Starting /dee2/code/volunteer_pipeline.sh SRR8846521 current disk space = 1506020503552 free memory = 1370353352 SRR8846521 SRAfilesize 529846825e4db671589c1e9262b7bde1 SRR8846521.sra SRR8846521.sra file validated SRR8846521 is paired end SRR8846521 is conventional basespace SRR8846521 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846521_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.682 25.0 18.0 32.0 18.0 33.0 2 24.08975 25.0 18.0 30.0 18.0 33.0 3 27.78625 29.0 27.0 31.0 18.0 33.0 4 30.648 31.0 29.0 33.0 27.0 33.0 5 32.042 33.0 32.0 33.0 31.0 33.0 6 35.88075 38.0 36.0 38.0 33.0 38.0 7 36.76125 38.0 38.0 38.0 34.0 38.0 8 36.79875 38.0 38.0 38.0 34.0 38.0 9 37.0755 38.0 38.0 38.0 36.0 38.0 10-14 37.192499999999995 38.0 38.0 38.0 36.2 38.0 15-19 37.479749999999996 38.0 38.0 38.0 37.2 38.0 20-24 37.53855 38.0 38.0 38.0 37.6 38.0 25-29 37.3581 38.0 38.0 38.0 37.0 38.0 30-34 37.1394 38.0 38.0 38.0 36.4 38.0 35-39 37.1808 38.0 38.0 38.0 36.2 38.0 40-44 37.3472 38.0 38.0 38.0 37.0 38.0 45-49 37.225100000000005 38.0 38.0 38.0 36.4 38.0 50-54 37.077600000000004 38.0 38.0 38.0 36.0 38.0 55-59 36.95195 38.0 38.0 38.0 35.8 38.0 60-64 36.9843 38.0 38.0 38.0 35.6 38.0 65-69 37.03805 38.0 38.0 38.0 36.0 38.0 70-74 36.93755 38.0 38.0 38.0 35.4 38.0 75-79 36.7986 38.0 38.0 38.0 34.8 38.0 80-84 36.2088 38.0 37.0 38.0 32.6 38.0 85-89 36.12165 38.0 37.0 38.0 33.0 38.0 90-94 36.402699999999996 38.0 37.6 38.0 33.8 38.0 95-99 36.42235 38.0 37.6 38.0 34.0 38.0 100-104 35.8827 38.0 36.8 38.0 32.0 38.0 105-109 34.88585 38.0 35.2 38.0 26.6 38.0 110-114 35.59315 38.0 36.2 38.0 30.6 38.0 115-119 35.69045 38.0 36.4 38.0 31.4 38.0 120-124 35.275349999999996 38.0 35.4 38.0 29.6 38.0 125-129 34.34355 38.0 34.4 38.0 24.8 38.0 130-134 33.9002 38.0 34.0 38.0 23.0 38.0 135-139 34.33355 38.0 34.6 38.0 25.6 38.0 140-144 33.769499999999994 38.0 34.0 38.0 23.0 38.0 145-149 32.973 38.0 33.6 38.0 18.6 38.0 150-151 27.785 34.5 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 1.0 15 1.0 16 3.0 17 0.0 18 1.0 19 2.0 20 4.0 21 2.0 22 5.0 23 7.0 24 8.0 25 7.0 26 9.0 27 26.0 28 36.0 29 43.0 30 64.0 31 83.0 32 124.0 33 157.0 34 247.0 35 492.0 36 1166.0 37 1510.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.25 25.724999999999998 5.55 50.475 2 17.424999999999997 30.125 28.825 23.625 3 19.55 27.450000000000003 27.55 25.45 4 25.18129532383096 30.332583145786447 20.80520130032508 23.680920230057513 5 23.45 33.800000000000004 23.05 19.7 6 19.2453785768549 33.80602684223854 24.335274753102052 22.613319827804506 7 15.35 20.25 41.325 23.075000000000003 8 19.925 21.65 26.200000000000003 32.225 9 19.05 19.175 32.475 29.299999999999997 10-14 22.470000000000002 26.174999999999997 24.38 26.974999999999998 15-19 22.21 26.025 26.040000000000003 25.724999999999998 20-24 21.865000000000002 27.229999999999997 25.585 25.319999999999997 25-29 21.69 26.584999999999997 25.924999999999997 25.8 30-34 22.21 26.41 26.029999999999998 25.35 35-39 21.97 25.89 26.575 25.564999999999998 40-44 22.88 26.245 25.52 25.355 45-49 22.105 26.424999999999997 25.77 25.7 50-54 22.79 25.905 26.14 25.165 55-59 22.62 26.275 25.255 25.85 60-64 22.445 26.43 26.08 25.045 65-69 22.189999999999998 26.185000000000002 26.56 25.064999999999998 70-74 22.09 25.814999999999998 26.365 25.729999999999997 75-79 22.52 25.55 26.174999999999997 25.755 80-84 22.578386758013703 24.898734810221534 26.623993599039856 25.89888483272491 85-89 22.174978740433197 25.596518433294985 26.046721024461007 26.181781801810818 90-94 22.225556389097274 25.641410352588146 26.556639159789945 25.57639409852463 95-99 22.911145557277866 25.386269313465675 26.14130706535327 25.5612780639032 100-104 23.07 26.095000000000002 26.22 24.615000000000002 105-109 23.385 25.14 25.94 25.535000000000004 110-114 22.46 25.885 26.07 25.585 115-119 22.78 25.855 25.319999999999997 26.045 120-124 23.14 24.81 25.885 26.165 125-129 23.365 25.77 25.71 25.155 130-134 23.074614922984598 25.23004600920184 26.12022404480896 25.575115023004603 135-139 23.438203371179913 25.06377232031211 25.784024408542987 25.71399989996499 140-144 23.205442449102094 25.45645540493222 25.986694012305538 25.351408133660147 145-149 23.145 25.715 25.31 25.83 150-151 23.62589207462126 25.328659070990362 25.81695254789032 25.22849630649806 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 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 0.5 21 0.5 22 0.5 23 0.5 24 0.5 25 1.0 26 3.5 27 4.0 28 5.0 29 8.0 30 11.0 31 13.5 32 11.5 33 21.5 34 31.0 35 43.0 36 60.5 37 74.0 38 89.0 39 106.0 40 138.0 41 181.0 42 210.0 43 209.5 44 204.0 45 205.0 46 207.0 47 203.5 48 213.5 49 201.0 50 157.0 51 149.5 52 138.0 53 114.5 54 104.5 55 95.0 56 91.5 57 86.5 58 76.0 59 64.5 60 55.0 61 53.0 62 55.5 63 51.0 64 42.0 65 33.5 66 27.5 67 24.5 68 25.0 69 26.5 70 20.5 71 14.0 72 12.0 73 10.0 74 6.5 75 4.0 76 2.5 77 0.5 78 0.0 79 0.5 80 1.0 81 0.5 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.025 5 0.0 6 1.275 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 0.015 85-89 0.045 90-94 0.025 95-99 0.005 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.02 135-139 0.034999999999999996 140-144 0.045 145-149 0.0 150-151 0.1625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.65 #Duplication Level Percentage of deduplicated Percentage of total 1 99.64877069744105 99.3 2 0.35122930255895635 0.7000000000000001 3 0.0 0.0 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 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 0.0 0.0 0.0 0.0 0.0 84-85 0.0125 0.0 0.0 0.0 0.0 86-87 0.025 0.0 0.0 0.0 0.0 88-89 0.05 0.0 0.0 0.0 0.0 90-91 0.05 0.0 0.0 0.0 0.0 92-93 0.05 0.0 0.0 0.0 0.0 94-95 0.0625 0.0 0.0 0.0 0.0 96-97 0.0875 0.0 0.0 0.0 0.0 98-99 0.1 0.0 0.0 0.0 0.0 100-101 0.1375 0.0 0.0 0.0 0.0 102-103 0.15 0.0 0.0 0.0 0.0 104-105 0.25 0.0 0.0 0.0 0.0 106-107 0.30000000000000004 0.0 0.0 0.0 0.0 108-109 0.3875 0.0 0.0 0.0 0.0 110-111 0.4625 0.0 0.0 0.0 0.0 112-113 0.5125 0.0 0.0 0.0 0.0 114-115 0.6 0.0 0.0 0.0 0.0 116-117 0.65 0.0 0.0 0.0 0.0 118-119 0.75 0.0 0.0 0.0 0.0 120-121 0.8875 0.0 0.0 0.0 0.0 122-123 1.0375 0.0 0.0 0.0 0.0 124-125 1.2999999999999998 0.0 0.0 0.0 0.0 126-127 1.4125 0.0 0.0 0.0 0.0 128-129 1.525 0.0 0.0 0.0 0.0 130-131 1.7 0.0 0.0 0.0 0.0 132-133 1.8624999999999998 0.0 0.0 0.0 0.0 134-135 2.0 0.0 0.0 0.0 0.0 136-137 2.1375 0.0 0.0 0.0 0.0 138-139 2.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCGGAG 10 0.006830828 145.0 6 >>END_MODULE SRR8846521 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846521_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.778 33.0 33.0 34.0 32.0 34.0 2 32.63975 33.0 33.0 34.0 32.0 34.0 3 32.94475 34.0 33.0 34.0 32.0 34.0 4 33.03075 34.0 33.0 34.0 32.0 34.0 5 33.0355 34.0 33.0 34.0 32.0 34.0 6 37.32525 38.0 38.0 38.0 37.0 38.0 7 37.2765 38.0 38.0 38.0 37.0 38.0 8 37.36175 38.0 38.0 38.0 37.0 38.0 9 37.31925 38.0 38.0 38.0 37.0 38.0 10-14 37.2542 38.0 38.0 38.0 37.0 38.0 15-19 37.04795 38.0 38.0 38.0 36.2 38.0 20-24 36.9225 38.0 38.0 38.0 35.8 38.0 25-29 36.8938 38.0 38.0 38.0 35.6 38.0 30-34 36.990300000000005 38.0 38.0 38.0 35.8 38.0 35-39 37.0021 38.0 38.0 38.0 36.0 38.0 40-44 36.763099999999994 38.0 38.0 38.0 35.0 38.0 45-49 36.4597 38.0 38.0 38.0 33.8 38.0 50-54 36.635149999999996 38.0 38.0 38.0 34.4 38.0 55-59 36.6563 38.0 38.0 38.0 34.6 38.0 60-64 36.3959 38.0 38.0 38.0 33.8 38.0 65-69 36.45725 38.0 38.0 38.0 33.8 38.0 70-74 36.755 38.0 38.0 38.0 35.0 38.0 75-79 36.8059 38.0 38.0 38.0 35.2 38.0 80-84 36.662400000000005 38.0 38.0 38.0 34.6 38.0 85-89 36.5072 38.0 38.0 38.0 34.0 38.0 90-94 36.31805000000001 38.0 38.0 38.0 33.8 38.0 95-99 36.0888 38.0 37.2 38.0 33.2 38.0 100-104 36.0431 38.0 37.0 38.0 33.0 38.0 105-109 35.6344 38.0 36.6 38.0 31.4 38.0 110-114 35.4423 38.0 36.0 38.0 30.0 38.0 115-119 35.43655 38.0 36.0 38.0 30.2 38.0 120-124 35.53125000000001 38.0 36.0 38.0 31.0 38.0 125-129 35.42195 38.0 36.0 38.0 30.6 38.0 130-134 34.8058 38.0 35.0 38.0 27.4 38.0 135-139 34.47535 38.0 35.0 38.0 25.2 38.0 140-144 34.4571 38.0 34.6 38.0 27.0 38.0 145-149 33.6219 38.0 33.0 38.0 23.4 38.0 150-151 29.106499999999997 36.0 18.0 37.5 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 3 1.0 4 0.0 5 1.0 6 2.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 2.0 13 4.0 14 0.0 15 1.0 16 0.0 17 2.0 18 8.0 19 2.0 20 2.0 21 3.0 22 12.0 23 11.0 24 6.0 25 24.0 26 19.0 27 32.0 28 27.0 29 53.0 30 62.0 31 83.0 32 90.0 33 131.0 34 165.0 35 315.0 36 706.0 37 2234.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.625 13.65 11.5 36.225 2 28.9 19.55 31.45 20.1 3 21.325 23.9 29.875 24.9 4 26.474999999999998 32.625 18.375 22.525000000000002 5 27.1 32.95 18.875 21.075 6 20.275000000000002 35.075 21.25 23.400000000000002 7 20.7 15.475 39.2 24.625 8 21.925 22.225 24.45 31.4 9 22.675 20.200000000000003 28.475 28.65 10-14 26.790000000000003 24.465 23.01 25.735000000000003 15-19 25.64756475647565 24.682468246824683 24.722472247224722 24.947494749474945 20-24 25.415 25.759999999999998 24.975 23.849999999999998 25-29 25.509999999999998 25.319999999999997 25.045 24.125 30-34 25.745 25.28 24.965 24.01 35-39 25.445 25.66 24.87 24.025 40-44 26.009999999999998 25.545 24.39 24.055 45-49 25.240000000000002 25.474999999999998 25.14 24.145 50-54 25.50755075507551 25.26252625262526 25.227522752275227 24.002400240024002 55-59 25.716429107276817 25.63640910227557 24.98624656164041 23.6609152288072 60-64 24.991249562478124 25.5612780639032 25.496274813740687 23.951197559877993 65-69 25.81 25.535000000000004 24.884999999999998 23.77 70-74 26.005 25.715 24.81 23.47 75-79 25.27 25.790000000000003 25.055 23.885 80-84 26.029999999999998 26.14 24.104999999999997 23.724999999999998 85-89 25.779999999999998 26.064999999999998 24.945 23.21 90-94 25.73257325732573 25.717571757175715 24.947494749474945 23.602360236023603 95-99 26.175470188075227 25.26010404161665 24.899959983993597 23.664465786314526 100-104 26.218352846992893 25.637946562593818 25.367757430201145 22.775943160212147 105-109 25.79450477954056 26.530203693508835 24.748511085531256 22.926780441419346 110-114 25.68811930737664 25.963367030327294 24.80732659393454 23.541187068361523 115-119 25.780312124849942 25.755302120848338 25.245098039215684 23.219287715086033 120-124 25.792737821346407 25.852755826748027 25.07752325697709 23.27698309492848 125-129 26.15284585375613 25.76272881864559 25.307592277683305 22.776833049914973 130-134 26.006703016357363 25.951678255214844 24.971237056675506 23.070381671752287 135-139 26.033905085762864 25.808871330699606 25.38380757113567 22.77341601240186 140-144 26.215486194477787 26.355542216886757 24.9499799919968 22.478991596638657 145-149 26.34158539634909 26.076519129782444 25.0112528132033 22.570642660665165 150-151 26.72338296009008 25.58488677592894 25.684974352558488 22.006755911422495 >>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 0.5 21 0.5 22 0.0 23 0.5 24 0.5 25 0.0 26 0.0 27 0.0 28 1.5 29 5.5 30 10.0 31 10.5 32 9.0 33 10.0 34 18.0 35 26.5 36 40.5 37 63.5 38 75.5 39 93.5 40 121.5 41 138.0 42 167.5 43 179.0 44 177.5 45 201.0 46 208.5 47 193.5 48 185.5 49 178.5 50 163.5 51 149.5 52 138.5 53 132.5 54 109.5 55 99.0 56 99.0 57 88.5 58 98.5 59 95.5 60 82.0 61 75.5 62 67.0 63 71.0 64 66.0 65 57.0 66 51.0 67 48.0 68 49.0 69 36.0 70 24.5 71 23.0 72 19.5 73 14.5 74 9.5 75 4.0 76 4.0 77 4.0 78 1.0 79 0.5 80 0.5 81 0.0 82 0.5 83 0.5 84 0.5 85 0.5 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 0.0 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 0.01 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 0.01 55-59 0.025 60-64 0.005 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.01 95-99 0.04 100-104 0.06999999999999999 105-109 0.095 110-114 0.09 115-119 0.04 120-124 0.03 125-129 0.03 130-134 0.045 135-139 0.015 140-144 0.04 145-149 0.025 150-151 0.08750000000000001 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.225 #Duplication Level Percentage of deduplicated Percentage of total 1 99.37011841773746 98.6 2 0.5291005291005291 1.05 3 0.07558578987150416 0.22499999999999998 4 0.0 0.0 5 0.02519526329050139 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CCTCTTGTTAGCTATCTACGTACGTGTACGATGGCTCCCACAGTGATGTC 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 0.0 84-85 0.0125 0.0 0.0 0.0 0.0 86-87 0.025 0.0 0.0 0.0 0.0 88-89 0.05 0.0 0.0 0.0 0.0 90-91 0.05 0.0 0.0 0.0 0.0 92-93 0.05 0.0 0.0 0.0 0.0 94-95 0.0625 0.0 0.0 0.0 0.0 96-97 0.0875 0.0 0.0 0.0 0.0 98-99 0.1 0.0 0.0 0.0 0.0 100-101 0.15 0.0 0.0 0.0 0.0 102-103 0.175 0.0 0.0 0.0 0.0 104-105 0.25 0.0 0.0 0.0 0.0 106-107 0.30000000000000004 0.0 0.0 0.0 0.0 108-109 0.3875 0.0 0.0 0.0 0.0 110-111 0.44999999999999996 0.0 0.0 0.0 0.0 112-113 0.4875 0.0 0.0 0.0 0.0 114-115 0.575 0.0 0.0 0.0 0.0 116-117 0.625 0.0 0.0 0.0 0.0 118-119 0.7250000000000001 0.0 0.0 0.0 0.0 120-121 0.8625 0.0 0.0 0.0 0.0 122-123 1.0125 0.0 0.0 0.0 0.0 124-125 1.275 0.0 0.0 0.0 0.0 126-127 1.3875 0.0 0.0 0.0 0.0 128-129 1.5 0.0 0.0 0.0 0.0 130-131 1.675 0.0 0.0 0.0 0.0 132-133 1.8375 0.0 0.0 0.0 0.0 134-135 1.975 0.0 0.0 0.0 0.0 136-137 2.1375 0.0 0.0 0.0 0.0 138-139 2.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659124 spots for SRR8846521.sra Written 1659124 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra Read 1659105 spots for SRR8846521.sra Written 1659105 spots for SRR8846521.sra SRR ids: ['SRR8846521.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fkz1hbpq SRR8846521.sra spots: 33182119 blocks: [[1, 1659105], [1659106, 3318210], [3318211, 4977315], [4977316, 6636420], [6636421, 8295525], [8295526, 9954630], [9954631, 11613735], [11613736, 13272840], [13272841, 14931945], [14931946, 16591050], [16591051, 18250155], [18250156, 19909260], [19909261, 21568365], [21568366, 23227470], [23227471, 24886575], [24886576, 26545680], [26545681, 28204785], [28204786, 29863890], [29863891, 31522995], [31522996, 33182119]] SRR8846521 file size 11222630 SRR8846521 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 SRR8846521 SRR8846521_1.fastq SRR8846521_2.fastq Input file: SRR8846521_1.fastq Paired file: SRR8846521_2.fastq trimmed: SRR8846521-trimmed-pair1.fastq, SRR8846521-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 Mon Dec 9 05:47:03 2024 >> started Mon Dec 9 05:51:04 2024 >> done (241.378s) 33182119 read pairs processed; of these: 11985 ( 0.04%) short read pairs filtered out after trimming by size control 7626 ( 0.02%) empty read pairs filtered out after trimming by size control 33162508 (99.94%) read pairs available; of these: 13337290 (40.22%) trimmed read pairs available after processing 19825218 (59.78%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 16 0.00% 19 14 0.00% 20 10 0.00% 21 13 0.00% 22 8 0.00% 23 12 0.00% 24 10 0.00% 25 18 0.00% 26 18 0.00% 27 11 0.00% 28 14 0.00% 29 15 0.00% 30 23 0.00% 31 22 0.00% 32 13 0.00% 33 13 0.00% 34 15 0.00% 35 19 0.00% 36 11 0.00% 37 20 0.00% 38 29 0.00% 39 28 0.00% 40 26 0.00% 41 25 0.00% 42 24 0.00% 43 26 0.00% 44 33 0.00% 45 36 0.00% 46 35 0.00% 47 38 0.00% 48 46 0.00% 49 40 0.00% 50 59 0.00% 51 57 0.00% 52 55 0.00% 53 73 0.00% 54 66 0.00% 55 75 0.00% 56 78 0.00% 57 94 0.00% 58 88 0.00% 59 114 0.00% 60 133 0.00% 61 133 0.00% 62 169 0.00% 63 187 0.00% 64 166 0.00% 65 187 0.00% 66 226 0.00% 67 248 0.00% 68 301 0.00% 69 314 0.00% 70 353 0.00% 71 405 0.00% 72 406 0.00% 73 541 0.00% 74 549 0.00% 75 639 0.00% 76 703 0.00% 77 770 0.00% 78 849 0.00% 79 977 0.00% 80 1125 0.00% 81 1274 0.00% 82 1370 0.00% 83 1654 0.00% 84 2353 0.01% 85 2783 0.01% 86 2992 0.01% 87 3069 0.01% 88 3419 0.01% 89 3626 0.01% 90 3913 0.01% 91 4160 0.01% 92 4565 0.01% 93 5045 0.02% 94 5561 0.02% 95 5781 0.02% 96 6354 0.02% 97 6693 0.02% 98 7277 0.02% 99 7734 0.02% 100 8364 0.03% 101 9093 0.03% 102 9843 0.03% 103 10545 0.03% 104 11053 0.03% 105 11922 0.04% 106 13036 0.04% 107 13745 0.04% 108 15184 0.05% 109 16050 0.05% 110 16874 0.05% 111 17642 0.05% 112 18823 0.06% 113 20018 0.06% 114 21032 0.06% 115 22621 0.07% 116 24082 0.07% 117 25244 0.08% 118 26853 0.08% 119 27845 0.08% 120 29702 0.09% 121 32015 0.10% 122 33384 0.10% 123 34553 0.10% 124 36815 0.11% 125 38815 0.12% 126 41058 0.12% 127 44006 0.13% 128 46347 0.14% 129 49039 0.15% 130 52315 0.16% 131 56046 0.17% 132 59273 0.18% 133 63589 0.19% 134 68627 0.21% 135 74178 0.22% 136 80164 0.24% 137 86214 0.26% 138 94461 0.28% 139 104859 0.32% 140 113449 0.34% 141 126741 0.38% 142 144988 0.44% 143 167342 0.50% 144 198470 0.60% 145 251296 0.76% 146 342834 1.03% 147 510238 1.54% 148 714048 2.15% 149 1575924 4.75% 150 7636187 23.03% 151 19825218 59.78% 33162508 reads passed initial QC criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=2.61 fanout-score-rank=26 prefix-density=0.79 prefix-fanout=2.5 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTCAGGGTACTCCTT criterion=fanout-score sequence-density=0.03 sequence-density-rank=30 fanout-score=105.70 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=9.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAA criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=3.24 fanout-score-rank=20 prefix-density=0.69 prefix-fanout=3.0 sequence=GAGTTCAGCAAGGTCGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=24 fanout-score=669.76 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=19.9 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR8846521 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 05:55:54 Started mapping on | Dec 09 05:55:56 Finished on | Dec 09 06:15:55 Mapping speed, Million of reads per hour | 99.57 Number of input reads | 33162508 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 32510789 Uniquely mapped reads % | 98.03% Average mapped length | 297.61 Number of splices: Total | 37518108 Number of splices: Annotated (sjdb) | 35442478 Number of splices: GT/AG | 37055880 Number of splices: GC/AG | 415273 Number of splices: AT/AC | 19198 Number of splices: Non-canonical | 27757 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.00% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 309495 % of reads mapped to multiple loci | 0.93% Number of reads mapped to too many loci | 26959 % of reads mapped to too many loci | 0.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.48% % of reads unmapped: other | 0.47% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 350398 350398 350398 N_multimapping 309495 309495 309495 N_noFeature 1240906 31688542 1483528 N_ambiguous 669935 4488 91799 UnstrandedReadsAssigned:30599948 PositiveStrandReadsAssigned:817759 NegativeStrandReadsAssigned:30935462 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR8846521 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: SRR8846521-trimmed-pair1.fastq SRR8846521-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,162,508 reads, 31,064,617 reads pseudoaligned [quant] estimated average fragment length: 281.583 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,179 rounds 52973 SRR8846521.ke.tsv 35125 SRR8846521.se.tsv 88098 total ==> SRR8846521.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 655.897 0.00253426 0.000178624 PNS24247 1044 763.417 118.641 7.18449 PNS24249 1928 1647.42 73.1493 2.05273 PNS24246 1044 763.417 118.641 7.18449 PNS24248 1044 763.417 118.641 7.18449 PNS24244 1471 1190.42 75.926 2.9486 PNS24243 293 77.0537 0 0 KQK14069 1603 1322.42 625.961 21.8828 KQK14071 474 212.661 2.59996 0.5652 ==> SRR8846521.se.tsv <== BRADI_1g14170v3 689 BRADI_1g53295v3 53 BRADI_1g59795v3 512 BRADI_1g07683v3 0 BRADI_1g00485v3 86 BRADI_1g20270v3 4188 BRADI_1g74790v3 467 BRADI_1g09890v3 2 BRADI_1g77505v3 398 BRADI_1g48960v3 1 SRR8846521 completed mapping pipeline successfully