 26.952125000000002 34.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 0.0 8 1.0 9 0.0 10 1.0 11 1.0 12 0.0 13 2.0 14 1.0 15 1.0 16 0.0 17 1.0 18 4.0 19 2.0 20 3.0 21 2.0 22 4.0 23 6.0 24 13.0 25 14.0 26 31.0 27 27.0 28 28.0 29 59.0 30 88.0 31 92.0 32 138.0 33 159.0 34 260.0 35 428.0 36 965.0 37 1668.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.94229206177187 11.731238146843674 9.590896775941479 35.73557301544297 2 25.35 10.975 32.125 31.55 3 21.2 14.7 26.025 38.074999999999996 4 24.45 20.674999999999997 23.599999999999998 31.275 5 25.525 26.25 23.1 25.124999999999996 6 26.075 29.675 22.525000000000002 21.725 7 18.2 25.775 37.55 18.475 8 20.775 23.7 27.950000000000003 27.575 9 21.0 22.425 30.599999999999998 25.974999999999998 10-14 22.895 26.240000000000002 25.835 25.03 15-19 22.42 25.21 25.985000000000003 26.384999999999998 20-24 22.645 25.45 25.169999999999998 26.735 25-29 22.855 25.34 25.105 26.700000000000003 30-34 23.465 24.98 25.259999999999998 26.295 35-39 23.294999999999998 24.72 25.52 26.465 40-44 23.46 25.6 24.375 26.565 45-49 23.64 24.58 24.825 26.955000000000002 50-54 22.555 25.900000000000002 24.709999999999997 26.834999999999997 55-59 23.445 24.935 25.505 26.115 60-64 23.605 25.540000000000003 24.67 26.185000000000002 65-69 23.525 24.610000000000003 25.330000000000002 26.534999999999997 70-74 23.925 25.135 24.65 26.290000000000003 75-79 24.16 24.025 24.775 27.04 80-84 23.335 25.064999999999998 24.51 27.089999999999996 85-89 23.835 24.285 25.185000000000002 26.695 90-94 24.615000000000002 24.18 24.875 26.33 95-99 24.07 24.104999999999997 25.119999999999997 26.705000000000002 100-104 24.125 24.59 25.124999999999996 26.16 105-109 24.01 24.995 24.645 26.35 110-114 23.825 24.6 24.535 27.04 115-119 23.945 24.4 25.009999999999998 26.645000000000003 120-124 24.08 25.014999999999997 24.515 26.39 125-129 24.65 24.27 24.11 26.97 130-134 24.295 24.18 24.86 26.665 135-139 24.47 24.529999999999998 24.69 26.31 140-144 24.165 24.27 24.93 26.634999999999998 145-149 24.325 24.375 24.145 27.155 150-151 24.4 24.825 24.375 26.400000000000002 >>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 0.5 6 0.5 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 0.0 18 0.5 19 0.5 20 0.0 21 0.0 22 0.5 23 0.5 24 0.0 25 0.0 26 1.5 27 2.0 28 2.5 29 6.0 30 7.5 31 9.0 32 15.5 33 20.0 34 24.5 35 32.5 36 45.5 37 63.0 38 89.0 39 112.5 40 125.5 41 135.5 42 142.5 43 172.0 44 193.5 45 188.0 46 186.0 47 180.0 48 166.0 49 160.5 50 162.0 51 148.5 52 138.0 53 129.0 54 112.5 55 105.5 56 106.5 57 95.5 58 78.5 59 72.0 60 63.0 61 58.5 62 62.0 63 55.0 64 47.5 65 52.5 66 50.0 67 44.0 68 43.5 69 46.0 70 48.0 71 40.5 72 34.0 73 29.0 74 23.0 75 22.0 76 18.0 77 13.0 78 9.5 79 5.0 80 2.0 81 1.0 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 warn #Base N-Count 1 7.725 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 99.425 #Duplication Level Percentage of deduplicated Percentage of total 1 99.49710837314558 98.925 2 0.4526024641689716 0.8999999999999999 3 0.025144581342720643 0.075 4 0.025144581342720643 0.1 5 0.0 0.0 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 pass >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0125 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.037500000000000006 0.0 0.0 0.0 0.0 88-89 0.0875 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.225 0.0 0.0 0.0 0.0 98-99 0.2625 0.0 0.0 0.0 0.0 100-101 0.35 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.44999999999999996 0.0 0.0 0.0 0.0 106-107 0.4875 0.0 0.0 0.0 0.0 108-109 0.5875 0.0 0.0 0.0 0.0 110-111 0.65 0.0 0.0 0.0 0.0 112-113 0.775 0.0 0.0 0.0 0.0 114-115 0.8625 0.0 0.0 0.0 0.0 116-117 1.0875 0.0 0.0 0.0 0.0 118-119 1.4125 0.0 0.0 0.0 0.0 120-121 1.725 0.0 0.0 0.0 0.0 122-123 1.9125 0.0 0.0 0.0 0.0 124-125 2.1375 0.0 0.0 0.0 0.0 126-127 2.4625 0.0 0.0 0.0 0.0 128-129 2.7125 0.0 0.0 0.0 0.0 130-131 2.9375 0.0 0.0 0.0 0.0 132-133 3.1500000000000004 0.0 0.0 0.0 0.0 134-135 3.5374999999999996 0.0 0.0 0.0 0.0 136-137 3.9875 0.0 0.0 0.0 0.0 138-139 4.387499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTATGCA 10 0.0051850425 158.80821 1 GGAAACA 10 0.006843168 144.91249 3 >>END_MODULE SRR6958458 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958458_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 32.2295 33.0 33.0 34.0 31.0 34.0 2 32.27825 33.0 33.0 34.0 31.0 34.0 3 32.27275 33.0 33.0 34.0 31.0 34.0 4 32.2895 33.0 33.0 34.0 31.0 34.0 5 32.22875 33.0 33.0 34.0 31.0 34.0 6 36.263 38.0 38.0 38.0 33.0 38.0 7 35.69575 38.0 37.0 38.0 30.0 38.0 8 36.40825 38.0 38.0 38.0 34.0 38.0 9 36.2515 38.0 38.0 38.0 34.0 38.0 10-14 36.325450000000004 38.0 38.0 38.0 34.0 38.0 15-19 36.5465 38.0 38.0 38.0 34.4 38.0 20-24 36.4721 38.0 38.0 38.0 34.6 38.0 25-29 36.558299999999996 38.0 38.0 38.0 35.0 38.0 30-34 36.5647 38.0 38.0 38.0 35.0 38.0 35-39 36.369600000000005 38.0 38.0 38.0 34.6 38.0 40-44 36.25085 38.0 38.0 38.0 33.8 38.0 45-49 36.11805 38.0 38.0 38.0 33.6 38.0 50-54 36.274950000000004 38.0 38.0 38.0 34.0 38.0 55-59 36.1139 38.0 38.0 38.0 33.4 38.0 60-64 35.95715 38.0 37.8 38.0 33.0 38.0 65-69 35.92635 38.0 38.0 38.0 33.0 38.0 70-74 35.7688 38.0 37.6 38.0 32.0 38.0 75-79 35.706849999999996 38.0 37.2 38.0 31.6 38.0 80-84 35.676649999999995 38.0 37.2 38.0 31.8 38.0 85-89 35.701800000000006 38.0 37.4 38.0 32.0 38.0 90-94 35.400600000000004 38.0 36.8 38.0 30.4 38.0 95-99 34.834199999999996 38.0 36.0 38.0 27.6 38.0 100-104 34.38155 38.0 35.2 38.0 24.2 38.0 105-109 34.35485 38.0 35.0 38.0 24.8 38.0 110-114 34.11955 38.0 34.6 38.0 23.6 38.0 115-119 33.999199999999995 38.0 34.8 38.0 23.2 38.0 120-124 33.83005 38.0 34.2 38.0 22.2 38.0 125-129 33.3246 38.0 34.0 38.0 18.6 38.0 130-134 32.523399999999995 38.0 33.0 38.0 14.2 38.0 135-139 32.26025 37.6 31.6 38.0 13.4 38.0 140-144 31.458199999999998 36.4 30.6 38.0 13.0 38.0 145-149 29.96215 36.0 29.4 38.0 6.4 38.0 150-151 24.029 31.0 13.5 36.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 20.0 3 11.0 4 8.0 5 4.0 6 4.0 7 3.0 8 2.0 9 3.0 10 4.0 11 2.0 12 3.0 13 4.0 14 3.0 15 2.0 16 8.0 17 9.0 18 8.0 19 5.0 20 17.0 21 11.0 22 18.0 23 16.0 24 21.0 25 25.0 26 31.0 27 37.0 28 37.0 29 62.0 30 81.0 31 101.0 32 150.0 33 173.0 34 262.0 35 422.0 36 829.0 37 1604.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.025 18.775 13.825000000000001 29.375 2 30.375000000000004 24.65 25.074999999999996 19.900000000000002 3 23.325000000000003 25.575 27.400000000000002 23.7 4 25.75 30.525000000000002 21.325 22.400000000000002 5 26.674999999999997 31.324999999999996 20.5 21.5 6 25.831457864466117 33.05826456614154 20.10502625656414 21.005251312828207 7 23.605901475368842 20.330082520630157 32.78319579894974 23.280820205051263 8 26.281570392598148 22.455613903475868 22.73068267066767 28.532133033258315 9 25.18129532383096 23.40585146286572 26.106526631657918 25.30632658164541 10-14 26.34158539634909 25.621405351337835 22.685671417854465 25.351337834458615 15-19 26.00280084025208 25.367610283084925 23.76713013904171 24.86245873762129 20-24 26.241560390097522 25.256314078519633 23.885971492873217 24.616154038509627 25-29 26.78169542385596 24.896224056014006 23.795948987246813 24.526131532883223 30-34 26.841710427606902 25.1262815703926 23.575893973493372 24.456114028507127 35-39 26.941735433858465 24.50112528132033 24.15603900975244 24.401100275068767 40-44 26.65666416604151 25.43635908977244 23.195798949737434 24.711177794448613 45-49 26.80170042510628 24.486121530382597 24.07101775443861 24.641160290072516 50-54 27.058117435230567 24.667400220066018 24.347304191257376 23.927178153446032 55-59 26.83670917729432 24.88122030507627 23.875968992248062 24.406101525381345 60-64 27.101775443860966 24.50112528132033 24.10602650662666 24.29107276819205 65-69 27.021755438859714 24.681170292573142 24.281070267566893 24.016004001000248 70-74 26.89672418104526 25.036259064766192 23.77094273568392 24.296074018504626 75-79 26.881720430107524 24.29107276819205 24.47111777944486 24.356089022255563 80-84 26.571642910727682 24.756189047261813 24.426106526631656 24.246061515378845 85-89 27.29682420605151 24.526131532883223 23.935983995999 24.241060265066267 90-94 27.136784196049014 24.711177794448613 24.36609152288072 23.785946486621658 95-99 27.286821705426355 24.646161540385098 23.58089522380595 24.486121530382597 100-104 27.09177294323581 25.241310327581896 24.04101025256314 23.625906476619154 105-109 26.500300060012 24.72994598919784 24.26485297059412 24.50490098019604 110-114 26.961740435108776 24.736184046011502 24.401100275068767 23.900975243810954 115-119 27.551887971993 24.746186546636658 23.765941485371343 23.935983995999 120-124 27.991997999499873 24.896224056014006 23.060765191297826 24.051012753188296 125-129 27.246811702925733 25.041260315078766 23.63590897724431 24.07601900475119 130-134 27.62690672668167 24.58614653663416 24.406101525381345 23.380845211302827 135-139 27.429114367155073 24.693704055608343 24.80872130819623 23.068460269040354 140-144 27.91 24.495 24.515 23.080000000000002 145-149 27.975595119023804 24.82996599319864 24.08981796359272 23.104620924184836 150-151 28.253531691461433 25.465683210401302 23.71546443305413 22.565320665083135 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 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 0.5 18 0.5 19 0.0 20 0.0 21 0.5 22 0.5 23 0.0 24 1.5 25 2.5 26 2.0 27 2.0 28 1.0 29 2.0 30 3.0 31 4.5 32 9.0 33 15.5 34 23.5 35 26.0 36 34.5 37 51.5 38 64.5 39 83.0 40 106.0 41 130.0 42 148.5 43 152.5 44 160.5 45 189.5 46 189.0 47 173.0 48 179.0 49 173.0 50 163.5 51 151.0 52 144.5 53 134.5 54 111.5 55 107.0 56 109.5 57 95.5 58 79.5 59 74.5 60 73.0 61 67.5 62 75.5 63 74.0 64 59.5 65 60.5 66 57.5 67 57.5 68 58.5 69 51.5 70 47.5 71 41.5 72 37.5 73 33.5 74 29.0 75 26.5 76 18.5 77 11.5 78 7.0 79 3.5 80 2.5 81 2.5 82 1.0 83 0.5 84 0.5 85 0.0 86 0.0 87 0.5 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 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 0.025 7 0.025 8 0.025 9 0.025 10-14 0.025 15-19 0.03 20-24 0.025 25-29 0.025 30-34 0.025 35-39 0.025 40-44 0.025 45-49 0.025 50-54 0.03 55-59 0.025 60-64 0.025 65-69 0.025 70-74 0.025 75-79 0.025 80-84 0.025 85-89 0.025 90-94 0.025 95-99 0.025 100-104 0.025 105-109 0.02 110-114 0.025 115-119 0.025 120-124 0.025 125-129 0.025 130-134 0.025 135-139 0.015 140-144 0.0 145-149 0.02 150-151 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.375 #Duplication Level Percentage of deduplicated Percentage of total 1 99.49685534591195 98.875 2 0.42767295597484273 0.8500000000000001 3 0.025157232704402514 0.075 4 0.05031446540880503 0.2 5 0.0 0.0 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 pass >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0125 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.037500000000000006 0.0 0.0 0.0 0.0 88-89 0.0875 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.125 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.225 0.0 0.0 0.0 0.0 98-99 0.2625 0.0 0.0 0.0 0.0 100-101 0.35 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.44999999999999996 0.0 0.0 0.0 0.0 106-107 0.5 0.0 0.0 0.0 0.0 108-109 0.6000000000000001 0.0 0.0 0.0 0.0 110-111 0.675 0.0 0.0 0.0 0.0 112-113 0.825 0.0 0.0 0.0 0.0 114-115 0.925 0.0 0.0 0.0 0.0 116-117 1.1375000000000002 0.0 0.0 0.0 0.0 118-119 1.4625 0.0 0.0 0.0 0.0 120-121 1.775 0.0 0.0 0.0 0.0 122-123 1.9874999999999998 0.0 0.0 0.0 0.0 124-125 2.2125 0.0 0.0 0.0 0.0 126-127 2.55 0.0 0.0 0.0 0.0 128-129 2.8125 0.0 0.0 0.0 0.0 130-131 3.0125 0.0 0.0 0.0 0.0 132-133 3.175 0.0 0.0 0.0 0.0 134-135 3.55 0.0 0.0 0.0 0.0 136-137 3.9625000000000004 0.0 0.0 0.0 0.0 138-139 4.362500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACCACAC 10 0.006830828 145.0 3 >>END_MODULE Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001561 spots for SRR6958458.sra Written 1001561 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra Read 1001546 spots for SRR6958458.sra Written 1001546 spots for SRR6958458.sra SRR ids: ['SRR6958458.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zj3z000g SRR6958458.sra spots: 20030935 blocks: [[1, 1001546], [1001547, 2003092], [2003093, 3004638], [3004639, 4006184], [4006185, 5007730], [5007731, 6009276], [6009277, 7010822], [7010823, 8012368], [8012369, 9013914], [9013915, 10015460], [10015461, 11017006], [11017007, 12018552], [12018553, 13020098], [13020099, 14021644], [14021645, 15023190], [15023191, 16024736], [16024737, 17026282], [17026283, 18027828], [18027829, 19029374], [19029375, 20030935]] SRR6958458 file size 6766126 SRR6958458 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 SRR6958458 SRR6958458_1.fastq SRR6958458_2.fastq Input file: SRR6958458_1.fastq Paired file: SRR6958458_2.fastq trimmed: SRR6958458-trimmed-pair1.fastq, SRR6958458-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 Fri Dec 6 23:35:14 2024 >> started Fri Dec 6 23:35:34 2024 >> done (20.417s) 20030935 read pairs processed; of these: 42917 ( 0.21%) short read pairs filtered out after trimming by size control 28694 ( 0.14%) empty read pairs filtered out after trimming by size control 19959324 (99.64%) read pairs available; of these: 8871444 (44.45%) trimmed read pairs available after processing 11087880 (55.55%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 8 0.00% 20 3 0.00% 21 8 0.00% 22 6 0.00% 23 6 0.00% 24 7 0.00% 25 10 0.00% 26 10 0.00% 27 12 0.00% 28 6 0.00% 29 9 0.00% 30 12 0.00% 31 11 0.00% 32 5 0.00% 33 11 0.00% 34 15 0.00% 35 9 0.00% 36 10 0.00% 37 15 0.00% 38 14 0.00% 39 14 0.00% 40 21 0.00% 41 18 0.00% 42 14 0.00% 43 18 0.00% 44 21 0.00% 45 18 0.00% 46 24 0.00% 47 25 0.00% 48 27 0.00% 49 38 0.00% 50 34 0.00% 51 50 0.00% 52 40 0.00% 53 47 0.00% 54 57 0.00% 55 61 0.00% 56 77 0.00% 57 91 0.00% 58 104 0.00% 59 110 0.00% 60 109 0.00% 61 139 0.00% 62 115 0.00% 63 159 0.00% 64 172 0.00% 65 186 0.00% 66 218 0.00% 67 260 0.00% 68 265 0.00% 69 263 0.00% 70 320 0.00% 71 412 0.00% 72 445 0.00% 73 485 0.00% 74 584 0.00% 75 630 0.00% 76 638 0.00% 77 790 0.00% 78 828 0.00% 79 1006 0.01% 80 1158 0.01% 81 1287 0.01% 82 1523 0.01% 83 1903 0.01% 84 3551 0.02% 85 4586 0.02% 86 4307 0.02% 87 4659 0.02% 88 4766 0.02% 89 4638 0.02% 90 4864 0.02% 91 5545 0.03% 92 5582 0.03% 93 5844 0.03% 94 6315 0.03% 95 6638 0.03% 96 7345 0.04% 97 7598 0.04% 98 8277 0.04% 99 9040 0.05% 100 9648 0.05% 101 10152 0.05% 102 11236 0.06% 103 11821 0.06% 104 12540 0.06% 105 13184 0.07% 106 14337 0.07% 107 15139 0.08% 108 15987 0.08% 109 17011 0.09% 110 17693 0.09% 111 19061 0.10% 112 20199 0.10% 113 21366 0.11% 114 23098 0.12% 115 24714 0.12% 116 25962 0.13% 117 27138 0.14% 118 28418 0.14% 119 29806 0.15% 120 31091 0.16% 121 32544 0.16% 122 34720 0.17% 123 36242 0.18% 124 39063 0.20% 125 40965 0.21% 126 43051 0.22% 127 45680 0.23% 128 47001 0.24% 129 49868 0.25% 130 52282 0.26% 131 54770 0.27% 132 57664 0.29% 133 61367 0.31% 134 64480 0.32% 135 68777 0.34% 136 72891 0.37% 137 77355 0.39% 138 82144 0.41% 139 87330 0.44% 140 94221 0.47% 141 102212 0.51% 142 113822 0.57% 143 125720 0.63% 144 144608 0.72% 145 173317 0.87% 146 215703 1.08% 147 289603 1.45% 148 440757 2.21% 149 890247 4.46% 150 4724892 23.67% 151 11087880 55.55% 19959324 reads passed initial QC criterion=sequence-density sequence-density=0.74 sequence-density-rank=1 fanout-score=2.55 fanout-score-rank=34 prefix-density=0.82 prefix-fanout=2.3 sequence=GAGCTGGAGCTG criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=244.28 fanout-score-rank=1 prefix-density=0.64 prefix-fanout=11.1 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.71 sequence-density-rank=1 fanout-score=5.38 fanout-score-rank=15 prefix-density=0.89 prefix-fanout=4.2 sequence=AAGATCAAGGAGAAGCTCCCTGGTGGTGGCCACAAAGACGGGCAGCAGACCACGGCGACCGGTGGCACCTACGGGCAGCAAACAGGCCATACTGGGGTTGCTGGCACCGGGGCGCATGGCACCGGCAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=74.88 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=7.9 sequence=AAGAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGTTCGAGCACTCGACCGAAGATGTCTT SRR6958458 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:36:29 Started mapping on | Dec 06 23:36:29 Finished on | Dec 06 23:37:37 Mapping speed, Million of reads per hour | 1056.67 Number of input reads | 19959324 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 19355570 Uniquely mapped reads % | 96.98% Average mapped length | 295.86 Number of splices: Total | 17447025 Number of splices: Annotated (sjdb) | 16283124 Number of splices: GT/AG | 17250784 Number of splices: GC/AG | 161736 Number of splices: AT/AC | 7119 Number of splices: Non-canonical | 27386 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.01% Deletion average length | 1.43 Insertion rate per base | 0.00% Insertion average length | 1.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 107124 % of reads mapped to multiple loci | 0.54% Number of reads mapped to too many loci | 36569 % of reads mapped to too many loci | 0.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.93% % of reads unmapped: other | 1.38% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 519408 519408 519408 N_multimapping 107124 107124 107124 N_noFeature 855035 18698810 1130490 N_ambiguous 435640 2963 55245 UnstrandedReadsAssigned:18064895 PositiveStrandReadsAssigned:653797 NegativeStrandReadsAssigned:18169835 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR6958458 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: SRR6958458-trimmed-pair1.fastq SRR6958458-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,959,324 reads, 18,124,436 reads pseudoaligned [quant] estimated average fragment length: 246.044 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,219 rounds 52973 SRR6958458.ke.tsv 35125 SRR6958458.se.tsv 88098 total ==> SRR6958458.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 691.229 191.519 19.7998 PNS24247 1044 798.956 45.8214 4.09841 PNS24249 1928 1682.96 277.309 11.775 PNS24246 1044 798.956 45.8214 4.09841 PNS24248 1044 798.956 45.8214 4.09841 PNS24244 1471 1225.96 98.7075 5.75367 PNS24243 293 88.3367 2 1.61793 KQK14069 1603 1357.96 342.072 18.0012 KQK14071 474 238.313 14.5862 4.37385 ==> SRR6958458.se.tsv <== BRADI_1g14170v3 375 BRADI_1g53295v3 282 BRADI_1g59795v3 62 BRADI_1g07683v3 0 BRADI_1g00485v3 17 BRADI_1g20270v3 973 BRADI_1g74790v3 1318 BRADI_1g09890v3 1 BRADI_1g77505v3 70 BRADI_1g48960v3 0 SRR6958458 completed mapping pipeline successfully