Starting /dee2/code/volunteer_pipeline.sh SRR7169939 current disk space = 3048975761408 free memory = 754091528 SRR7169939 SRAfilesize 8cb13cb2b633ebc25beb94210059e992 SRR7169939.sra SRR7169939.sra file validated SRR7169939 is paired end SRR7169939 is conventional basespace SRR7169939 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169939_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 32.84 34.0 33.0 34.0 33.0 34.0 2 33.41125 34.0 34.0 34.0 33.0 34.0 3 33.51175 34.0 34.0 34.0 33.0 34.0 4 33.552 34.0 34.0 34.0 33.0 34.0 5 33.43225 34.0 34.0 34.0 33.0 34.0 6 37.23175 38.0 37.0 38.0 36.0 38.0 7 37.5365 38.0 38.0 38.0 37.0 38.0 8 37.5885 38.0 38.0 38.0 38.0 38.0 9 37.68 38.0 38.0 38.0 38.0 38.0 10-14 37.5776 38.0 38.0 38.0 38.0 38.0 15-19 37.5978 38.0 38.0 38.0 38.0 38.0 20-24 37.52675000000001 38.0 38.0 38.0 38.0 38.0 25-29 37.466499999999996 38.0 38.0 38.0 38.0 38.0 30-34 37.51345 38.0 38.0 38.0 38.0 38.0 35-39 37.292899999999996 38.0 38.0 38.0 37.4 38.0 40-44 37.1851 38.0 38.0 38.0 37.0 38.0 45-49 37.0749 38.0 38.0 38.0 36.4 38.0 50-54 37.02275 38.0 38.0 38.0 36.0 38.0 55-59 36.9732 38.0 38.0 38.0 36.0 38.0 60-64 36.926899999999996 38.0 38.0 38.0 36.0 38.0 65-69 36.8663 38.0 38.0 38.0 35.8 38.0 70-74 36.71925 38.0 38.0 38.0 35.4 38.0 75-79 36.4056 38.0 38.0 38.0 34.4 38.0 80-84 36.278650000000006 38.0 38.0 38.0 34.0 38.0 85-89 36.2011 38.0 38.0 38.0 34.0 38.0 90-94 36.08015 38.0 38.0 38.0 33.8 38.0 95-99 35.904450000000004 38.0 38.0 38.0 33.0 38.0 100-104 35.69565 38.0 37.6 38.0 31.4 38.0 105-109 35.46055 38.0 37.0 38.0 30.2 38.0 110-114 35.36735 38.0 37.0 38.0 29.8 38.0 115-119 35.078500000000005 38.0 36.6 38.0 27.8 38.0 120-124 35.21725 38.0 37.0 38.0 28.8 38.0 125-129 35.00335 38.0 36.2 38.0 28.2 38.0 130-134 34.31085 38.0 35.2 38.0 24.4 38.0 135-139 33.6588 38.0 35.0 38.0 20.2 38.0 140-144 33.5511 38.0 35.0 38.0 19.8 38.0 145-149 32.93 38.0 34.2 38.0 13.2 38.0 150-151 28.542875000000002 35.5 24.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 0.0 8 0.0 9 2.0 10 2.0 11 2.0 12 3.0 13 1.0 14 2.0 15 3.0 16 8.0 17 2.0 18 14.0 19 17.0 20 10.0 21 7.0 22 12.0 23 24.0 24 15.0 25 25.0 26 31.0 27 25.0 28 31.0 29 40.0 30 53.0 31 50.0 32 54.0 33 89.0 34 130.0 35 237.0 36 549.0 37 2561.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.6414708886619 13.100102145045966 10.112359550561797 33.146067415730336 2 23.599999999999998 15.2 30.625000000000004 30.575000000000003 3 18.9 20.625 25.775 34.699999999999996 4 20.599999999999998 27.700000000000003 23.225 28.475 5 22.025 31.874999999999996 24.525 21.575 6 20.9 34.425 25.0 19.675 7 14.424999999999999 30.025000000000002 38.375 17.175 8 17.5 28.425 30.45 23.625 9 17.9 27.150000000000002 32.0 22.95 10-14 18.884999999999998 31.61 26.825 22.68 15-19 19.335 30.235 27.839999999999996 22.59 20-24 19.67 30.275000000000002 26.955000000000002 23.1 25-29 19.5 30.470000000000002 26.595000000000002 23.435 30-34 18.57 30.564999999999998 27.26 23.605 35-39 19.09 29.609999999999996 27.265 24.035 40-44 19.53 29.915000000000003 27.005000000000003 23.549999999999997 45-49 19.420826247874363 29.908972691807545 27.38821646493948 23.281984595378614 50-54 19.68 29.525000000000002 26.979999999999997 23.815 55-59 19.77 28.895 27.195000000000004 24.14 60-64 19.365 28.904999999999998 27.465 24.265 65-69 19.314999999999998 29.599999999999998 27.065 24.02 70-74 19.695 29.84 26.625 23.84 75-79 19.665 29.335 26.979999999999997 24.02 80-84 19.88 29.794999999999998 26.375 23.95 85-89 19.968970521995896 28.87743356188379 27.376007206846502 23.77758870927381 90-94 20.47599919662583 29.06206065474995 26.571600723036752 23.890339425587467 95-99 20.497112729098667 28.968114486567913 26.53276424805423 24.002008536279188 100-104 20.642385431258756 28.907344406643986 26.46087652591555 23.989393636181706 105-109 20.681034051702586 29.071453572678635 26.606330316515823 23.641182059102956 110-114 20.68 29.73 25.47 24.12 115-119 20.191009550477524 29.43647182359118 25.906295314765735 24.466223311165557 120-124 20.919999999999998 28.999999999999996 25.97 24.11 125-129 20.304060812162433 28.860772154430887 26.540308061612322 24.29485897179436 130-134 21.213031076414953 28.19896912375519 25.626782765350548 24.961217034479308 135-139 20.766068384638526 28.702496741201244 25.68434773889502 24.847087135265216 140-144 20.565424068051037 28.516387290467847 25.57418063547661 25.344008006004504 145-149 20.99074305729297 28.766574931198395 25.629221916437327 24.613460095071304 150-151 21.875 27.8875 26.2125 24.025 >>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 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 1.0 16 1.0 17 0.5 18 0.0 19 0.0 20 0.5 21 1.0 22 1.0 23 0.5 24 3.0 25 9.0 26 15.0 27 15.5 28 12.0 29 15.5 30 24.0 31 41.0 32 54.0 33 56.0 34 69.0 35 86.5 36 104.0 37 131.5 38 149.0 39 168.5 40 199.0 41 200.0 42 202.0 43 227.5 44 248.0 45 250.5 46 248.0 47 247.5 48 205.5 49 167.0 50 158.0 51 139.0 52 118.0 53 107.5 54 91.5 55 61.5 56 40.0 57 32.0 58 24.5 59 16.5 60 13.0 61 9.0 62 6.5 63 5.0 64 6.0 65 5.0 66 2.5 67 1.5 68 1.0 69 1.5 70 1.0 71 0.0 72 0.5 73 1.0 74 1.0 75 0.5 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 2.1 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 0.03 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 0.095 90-94 0.42 95-99 0.42500000000000004 100-104 0.06 105-109 0.005 110-114 0.0 115-119 0.005 120-124 0.0 125-129 0.02 130-134 0.08499999999999999 135-139 0.27 140-144 0.075 145-149 0.075 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.175 #Duplication Level Percentage of deduplicated Percentage of total 1 98.62490450725745 96.825 2 1.2987012987012987 2.55 3 0.05092946269416857 0.15 4 0.0 0.0 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 0.025464731347084286 0.475 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCCATATCTCGTATGC 19 0.475 TruSeq Adapter, Index 4 (97% over 37bp) >>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 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.16249999999999998 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.275 0.0 0.0 0.0 0.0 76-77 0.35 0.0 0.0 0.0 0.0 78-79 0.375 0.0 0.0 0.0 0.0 80-81 0.5 0.0 0.0 0.0 0.0 82-83 0.55 0.0 0.0 0.0 0.0 84-85 0.7125 0.0 0.0 0.0 0.0 86-87 0.8625 0.0 0.0 0.0 0.0 88-89 1.15 0.0 0.0 0.0 0.0 90-91 1.475 0.0 0.0 0.0 0.0 92-93 1.7 0.0 0.0 0.0 0.0 94-95 2.0375 0.0 0.0 0.0 0.0 96-97 2.2750000000000004 0.0 0.0 0.0 0.0 98-99 2.75 0.0 0.0 0.0 0.0 100-101 3.225 0.0 0.0 0.0 0.0 102-103 3.9625000000000004 0.0 0.0 0.0 0.0 104-105 4.675000000000001 0.0 0.0 0.0 0.0 106-107 5.2625 0.0 0.0 0.0 0.0 108-109 6.0125 0.0 0.0 0.0 0.0 110-111 6.675 0.0 0.0 0.0 0.0 112-113 7.4375 0.0 0.0 0.0 0.0 114-115 7.975 0.0 0.0 0.0 0.0 116-117 8.899999999999999 0.0 0.0 0.0 0.0 118-119 9.5625 0.0 0.0 0.0 0.0 120-121 10.2375 0.0 0.0 0.0 0.0 122-123 10.925 0.0 0.0 0.0 0.0 124-125 11.6875 0.0 0.0 0.0 0.0 126-127 12.675 0.0 0.0 0.0 0.0 128-129 13.65 0.0 0.0 0.0 0.0 130-131 14.375 0.0 0.0 0.0 0.0 132-133 15.1625 0.0 0.0 0.0 0.0 134-135 16.0 0.0 0.0 0.0 0.0 136-137 16.737499999999997 0.0 0.0 0.0 0.0 138-139 17.7125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAGTCTT 10 0.006832588 144.9875 6 TCAGTCT 10 0.006832588 144.9875 5 >>END_MODULE SRR7169939 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169939_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 31.8145 33.0 33.0 34.0 32.0 34.0 2 32.12225 34.0 33.0 34.0 31.0 34.0 3 32.09425 34.0 33.0 34.0 32.0 34.0 4 31.99375 34.0 33.0 34.0 32.0 34.0 5 31.86375 34.0 33.0 34.0 32.0 34.0 6 35.86375 38.0 38.0 38.0 35.0 38.0 7 35.9735 38.0 38.0 38.0 35.0 38.0 8 36.05275 38.0 38.0 38.0 36.0 38.0 9 36.06625 38.0 38.0 38.0 36.0 38.0 10-14 36.045 38.0 38.0 38.0 36.0 38.0 15-19 35.8911 38.0 38.0 38.0 35.8 38.0 20-24 35.9636 38.0 38.0 38.0 36.0 38.0 25-29 36.064299999999996 38.0 38.0 38.0 36.0 38.0 30-34 36.0539 38.0 38.0 38.0 36.0 38.0 35-39 36.035199999999996 38.0 38.0 38.0 36.0 38.0 40-44 35.877599999999994 38.0 38.0 38.0 36.0 38.0 45-49 35.7678 38.0 38.0 38.0 35.2 38.0 50-54 35.9211 38.0 38.0 38.0 35.8 38.0 55-59 35.8492 38.0 38.0 38.0 35.4 38.0 60-64 35.845749999999995 38.0 38.0 38.0 35.4 38.0 65-69 35.8238 38.0 38.0 38.0 35.6 38.0 70-74 35.6981 38.0 38.0 38.0 34.8 38.0 75-79 35.6323 38.0 38.0 38.0 34.2 38.0 80-84 35.553450000000005 38.0 38.0 38.0 34.0 38.0 85-89 35.245200000000004 38.0 38.0 38.0 33.0 38.0 90-94 34.855650000000004 38.0 38.0 38.0 29.2 38.0 95-99 35.2088 38.0 38.0 38.0 30.6 38.0 100-104 35.2465 38.0 38.0 38.0 31.8 38.0 105-109 35.177949999999996 38.0 38.0 38.0 31.8 38.0 110-114 35.08865 38.0 38.0 38.0 31.4 38.0 115-119 34.798550000000006 38.0 38.0 38.0 28.6 38.0 120-124 34.56915 38.0 37.2 38.0 27.0 38.0 125-129 34.1365 38.0 36.6 38.0 23.6 38.0 130-134 32.940999999999995 38.0 35.2 38.0 11.0 38.0 135-139 31.880350000000004 38.0 34.8 38.0 2.0 38.0 140-144 30.8923 38.0 32.8 38.0 2.0 38.0 145-149 30.202049999999996 38.0 31.8 38.0 2.0 38.0 150-151 26.440875 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 128.0 3 3.0 4 6.0 5 2.0 6 4.0 7 2.0 8 3.0 9 3.0 10 0.0 11 4.0 12 0.0 13 4.0 14 7.0 15 4.0 16 5.0 17 16.0 18 9.0 19 6.0 20 8.0 21 5.0 22 12.0 23 22.0 24 14.0 25 19.0 26 23.0 27 32.0 28 24.0 29 31.0 30 39.0 31 63.0 32 89.0 33 116.0 34 142.0 35 164.0 36 417.0 37 2574.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.33367929423975 21.613907628437985 14.218993253762324 22.83341982355994 2 28.70182555780933 25.88742393509128 27.789046653144016 17.621703853955374 3 21.73690932311622 27.15197956577267 30.574712643678158 20.53639846743295 4 25.15495867768595 33.16115702479338 22.57231404958678 19.111570247933884 5 25.738724727838257 34.18869880767237 23.068947641264902 17.003628823224467 6 22.83057851239669 35.33057851239669 24.25103305785124 17.587809917355372 7 21.575695159629248 23.01750772399588 36.122554067971166 19.284243048403706 8 23.403707518022657 25.257466529351184 26.853759011328528 24.48506694129763 9 23.04336669232743 26.071336925840388 27.816268924813958 23.06902745701822 10-14 24.684034046943513 28.207376837761156 25.953056486974464 21.155532628320866 15-19 24.08049247322953 27.56712016967565 27.62919662717914 20.72319072991568 20-24 24.85295635125374 28.00536580332267 26.87545144979878 20.266226395624805 25-29 24.668516805427075 27.746942131770997 27.053140096618357 20.531400966183575 30-34 24.645790554414784 27.895277207392198 27.05852156057495 20.40041067761807 35-39 24.600803543834346 27.979808385701038 26.846605542392087 20.572782528072526 40-44 25.05945610588357 27.747906111053666 26.91552062868369 20.27711715437907 45-49 24.667666683908344 27.471163295918892 26.793565406300107 21.067604613872653 50-54 24.10705095213587 27.900154400411736 27.596500257334018 20.396294390118374 55-59 24.59320288362513 27.744593202883628 27.301750772399586 20.360453141091657 60-64 24.09830997526793 28.282151690024733 27.560799670239078 20.058738664468258 65-69 24.31169098006986 28.02034107252928 27.619683583316213 20.04828436408465 70-74 24.34862572800654 27.48543986921426 27.556963318688055 20.60897108409114 75-79 23.949859299053465 27.689946277820415 28.03274494755692 20.3274494755692 80-84 24.41134316134316 26.863226863226863 28.31695331695332 20.40847665847666 85-89 24.664935064935065 27.66233766233766 28.103896103896105 19.568831168831167 90-94 24.60338237604063 27.629718833446777 27.865333263521652 19.901565526990943 95-99 24.552377032311178 27.490224325993 28.30314879604857 19.654249845647254 100-104 25.514128929688702 27.52961690343095 27.262936560849276 19.693317606031076 105-109 25.149146266200372 27.926352602345194 27.592059247068505 19.33244188438593 110-114 25.314109165808446 27.842430484037074 27.399588053553035 19.44387229660144 115-119 25.164885730354314 27.665013548749933 27.823508359323075 19.34659236157268 120-124 26.19811560988032 27.710720651897127 27.069009421950597 19.022154316271962 125-129 26.493694438701677 27.713458755426917 27.144924540004133 18.647922265867273 130-134 26.28893377272244 27.591155522483255 27.543318805145105 18.5765918996492 135-139 26.276896326885456 27.74940230384699 27.559226255161924 18.41447511410563 140-144 26.896779885310984 26.968460520511687 27.756947507719453 18.377812086457872 145-149 26.991221069433358 28.502261239691407 26.453844107475394 18.05267358339984 150-151 27.11864406779661 27.998447405873982 26.51054470177254 18.372363824556864 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 65.0 1 40.5 2 9.0 3 3.5 4 3.5 5 2.5 6 1.5 7 0.5 8 2.0 9 3.0 10 2.0 11 1.5 12 1.5 13 1.0 14 2.5 15 2.5 16 1.0 17 1.5 18 2.0 19 1.0 20 1.0 21 1.5 22 1.0 23 0.5 24 1.0 25 2.5 26 3.5 27 3.5 28 4.0 29 8.0 30 9.0 31 8.0 32 9.5 33 19.5 34 35.5 35 45.0 36 65.0 37 88.5 38 112.0 39 142.5 40 174.5 41 222.0 42 252.0 43 268.0 44 282.0 45 267.5 46 257.5 47 268.0 48 252.5 49 217.5 50 183.0 51 143.5 52 119.0 53 109.5 54 88.5 55 59.0 56 41.5 57 32.0 58 22.0 59 14.5 60 10.5 61 8.0 62 8.0 63 5.5 64 4.5 65 4.0 66 1.5 67 1.5 68 1.5 69 1.0 70 1.0 71 0.0 72 0.5 73 0.5 74 0.5 75 0.5 76 0.5 77 0.5 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 warn #Base N-Count 1 3.65 2 1.4000000000000001 3 2.125 4 3.2 5 3.55 6 3.2 7 2.9000000000000004 8 2.9000000000000004 9 2.5749999999999997 10-14 3.075 15-19 3.345 20-24 3.09 25-29 2.71 30-34 2.6 35-39 2.93 40-44 3.29 45-49 3.335 50-54 2.85 55-59 2.9000000000000004 60-64 2.96 65-69 2.6599999999999997 70-74 2.13 75-79 2.275 80-84 2.32 85-89 3.75 90-94 4.505 95-99 2.82 100-104 2.505 105-109 2.78 110-114 2.9000000000000004 115-119 2.205 120-124 1.825 125-129 3.26 130-134 5.93 135-139 7.9799999999999995 140-144 9.32 145-149 6.0249999999999995 150-151 3.3875 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.25 #Duplication Level Percentage of deduplicated Percentage of total 1 98.57142857142858 94.875 2 1.194805194805195 2.3 3 0.05194805194805195 0.15 4 0.0 0.0 5 0.05194805194805195 0.25 6 0.025974025974025976 0.15 7 0.0 0.0 8 0.025974025974025976 0.2 9 0.0 0.0 >10 0.05194805194805195 0.675 >50 0.025974025974025976 1.4000000000000001 >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 fail #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 56 1.4000000000000001 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 17 0.42500000000000004 Illumina Single End PCR Primer 1 (100% over 50bp) NTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 10 0.25 No Hit NGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 8 0.2 No Hit NCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 6 0.15 No Hit NANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 5 0.125 No Hit GGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACA 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 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1375 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2375 0.0 0.0 0.0 0.0 76-77 0.2875 0.0 0.0 0.0 0.0 78-79 0.3 0.0 0.0 0.0 0.0 80-81 0.3875 0.0 0.0 0.0 0.0 82-83 0.425 0.0 0.0 0.0 0.0 84-85 0.5875 0.0 0.0 0.0 0.0 86-87 0.7375 0.0 0.0 0.0 0.0 88-89 1.025 0.0 0.0 0.0 0.0 90-91 1.375 0.0 0.0 0.0 0.0 92-93 1.5625 0.0 0.0 0.0 0.0 94-95 1.9 0.0 0.0 0.0 0.0 96-97 2.0999999999999996 0.0 0.0 0.0 0.0 98-99 2.6 0.0 0.0 0.0 0.0 100-101 3.0625 0.0 0.0 0.0 0.0 102-103 3.7875 0.0 0.0 0.0 0.0 104-105 4.425 0.0 0.0 0.0 0.0 106-107 4.9875 0.0 0.0 0.0 0.0 108-109 5.7625 0.0 0.0 0.0 0.0 110-111 6.45 0.0 0.0 0.0 0.0 112-113 7.2375 0.0 0.0 0.0 0.0 114-115 7.825 0.0 0.0 0.0 0.0 116-117 8.6125 0.0 0.0 0.0 0.0 118-119 9.274999999999999 0.0 0.0 0.0 0.0 120-121 9.899999999999999 0.0 0.0 0.0 0.0 122-123 10.55 0.0 0.0 0.0 0.0 124-125 11.25 0.0 0.0 0.0 0.0 126-127 12.075 0.0 0.0 0.0 0.0 128-129 12.975 0.0 0.0 0.0 0.0 130-131 13.6625 0.0 0.0 0.0 0.0 132-133 14.5125 0.0 0.0 0.0 0.0 134-135 15.2375 0.0 0.0 0.0 0.0 136-137 16.012500000000003 0.0 0.0 0.0 0.0 138-139 16.799999999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761659 spots for SRR7169939.sra Written 761659 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra Read 761642 spots for SRR7169939.sra Written 761642 spots for SRR7169939.sra SRR ids: ['SRR7169939.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_sqabnq1s SRR7169939.sra spots: 15232857 blocks: [[1, 761642], [761643, 1523284], [1523285, 2284926], [2284927, 3046568], [3046569, 3808210], [3808211, 4569852], [4569853, 5331494], [5331495, 6093136], [6093137, 6854778], [6854779, 7616420], [7616421, 8378062], [8378063, 9139704], [9139705, 9901346], [9901347, 10662988], [10662989, 11424630], [11424631, 12186272], [12186273, 12947914], [12947915, 13709556], [13709557, 14471198], [14471199, 15232857]] SRR7169939 file size 5140215 SRR7169939 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 SRR7169939 SRR7169939_1.fastq SRR7169939_2.fastq Input file: SRR7169939_1.fastq Paired file: SRR7169939_2.fastq trimmed: SRR7169939-trimmed-pair1.fastq, SRR7169939-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 03:39:43 2025 >> started Wed Feb 12 03:39:58 2025 >> done (15.706s) 15232857 read pairs processed; of these: 31473 ( 0.21%) short read pairs filtered out after trimming by size control 110623 ( 0.73%) empty read pairs filtered out after trimming by size control 15090761 (99.07%) read pairs available; of these: 8287938 (54.92%) trimmed read pairs available after processing 6802823 (45.08%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 7 0.00% 20 7 0.00% 21 11 0.00% 22 10 0.00% 23 25 0.00% 24 25 0.00% 25 10 0.00% 26 13 0.00% 27 24 0.00% 28 17 0.00% 29 21 0.00% 30 26 0.00% 31 30 0.00% 32 31 0.00% 33 31 0.00% 34 38 0.00% 35 40 0.00% 36 38 0.00% 37 49 0.00% 38 56 0.00% 39 49 0.00% 40 85 0.00% 41 78 0.00% 42 102 0.00% 43 135 0.00% 44 109 0.00% 45 146 0.00% 46 155 0.00% 47 186 0.00% 48 196 0.00% 49 197 0.00% 50 260 0.00% 51 322 0.00% 52 356 0.00% 53 371 0.00% 54 396 0.00% 55 407 0.00% 56 454 0.00% 57 520 0.00% 58 636 0.00% 59 662 0.00% 60 710 0.00% 61 925 0.01% 62 1025 0.01% 63 1119 0.01% 64 1277 0.01% 65 1427 0.01% 66 1868 0.01% 67 2404 0.02% 68 3061 0.02% 69 4378 0.03% 70 6557 0.04% 71 5094 0.03% 72 4207 0.03% 73 4211 0.03% 74 4334 0.03% 75 4963 0.03% 76 5310 0.04% 77 5685 0.04% 78 6174 0.04% 79 7145 0.05% 80 7844 0.05% 81 8847 0.06% 82 10412 0.07% 83 11465 0.08% 84 14121 0.09% 85 16299 0.11% 86 16981 0.11% 87 18374 0.12% 88 20036 0.13% 89 21106 0.14% 90 22446 0.15% 91 23717 0.16% 92 25242 0.17% 93 27942 0.19% 94 29779 0.20% 95 32371 0.21% 96 33901 0.22% 97 35444 0.23% 98 35979 0.24% 99 36555 0.24% 100 38839 0.26% 101 40578 0.27% 102 43151 0.29% 103 44714 0.30% 104 47176 0.31% 105 50222 0.33% 106 51669 0.34% 107 52502 0.35% 108 53574 0.36% 109 55470 0.37% 110 56509 0.37% 111 57852 0.38% 112 59819 0.40% 113 63636 0.42% 114 64910 0.43% 115 68376 0.45% 116 70020 0.46% 117 71086 0.47% 118 72101 0.48% 119 71275 0.47% 120 72844 0.48% 121 73187 0.48% 122 75083 0.50% 123 77385 0.51% 124 80690 0.53% 125 82656 0.55% 126 84315 0.56% 127 85929 0.57% 128 87445 0.58% 129 88040 0.58% 130 90105 0.60% 131 89132 0.59% 132 92261 0.61% 133 94936 0.63% 134 97720 0.65% 135 100984 0.67% 136 104972 0.70% 137 107635 0.71% 138 111392 0.74% 139 115818 0.77% 140 118802 0.79% 141 122916 0.81% 142 129006 0.85% 143 135282 0.90% 144 145517 0.96% 145 158439 1.05% 146 180398 1.20% 147 218849 1.45% 148 286836 1.90% 149 504934 3.35% 150 2813877 18.65% 151 6802823 45.08% 15090761 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=4.74 fanout-score-rank=24 prefix-density=0.18 prefix-fanout=4.0 sequence=GTTGCATCCTGGTATTGCTGATATTC criterion=fanout-score sequence-density=0.14 sequence-density-rank=4 fanout-score=37.56 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=12.2 sequence=CAAAATCATAGCCCACTTAAAAAAACGAGAGCAATCCATGCAATAACCTCATCAAAACCTTCTGTGTCACAAAGAATATATTGCTGCAACCATGCAAACTCCAAAGAACACAACATTGTTCAGAACAGTAAAGCTTACTGCCCCAGAAGTATCCGCAGGAGATTCTGGACTCGCTGCAGCTTTGGATCTCTTCTTTGGCTTTTCAGGTGCTGGTGCTGGAGTAGGAGGTTTAGGTGTAAAGATATCAAGAGGAAGAAGCACCTTGTCAACCTGATAAACAGCTAACTGGCTATCAGTGTAGATAGTGCCGGATACGCTTGTATTTGTAAGCCCTGTAGTTATATTCACAGAGTTTCCTGTGGTGGTTACGTTAAGCTCTAACCTGCCACCTGATCCTGCTTGTGTGGTCAGAGGGTTGCTCACAGTCTGGAACTGGGAACTTGATAGAAATTGTGGTATAATGTGAAACTGTACTAGCTCAGCCTTTTCTTGATCGCTTAGGGAGTTGAGG criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=18.08 fanout-score-rank=12 prefix-density=0.41 prefix-fanout=7.9 sequence=TGCTGAGATCATTGTGCATGGAAAATCCGGATTCCATATTGATCCTTACCATGGAGTACAGGCTGCTGAACTCCTTGTTGACTTCTTTGAGAAGTGCAAGGCTGATCCCAGTTACTGGGACAAAATCTCCCAGGGAGGCCTGCAGCGAATCCAAGAGAAGTATACCTGGAAAATTTACTCTCAAAGGCTCCTGACTCTCACAGGAGTTTATGGCTTCTGGAAGCATGTTTCCAACCTTGATCATCGTGAGAGCCGTCGCTATCTGGAAATGTTCTATGCACTCAAATATCGCAAATTGGCTGATTCTGTTCCTTTGACTATCGAGTAAATGGAGCTGGAGAAATCAAGGAAACATGGGTTGGTTTGAGTCGGGTTCCGGGTCCAGAATAATGGTGTCATTTCACGATAGTGATTGGACAAGAAAGGCTTTGATCTTCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=43 fanout-score=48.48 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=5.9 sequence=TGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCG SRR7169939 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 03:40:41 Started mapping on | Feb 12 03:40:41 Finished on | Feb 12 03:42:13 Mapping speed, Million of reads per hour | 590.51 Number of input reads | 15090761 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 14068062 Uniquely mapped reads % | 93.22% Average mapped length | 285.06 Number of splices: Total | 10547532 Number of splices: Annotated (sjdb) | 10328603 Number of splices: GT/AG | 10383678 Number of splices: GC/AG | 121190 Number of splices: AT/AC | 10060 Number of splices: Non-canonical | 32604 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.04% Deletion average length | 2.81 Insertion rate per base | 0.03% Insertion average length | 2.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 252683 % of reads mapped to multiple loci | 1.67% Number of reads mapped to too many loci | 44474 % of reads mapped to too many loci | 0.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.73% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 794716 794716 794716 N_multimapping 252683 252683 252683 N_noFeature 338828 13829904 442488 N_ambiguous 190407 999 55342 UnstrandedReadsAssigned:13538827 PositiveStrandReadsAssigned:237159 NegativeStrandReadsAssigned:13570232 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=136 echo kmer=131 SRR7169939 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: SRR7169939-trimmed-pair1.fastq SRR7169939-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,090,761 reads, 13,593,625 reads pseudoaligned [quant] estimated average fragment length: 193.943 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,118 rounds 52401 SRR7169939.ke.tsv 34699 SRR7169939.se.tsv 87100 total ==> SRR7169939.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1825.06 244 8.89802 Potri.005G024800.1.v4.1 1035 842.057 10 0.790385 Potri.004G059700.1.v4.1 961 768.067 1 0.0866525 Potri.007G009000.2.v4.1 1416 1223.06 0 0 Potri.003G141000.2.v4.1 2943 2750.06 157 3.7996 Potri.016G087400.1.v4.1 270 101.181 1271 836.038 Potri.015G069301.1.v4.1 564 372.264 0 0 Potri.010G195200.1.v4.1 1773 1580.06 12 0.505462 Potri.012G127500.1.v4.1 977 784.062 5419 459.99 ==> SRR7169939.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 768 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 332 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 12 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 2 SRR7169939 completed mapping pipeline successfully