Starting /dee2/code/volunteer_pipeline.sh SRR7170197 current disk space = 3051419410432 free memory = 1467579888 SRR7170197 SRAfilesize 89a9b532f184901ab6020006c2150c8d SRR7170197.sra SRR7170197.sra file validated SRR7170197 is paired end SRR7170197 is conventional basespace SRR7170197 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170197_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 32.9115 34.0 33.0 34.0 33.0 34.0 2 33.43925 34.0 34.0 34.0 33.0 34.0 3 33.543 34.0 34.0 34.0 33.0 34.0 4 33.60525 34.0 34.0 34.0 33.0 34.0 5 33.629 34.0 34.0 34.0 33.0 34.0 6 37.377 38.0 38.0 38.0 37.0 38.0 7 37.5185 38.0 38.0 38.0 37.0 38.0 8 37.60375 38.0 38.0 38.0 38.0 38.0 9 37.66375 38.0 38.0 38.0 38.0 38.0 10-14 37.335300000000004 38.0 38.0 38.0 37.2 38.0 15-19 37.6422 38.0 38.0 38.0 38.0 38.0 20-24 37.6842 38.0 38.0 38.0 38.0 38.0 25-29 37.63935 38.0 38.0 38.0 38.0 38.0 30-34 37.646 38.0 38.0 38.0 38.0 38.0 35-39 37.46935 38.0 38.0 38.0 37.8 38.0 40-44 37.4674 38.0 38.0 38.0 38.0 38.0 45-49 37.382799999999996 38.0 38.0 38.0 37.0 38.0 50-54 37.374849999999995 38.0 38.0 38.0 37.0 38.0 55-59 37.3706 38.0 38.0 38.0 37.0 38.0 60-64 37.353899999999996 38.0 38.0 38.0 37.0 38.0 65-69 37.26174999999999 38.0 38.0 38.0 37.0 38.0 70-74 37.2571 38.0 38.0 38.0 37.0 38.0 75-79 36.9557 38.0 38.0 38.0 36.0 38.0 80-84 37.11705 38.0 38.0 38.0 36.0 38.0 85-89 37.05085 38.0 38.0 38.0 36.2 38.0 90-94 36.97885 38.0 38.0 38.0 36.0 38.0 95-99 36.92815 38.0 38.0 38.0 36.0 38.0 100-104 36.9044 38.0 38.0 38.0 35.8 38.0 105-109 36.73755 38.0 38.0 38.0 35.2 38.0 110-114 36.7051 38.0 38.0 38.0 35.0 38.0 115-119 36.62714999999999 38.0 38.0 38.0 34.6 38.0 120-124 36.4329 38.0 38.0 38.0 34.0 38.0 125-129 36.31195 38.0 38.0 38.0 34.0 38.0 130-134 36.12365 38.0 37.6 38.0 33.4 38.0 135-139 35.95635 38.0 37.2 38.0 33.2 38.0 140-144 35.77515 38.0 36.8 38.0 32.6 38.0 145-149 35.418099999999995 38.0 36.0 38.0 32.2 38.0 150-151 32.49875 37.0 33.5 38.0 16.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 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 2.0 14 4.0 15 1.0 16 2.0 17 1.0 18 2.0 19 3.0 20 3.0 21 5.0 22 3.0 23 0.0 24 3.0 25 15.0 26 4.0 27 17.0 28 15.0 29 20.0 30 34.0 31 34.0 32 32.0 33 69.0 34 99.0 35 185.0 36 412.0 37 3034.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.783715012722645 15.852417302798983 7.709923664122137 31.653944020356235 2 21.405351337834457 19.05476369092273 37.83445861465366 21.705426356589147 3 18.65 26.275 28.375 26.700000000000003 4 21.025 34.675 22.95 21.349999999999998 5 21.425 36.925000000000004 23.9 17.75 6 16.575 37.675 26.075 19.675 7 14.325 22.425 44.025 19.225 8 17.299999999999997 23.400000000000002 32.0 27.3 9 18.075 23.35 32.525 26.05 10-14 19.84 30.995 25.724999999999998 23.44 15-19 20.244999999999997 28.705000000000002 27.955000000000002 23.095 20-24 19.75 28.955 27.495000000000005 23.799999999999997 25-29 20.52 29.845 26.779999999999998 22.855 30-34 20.14 29.215000000000003 27.185 23.46 35-39 19.715 28.915000000000003 27.82 23.549999999999997 40-44 20.515 29.215000000000003 26.919999999999998 23.35 45-49 20.880220055013755 29.14228557139285 26.851712928232057 23.12578144536134 50-54 20.345 28.985 27.27 23.400000000000002 55-59 20.455000000000002 28.050000000000004 27.54 23.955000000000002 60-64 20.095 29.21 27.235 23.46 65-69 19.915 28.435 27.944999999999997 23.705000000000002 70-74 20.615 29.005 27.105 23.275000000000002 75-79 20.815 28.375 27.26 23.549999999999997 80-84 20.175 28.325 28.12 23.380000000000003 85-89 20.830000000000002 28.175 27.445000000000004 23.549999999999997 90-94 19.939999999999998 28.395 27.52 24.145 95-99 20.7 28.52 27.305 23.474999999999998 100-104 21.10344137655062 28.746498599439775 26.98079231692677 23.169267707082835 105-109 20.75 28.910000000000004 26.815 23.525 110-114 21.765 28.904999999999998 26.665 22.665 115-119 20.849999999999998 28.9 26.169999999999998 24.08 120-124 21.26 27.935 27.11 23.695 125-129 21.391069553477674 29.071453572678635 26.051302565128253 23.486174308715434 130-134 20.97 28.89 26.784999999999997 23.355 135-139 21.215 27.889999999999997 26.590000000000003 24.305 140-144 21.325 28.15 26.19 24.335 145-149 21.055 28.915000000000003 25.979999999999997 24.05 150-151 21.3 28.4 26.724999999999998 23.575 >>END_MODULE >>Per sequence GC content pass #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 0.5 17 0.5 18 1.0 19 1.0 20 0.0 21 0.5 22 0.5 23 0.0 24 3.0 25 4.5 26 4.5 27 7.5 28 9.0 29 13.0 30 20.5 31 30.0 32 40.0 33 46.0 34 60.5 35 76.5 36 88.5 37 109.0 38 142.0 39 172.5 40 189.0 41 205.5 42 239.5 43 269.5 44 266.0 45 273.5 46 276.5 47 254.0 48 223.0 49 193.5 50 168.5 51 135.5 52 116.5 53 94.0 54 65.5 55 46.5 56 35.5 57 28.5 58 23.5 59 18.0 60 13.0 61 10.5 62 5.5 63 4.5 64 4.5 65 3.5 66 2.0 67 1.0 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.7500000000000002 2 0.025 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 0.025 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 0.04 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.005 130-134 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 99.275 #Duplication Level Percentage of deduplicated Percentage of total 1 99.29488793754722 98.575 2 0.6799294887937547 1.35 3 0.02518257365902795 0.075 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 0.0 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 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 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.0875 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.225 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.35 0.0 0.0 0.0 0.0 90-91 0.5125 0.0 0.0 0.0 0.0 92-93 0.6000000000000001 0.0 0.0 0.0 0.0 94-95 0.8125 0.0 0.0 0.0 0.0 96-97 0.9750000000000001 0.0 0.0 0.0 0.0 98-99 1.25 0.0 0.0 0.0 0.0 100-101 1.5 0.0 0.0 0.0 0.0 102-103 1.8875 0.0 0.0 0.0 0.0 104-105 2.2 0.0 0.0 0.0 0.0 106-107 2.4125 0.0 0.0 0.0 0.0 108-109 2.6625 0.0 0.0 0.0 0.0 110-111 3.0 0.0 0.0 0.0 0.0 112-113 3.525 0.0 0.0 0.0 0.0 114-115 4.025 0.0 0.0 0.0 0.0 116-117 4.4625 0.0 0.0 0.0 0.0 118-119 5.025 0.0 0.0 0.0 0.0 120-121 5.6 0.0 0.0 0.0 0.0 122-123 6.1875 0.0 0.0 0.0 0.0 124-125 6.95 0.0 0.0 0.0 0.0 126-127 7.525 0.0 0.0 0.0 0.0 128-129 8.025 0.0 0.0 0.0 0.0 130-131 8.625 0.0 0.0 0.0 0.0 132-133 9.2375 0.0 0.0 0.0 0.0 134-135 9.975 0.0 0.0 0.0 0.0 136-137 10.7625 0.0 0.0 0.0 0.0 138-139 11.6125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCTTTCA 10 0.006830828 145.0 4 TGGCTTT 10 0.006830828 145.0 2 >>END_MODULE SRR7170197 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170197_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 33.18025 34.0 33.0 34.0 33.0 34.0 2 33.26375 34.0 33.0 34.0 33.0 34.0 3 33.33775 34.0 33.0 34.0 33.0 34.0 4 33.276 34.0 33.0 34.0 33.0 34.0 5 33.32275 34.0 33.0 34.0 33.0 34.0 6 37.501 38.0 38.0 38.0 38.0 38.0 7 37.43775 38.0 38.0 38.0 38.0 38.0 8 37.47225 38.0 38.0 38.0 38.0 38.0 9 37.43675 38.0 38.0 38.0 38.0 38.0 10-14 37.478449999999995 38.0 38.0 38.0 38.0 38.0 15-19 37.449 38.0 38.0 38.0 38.0 38.0 20-24 37.5047 38.0 38.0 38.0 38.0 38.0 25-29 37.44834999999999 38.0 38.0 38.0 38.0 38.0 30-34 37.39355 38.0 38.0 38.0 38.0 38.0 35-39 37.31365 38.0 38.0 38.0 37.8 38.0 40-44 37.367 38.0 38.0 38.0 37.8 38.0 45-49 37.364050000000006 38.0 38.0 38.0 38.0 38.0 50-54 37.34185 38.0 38.0 38.0 38.0 38.0 55-59 37.32009999999999 38.0 38.0 38.0 38.0 38.0 60-64 37.34994999999999 38.0 38.0 38.0 38.0 38.0 65-69 37.265499999999996 38.0 38.0 38.0 37.6 38.0 70-74 37.22205 38.0 38.0 38.0 37.8 38.0 75-79 37.2202 38.0 38.0 38.0 37.6 38.0 80-84 37.19985 38.0 38.0 38.0 37.0 38.0 85-89 37.1653 38.0 38.0 38.0 37.2 38.0 90-94 37.07375 38.0 38.0 38.0 37.0 38.0 95-99 37.05055 38.0 38.0 38.0 36.8 38.0 100-104 37.04299999999999 38.0 38.0 38.0 37.0 38.0 105-109 36.8814 38.0 38.0 38.0 36.0 38.0 110-114 36.79475 38.0 38.0 38.0 36.0 38.0 115-119 36.6205 38.0 38.0 38.0 35.6 38.0 120-124 36.5233 38.0 38.0 38.0 35.0 38.0 125-129 36.43625 38.0 38.0 38.0 34.8 38.0 130-134 36.20425 38.0 38.0 38.0 34.0 38.0 135-139 36.1028 38.0 38.0 38.0 34.0 38.0 140-144 35.75485 38.0 37.2 38.0 33.2 38.0 145-149 35.056999999999995 38.0 36.0 38.0 31.0 38.0 150-151 31.740250000000003 36.5 32.0 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 5.0 3 2.0 4 1.0 5 2.0 6 0.0 7 0.0 8 1.0 9 0.0 10 1.0 11 1.0 12 1.0 13 3.0 14 1.0 15 5.0 16 3.0 17 3.0 18 3.0 19 4.0 20 4.0 21 8.0 22 3.0 23 3.0 24 9.0 25 9.0 26 9.0 27 12.0 28 9.0 29 11.0 30 25.0 31 22.0 32 43.0 33 56.0 34 90.0 35 134.0 36 321.0 37 3196.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.38047559449312 21.126408010012515 10.262828535669586 24.23028785982478 2 23.754693366708384 24.881101376720903 34.618272841051315 16.7459324155194 3 20.82082082082082 27.027027027027028 32.35735735735736 19.794794794794797 4 24.281070267566893 34.98374593648413 22.930732683170792 17.804451112778192 5 23.729662077597 37.74718397997497 21.501877346683354 17.02127659574468 6 19.400000000000002 38.275 24.0 18.325 7 19.45 18.475 41.0 21.075 8 19.35 22.95 29.099999999999998 28.599999999999998 9 22.875 23.825 28.125 25.174999999999997 10-14 22.50562640660165 28.362090522630655 27.366841710427607 21.765441360340084 15-19 23.06307207522633 27.42459860951333 28.094833191617063 21.417496123643275 20-24 23.040760190047514 27.76194048512128 27.806951737934483 21.390347586896723 25-29 22.765 28.22 28.139999999999997 20.875 30-34 23.169999999999998 27.58 28.17 21.08 35-39 22.77841676251438 27.47912186828024 28.209231384707707 21.533229984497677 40-44 23.075000000000003 27.955000000000002 28.23 20.74 45-49 23.28 27.62 28.24 20.86 50-54 23.075000000000003 28.194999999999997 28.044999999999998 20.685000000000002 55-59 23.492349234923495 27.93279327932793 27.952795279527955 20.622062206220622 60-64 23.175 27.965 27.985 20.875 65-69 23.301165058252913 27.541377068853446 28.381419070953545 20.776038801940096 70-74 23.41 28.07 27.485 21.035 75-79 23.64 27.215 28.26 20.885 80-84 23.35 27.505000000000003 28.199999999999996 20.945 85-89 23.385 28.055000000000003 28.1 20.46 90-94 23.474999999999998 27.694999999999997 28.38 20.45 95-99 23.9221766529959 27.47324197259178 28.048414524357305 20.556166850055018 100-104 24.07361104165625 27.19407911186678 27.69415412311847 21.038155723358503 105-109 23.994597839135654 28.16126450580232 27.681072428971586 20.16306522609044 110-114 23.932522400760874 27.796966511488215 27.7919607548681 20.478550332882815 115-119 24.536897967357564 28.25673375388004 27.455692400120157 19.750675878642234 120-124 24.584750850510307 27.40144086451871 27.521512907744643 20.492295377226334 125-129 24.398539488821086 27.62466863402191 27.859750912819486 20.11704096433752 130-134 24.91496598639456 27.686074429771907 27.315926370548222 20.083033213285315 135-139 25.288793318997847 27.634145121768267 27.379106866029908 19.697954693203982 140-144 25.759999999999998 26.919999999999998 27.134999999999998 20.185 145-149 25.99169626331849 28.032614676604474 26.39187634435496 19.583812715722075 150-151 25.809678629486054 28.060522696011002 27.01012879829936 19.119669876203577 >>END_MODULE >>Per sequence GC content pass #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 0.5 18 0.5 19 0.0 20 0.5 21 0.5 22 0.0 23 0.5 24 1.5 25 2.0 26 2.5 27 3.0 28 3.5 29 6.5 30 9.0 31 16.5 32 24.0 33 31.5 34 42.5 35 54.0 36 70.0 37 100.0 38 144.5 39 178.5 40 197.5 41 223.5 42 259.5 43 293.5 44 300.5 45 291.5 46 281.5 47 256.0 48 227.0 49 203.0 50 170.0 51 142.0 52 117.5 53 88.0 54 63.5 55 49.5 56 44.0 57 27.5 58 14.5 59 12.5 60 9.0 61 7.0 62 8.5 63 7.0 64 4.5 65 1.5 66 0.0 67 2.5 68 2.5 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 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.125 2 0.125 3 0.1 4 0.025 5 0.125 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.025 15-19 0.034999999999999996 20-24 0.025 25-29 0.0 30-34 0.0 35-39 0.015 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.01 60-64 0.0 65-69 0.005 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.03 100-104 0.015 105-109 0.04 110-114 0.11499999999999999 115-119 0.13 120-124 0.06 125-129 0.034999999999999996 130-134 0.04 135-139 0.015 140-144 0.0 145-149 0.045 150-151 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.45 #Duplication Level Percentage of deduplicated Percentage of total 1 99.47209653092006 98.925 2 0.5027652086475616 1.0 3 0.025138260432378077 0.075 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 0.0 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 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 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.0875 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.225 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.35 0.0 0.0 0.0 0.0 90-91 0.5125 0.0 0.0 0.0 0.0 92-93 0.6000000000000001 0.0 0.0 0.0 0.0 94-95 0.8375 0.0 0.0 0.0 0.0 96-97 1.0375 0.0 0.0 0.0 0.0 98-99 1.325 0.0 0.0 0.0 0.0 100-101 1.575 0.0 0.0 0.0 0.0 102-103 1.9125 0.0 0.0 0.0 0.0 104-105 2.2249999999999996 0.0 0.0 0.0 0.0 106-107 2.4375 0.0 0.0 0.0 0.0 108-109 2.6875 0.0 0.0 0.0 0.0 110-111 3.0125 0.0 0.0 0.0 0.0 112-113 3.525 0.0 0.0 0.0 0.0 114-115 4.025 0.0 0.0 0.0 0.0 116-117 4.449999999999999 0.0 0.0 0.0 0.0 118-119 4.9875 0.0 0.0 0.0 0.0 120-121 5.55 0.0 0.0 0.0 0.0 122-123 6.125 0.0 0.0 0.0 0.0 124-125 6.8875 0.0 0.0 0.0 0.0 126-127 7.4375 0.0 0.0 0.0 0.0 128-129 7.9625 0.0 0.0 0.0 0.0 130-131 8.625 0.0 0.0 0.0 0.0 132-133 9.25 0.0 0.0 0.0 0.0 134-135 9.95 0.0 0.0 0.0 0.0 136-137 10.7 0.0 0.0 0.0 0.0 138-139 11.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAGAAAC 10 0.006830828 145.0 3 >>END_MODULE Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra Read 613331 spots for SRR7170197.sra Written 613331 spots for SRR7170197.sra Read 613323 spots for SRR7170197.sra Written 613323 spots for SRR7170197.sra SRR ids: ['SRR7170197.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_c__hto7t SRR7170197.sra spots: 12266468 blocks: [[1, 613323], [613324, 1226646], [1226647, 1839969], [1839970, 2453292], [2453293, 3066615], [3066616, 3679938], [3679939, 4293261], [4293262, 4906584], [4906585, 5519907], [5519908, 6133230], [6133231, 6746553], [6746554, 7359876], [7359877, 7973199], [7973200, 8586522], [8586523, 9199845], [9199846, 9813168], [9813169, 10426491], [10426492, 11039814], [11039815, 11653137], [11653138, 12266468]] SRR7170197 file size 4135003 SRR7170197 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 SRR7170197 SRR7170197_1.fastq SRR7170197_2.fastq Input file: SRR7170197_1.fastq Paired file: SRR7170197_2.fastq trimmed: SRR7170197-trimmed-pair1.fastq, SRR7170197-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 18:19:06 2025 >> started Wed Feb 12 18:19:20 2025 >> done (13.995s) 12266468 read pairs processed; of these: 10114 ( 0.08%) short read pairs filtered out after trimming by size control 8702 ( 0.07%) empty read pairs filtered out after trimming by size control 12247652 (99.85%) read pairs available; of these: 5339921 (43.60%) trimmed read pairs available after processing 6907731 (56.40%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 9 0.00% 20 9 0.00% 21 8 0.00% 22 12 0.00% 23 6 0.00% 24 11 0.00% 25 7 0.00% 26 12 0.00% 27 6 0.00% 28 15 0.00% 29 10 0.00% 30 9 0.00% 31 9 0.00% 32 10 0.00% 33 14 0.00% 34 10 0.00% 35 20 0.00% 36 8 0.00% 37 10 0.00% 38 18 0.00% 39 29 0.00% 40 28 0.00% 41 24 0.00% 42 28 0.00% 43 35 0.00% 44 37 0.00% 45 39 0.00% 46 61 0.00% 47 57 0.00% 48 85 0.00% 49 72 0.00% 50 92 0.00% 51 111 0.00% 52 94 0.00% 53 137 0.00% 54 133 0.00% 55 164 0.00% 56 172 0.00% 57 179 0.00% 58 196 0.00% 59 262 0.00% 60 301 0.00% 61 325 0.00% 62 354 0.00% 63 442 0.00% 64 469 0.00% 65 536 0.00% 66 580 0.00% 67 708 0.01% 68 945 0.01% 69 1162 0.01% 70 1624 0.01% 71 1661 0.01% 72 1622 0.01% 73 1652 0.01% 74 1778 0.01% 75 1986 0.02% 76 2144 0.02% 77 2440 0.02% 78 2650 0.02% 79 2940 0.02% 80 3337 0.03% 81 3791 0.03% 82 4242 0.03% 83 4982 0.04% 84 5896 0.05% 85 6527 0.05% 86 6940 0.06% 87 7547 0.06% 88 8132 0.07% 89 8952 0.07% 90 9681 0.08% 91 10126 0.08% 92 11337 0.09% 93 12163 0.10% 94 12985 0.11% 95 13906 0.11% 96 14505 0.12% 97 15261 0.12% 98 15857 0.13% 99 16701 0.14% 100 17708 0.14% 101 18412 0.15% 102 19898 0.16% 103 21037 0.17% 104 22129 0.18% 105 23049 0.19% 106 23745 0.19% 107 24487 0.20% 108 25769 0.21% 109 26030 0.21% 110 26655 0.22% 111 28004 0.23% 112 29764 0.24% 113 31095 0.25% 114 32268 0.26% 115 33570 0.27% 116 34014 0.28% 117 34911 0.29% 118 35048 0.29% 119 35768 0.29% 120 36575 0.30% 121 37805 0.31% 122 39342 0.32% 123 40656 0.33% 124 42440 0.35% 125 42800 0.35% 126 44876 0.37% 127 44717 0.37% 128 45658 0.37% 129 46452 0.38% 130 47023 0.38% 131 48010 0.39% 132 50274 0.41% 133 52268 0.43% 134 54000 0.44% 135 55734 0.46% 136 57468 0.47% 137 59016 0.48% 138 61223 0.50% 139 62889 0.51% 140 63973 0.52% 141 68045 0.56% 142 71239 0.58% 143 77298 0.63% 144 85258 0.70% 145 95233 0.78% 146 112175 0.92% 147 140316 1.15% 148 194705 1.59% 149 364073 2.97% 150 2333579 19.05% 151 6907731 56.40% 12247652 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=42 prefix-density=0.18 prefix-fanout=2.0 sequence=CCAACATACCAGTGCACAAACGCACGCTTGGCATACATGAGATCAAACTTGTGGTCAATGCGAGAGAAGACTTCTGCAACACTTGTGGAATTGGAAATCATGCAAACAGCCCTCTGAACCTTAGCAAGGTCGCCTCCTGGAACAACAGTTGGTGGCTGGTAGTTGATGCCACACTTGAACCCAGTTGGGCACCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=150.84 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=6.7 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCAC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=2.44 fanout-score-rank=37 prefix-density=0.25 prefix-fanout=2.0 sequence=TGCATTTCGATT criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=209.93 fanout-score-rank=1 prefix-density=0.21 prefix-fanout=13.9 sequence=GAGGAGAAGGAACACGAGGATACTAGTGTTCCTGTCGAGGTAGTCCATACAGAGACACCCCATGAACCAGAGGATAAGAAGGGTTTCCTTGACAAAATCAAGGAGAAATTGCCAGGACATAAGAAAGCTGACGAGGTCCCTCCTCCAGCTCCTGAACATGTTTCCCCTGAAGCTGCAGTTTCCCATGAAGGAGATGCCAAGGAGAAGAAGGGACTACTCGAGAAGATCAAGGAGA SRR7170197 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 18:20:02 Started mapping on | Feb 12 18:20:02 Finished on | Feb 12 18:21:25 Mapping speed, Million of reads per hour | 531.22 Number of input reads | 12247652 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 11525479 Uniquely mapped reads % | 94.10% Average mapped length | 291.06 Number of splices: Total | 10830880 Number of splices: Annotated (sjdb) | 10645715 Number of splices: GT/AG | 10669191 Number of splices: GC/AG | 127333 Number of splices: AT/AC | 9237 Number of splices: Non-canonical | 25119 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.03% Deletion average length | 2.74 Insertion rate per base | 0.02% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 201840 % of reads mapped to multiple loci | 1.65% Number of reads mapped to too many loci | 116284 % of reads mapped to too many loci | 0.95% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.19% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 530901 530901 530901 N_multimapping 201840 201840 201840 N_noFeature 300639 11405731 348562 N_ambiguous 115954 587 43747 UnstrandedReadsAssigned:11108886 PositiveStrandReadsAssigned:119161 NegativeStrandReadsAssigned:11133170 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR7170197 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: SRR7170197-trimmed-pair1.fastq SRR7170197-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,247,652 reads, 11,122,560 reads pseudoaligned [quant] estimated average fragment length: 222.883 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 999 rounds 52401 SRR7170197.ke.tsv 34699 SRR7170197.se.tsv 87100 total ==> SRR7170197.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1796.12 187 9.81141 Potri.005G024800.1.v4.1 1035 813.117 33 3.82459 Potri.004G059700.1.v4.1 961 739.198 1 0.127486 Potri.007G009000.2.v4.1 1416 1194.12 0 0 Potri.003G141000.2.v4.1 2943 2721.12 218.032 7.55089 Potri.016G087400.1.v4.1 270 93.5895 1276.23 1285.07 Potri.015G069301.1.v4.1 564 347.561 0 0 Potri.010G195200.1.v4.1 1773 1551.12 5 0.303773 Potri.012G127500.1.v4.1 977 755.158 4261 531.738 ==> SRR7170197.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1046 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 196 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 3 SRR7170197 completed mapping pipeline successfully