Starting /dee2/code/volunteer_pipeline.sh SRR6053274 current disk space = 3049400881152 free memory = 1507079860 SRR6053274 SRAfilesize 0b0d90bf0d1b5c7fcac615083dabd56c SRR6053274.sra SRR6053274.sra file validated SRR6053274 is paired end SRR6053274 is conventional basespace SRR6053274 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6053274_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.60325 34.0 33.0 34.0 32.0 34.0 2 33.01925 34.0 33.0 34.0 32.0 34.0 3 32.99525 34.0 33.0 34.0 32.0 34.0 4 32.982 34.0 33.0 34.0 32.0 34.0 5 32.88 34.0 33.0 34.0 32.0 34.0 6 36.5745 38.0 37.0 38.0 34.0 38.0 7 37.05725 38.0 38.0 38.0 36.0 38.0 8 37.18925 38.0 38.0 38.0 36.0 38.0 9 37.194 38.0 38.0 38.0 37.0 38.0 10-14 36.87325 38.0 37.8 38.0 35.0 38.0 15-19 37.03445 38.0 38.0 38.0 35.6 38.0 20-24 37.2232 38.0 38.0 38.0 37.0 38.0 25-29 34.950649999999996 37.0 32.6 38.0 29.8 38.0 30-34 36.9607 38.0 38.0 38.0 35.8 38.0 35-39 36.936350000000004 38.0 38.0 38.0 35.6 38.0 40-44 36.93675 38.0 38.0 38.0 36.0 38.0 45-49 36.96495 38.0 38.0 38.0 35.8 38.0 50-54 36.84125 38.0 38.0 38.0 35.6 38.0 55-59 36.8175 38.0 38.0 38.0 35.2 38.0 60-64 36.84499999999999 38.0 38.0 38.0 35.2 38.0 65-69 36.77255 38.0 38.0 38.0 34.8 38.0 70-74 36.775349999999996 38.0 38.0 38.0 35.0 38.0 75-79 36.6066 38.0 38.0 38.0 34.0 38.0 80-84 36.5982 38.0 38.0 38.0 34.0 38.0 85-89 36.55800000000001 38.0 38.0 38.0 34.0 38.0 90-94 36.5138 38.0 38.0 38.0 34.0 38.0 95-99 36.25235 38.0 37.8 38.0 33.6 38.0 100-104 36.128 38.0 37.2 38.0 33.2 38.0 105-109 36.117650000000005 38.0 37.4 38.0 33.2 38.0 110-114 35.7339 38.0 36.8 38.0 30.8 38.0 115-119 35.7673 38.0 37.0 38.0 31.0 38.0 120-124 35.664049999999996 38.0 36.8 38.0 30.8 38.0 125-129 34.987199999999994 38.0 35.4 38.0 27.2 38.0 130-134 35.16425 38.0 36.0 38.0 28.0 38.0 135-139 34.946799999999996 38.0 35.6 38.0 28.4 38.0 140-144 34.210249999999995 38.0 35.0 38.0 23.2 38.0 145-149 33.87599999999999 38.0 33.4 38.0 23.6 38.0 150-151 30.232625 35.5 28.0 38.0 8.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 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 2.0 12 0.0 13 3.0 14 0.0 15 2.0 16 0.0 17 0.0 18 3.0 19 2.0 20 2.0 21 4.0 22 7.0 23 13.0 24 18.0 25 11.0 26 17.0 27 32.0 28 35.0 29 40.0 30 76.0 31 87.0 32 115.0 33 118.0 34 196.0 35 290.0 36 614.0 37 2311.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.41428209673335 11.825778678146365 5.976196505444417 45.78374271967587 2 19.325 14.2 37.75 28.725 3 16.575 17.724999999999998 26.625 39.074999999999996 4 21.224999999999998 26.575 24.725 27.474999999999998 5 22.125 31.924999999999997 23.974999999999998 21.975 6 19.275000000000002 36.325 24.425 19.975 7 13.825000000000001 26.200000000000003 42.625 17.349999999999998 8 15.950000000000001 25.525 32.15 26.375 9 15.5 24.65 36.525 23.325000000000003 10-14 18.19 31.025000000000002 28.515 22.27 15-19 18.935 28.675 28.465 23.925 20-24 19.285 29.62 27.87 23.225 25-29 19.34 29.13 28.005000000000003 23.525 30-34 19.31 28.935 28.305000000000003 23.45 35-39 19.16 28.595 28.515 23.73 40-44 19.950000000000003 29.049999999999997 28.08 22.919999999999998 45-49 19.345000000000002 29.26 27.689999999999998 23.705000000000002 50-54 19.509999999999998 28.325 28.810000000000002 23.355 55-59 19.42 29.299999999999997 27.860000000000003 23.419999999999998 60-64 20.150000000000002 28.825 28.084999999999997 22.939999999999998 65-69 19.7 28.549999999999997 28.345 23.405 70-74 19.68 28.875 27.905 23.54 75-79 19.955000000000002 27.915 28.345 23.785 80-84 19.625 28.465 28.060000000000002 23.849999999999998 85-89 19.439999999999998 29.270000000000003 27.865000000000002 23.425 90-94 20.035 28.715000000000003 27.295 23.955000000000002 95-99 19.84 28.23 27.694999999999997 24.235 100-104 20.169999999999998 27.975 28.599999999999998 23.255 105-109 19.93 28.155 28.194999999999997 23.72 110-114 19.885 28.754999999999995 27.52 23.84 115-119 20.544999999999998 28.935 27.21 23.31 120-124 20.244999999999997 28.705000000000002 27.200000000000003 23.849999999999998 125-129 20.02 28.804999999999996 27.66 23.515 130-134 20.565 28.865000000000002 27.134999999999998 23.435 135-139 20.11 28.92 27.35 23.62 140-144 20.474999999999998 28.77 27.229999999999997 23.525 145-149 20.65 28.645 26.155 24.55 150-151 19.7375 29.5375 26.737499999999997 23.9875 >>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 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 1.0 20 1.5 21 1.5 22 1.5 23 2.0 24 2.0 25 2.5 26 5.5 27 7.5 28 10.5 29 13.5 30 20.5 31 33.5 32 39.0 33 56.0 34 76.5 35 85.5 36 102.0 37 121.0 38 152.0 39 178.5 40 218.5 41 253.5 42 254.5 43 255.0 44 244.0 45 249.5 46 254.0 47 246.0 48 235.5 49 197.0 50 155.0 51 105.0 52 82.0 53 87.0 54 67.0 55 43.5 56 32.5 57 29.0 58 22.0 59 13.0 60 10.0 61 8.0 62 6.0 63 5.0 64 4.0 65 3.0 66 1.5 67 1.5 68 0.5 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.5 76 0.5 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 1.275 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 99.8 #Duplication Level Percentage of deduplicated Percentage of total 1 99.8246492985972 99.625 2 0.15030060120240482 0.3 3 0.0250501002004008 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 0.0 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.3625 0.0 0.0 0.0 0.0 94-95 0.5249999999999999 0.0 0.0 0.0 0.0 96-97 0.8 0.0 0.0 0.0 0.0 98-99 1.05 0.0 0.0 0.0 0.0 100-101 1.3375 0.0 0.0 0.0 0.0 102-103 1.6875 0.0 0.0 0.0 0.0 104-105 1.9625 0.0 0.0 0.0 0.0 106-107 2.225 0.0 0.0 0.0 0.0 108-109 2.4875 0.0 0.0 0.0 0.0 110-111 2.875 0.0 0.0 0.0 0.0 112-113 3.2125 0.0 0.0 0.0 0.0 114-115 3.625 0.0 0.0 0.0 0.0 116-117 4.025 0.0 0.0 0.0 0.0 118-119 4.6 0.0 0.0 0.0 0.0 120-121 5.175000000000001 0.0 0.0 0.0 0.0 122-123 5.6625 0.0 0.0 0.0 0.0 124-125 6.4125 0.0 0.0 0.0 0.0 126-127 6.925 0.0 0.0 0.0 0.0 128-129 7.550000000000001 0.0 0.0 0.0 0.0 130-131 8.175 0.0 0.0 0.0 0.0 132-133 9.0125 0.0 0.0 0.0 0.0 134-135 9.7375 0.0 0.0 0.0 0.0 136-137 10.4125 0.0 0.0 0.0 0.0 138-139 11.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6053274 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6053274_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.45175 33.0 33.0 34.0 32.0 34.0 2 32.5695 33.0 33.0 34.0 32.0 34.0 3 32.6325 33.0 33.0 34.0 32.0 34.0 4 32.43725 33.0 33.0 34.0 32.0 34.0 5 32.216 33.0 33.0 34.0 31.0 34.0 6 36.45 38.0 38.0 38.0 34.0 38.0 7 36.41275 38.0 38.0 38.0 34.0 38.0 8 36.66025 38.0 38.0 38.0 35.0 38.0 9 36.606 38.0 38.0 38.0 34.0 38.0 10-14 36.6452 38.0 38.0 38.0 34.8 38.0 15-19 36.66754999999999 38.0 38.0 38.0 35.2 38.0 20-24 36.67815 38.0 38.0 38.0 35.2 38.0 25-29 36.65655 38.0 38.0 38.0 35.2 38.0 30-34 36.54515 38.0 38.0 38.0 34.8 38.0 35-39 36.47905 38.0 38.0 38.0 34.4 38.0 40-44 35.956849999999996 38.0 38.0 38.0 32.0 38.0 45-49 36.137350000000005 38.0 38.0 38.0 33.4 38.0 50-54 36.33885 38.0 38.0 38.0 34.0 38.0 55-59 36.3464 38.0 38.0 38.0 34.0 38.0 60-64 36.30975 38.0 38.0 38.0 34.0 38.0 65-69 35.734300000000005 38.0 37.2 38.0 30.6 38.0 70-74 36.25015 38.0 38.0 38.0 33.8 38.0 75-79 36.23215 38.0 38.0 38.0 34.0 38.0 80-84 36.121050000000004 38.0 38.0 38.0 33.4 38.0 85-89 35.9597 38.0 37.8 38.0 32.6 38.0 90-94 35.7196 38.0 37.4 38.0 31.0 38.0 95-99 35.19735 38.0 36.6 38.0 27.8 38.0 100-104 35.276799999999994 38.0 37.0 38.0 28.4 38.0 105-109 35.4402 38.0 37.0 38.0 29.6 38.0 110-114 35.27945 38.0 36.8 38.0 28.8 38.0 115-119 35.14065 38.0 36.2 38.0 28.2 38.0 120-124 35.077549999999995 38.0 36.2 38.0 28.0 38.0 125-129 34.54545 38.0 35.2 38.0 25.0 38.0 130-134 34.02145 38.0 34.2 38.0 22.8 38.0 135-139 33.24885 38.0 33.4 38.0 15.0 38.0 140-144 32.5805 38.0 33.0 38.0 13.0 38.0 145-149 31.5696 38.0 33.0 38.0 6.4 38.0 150-151 27.060499999999998 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 23.0 3 4.0 4 2.0 5 0.0 6 1.0 7 0.0 8 1.0 9 1.0 10 0.0 11 2.0 12 1.0 13 3.0 14 2.0 15 1.0 16 3.0 17 4.0 18 5.0 19 7.0 20 6.0 21 10.0 22 9.0 23 21.0 24 20.0 25 39.0 26 33.0 27 50.0 28 52.0 29 72.0 30 64.0 31 92.0 32 130.0 33 153.0 34 186.0 35 283.0 36 518.0 37 2202.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 32.824999999999996 25.3 10.625 31.25 2 26.343545956805624 26.594676042189853 32.345554997488705 14.716223003515822 3 18.709191361125065 28.980411853340033 31.391260673028633 20.91913611250628 4 21.597187343043696 35.18332496233049 24.962330487192368 18.25715720743345 5 25.251256281407038 36.733668341708544 20.829145728643216 17.185929648241206 6 21.3801756587202 39.849435382685066 22.534504391468005 16.23588456712673 7 20.045158053186153 21.976919217260413 39.53838434520823 18.43953838434521 8 20.92848180677541 25.144291091593473 29.962358845671268 23.96486825595985 9 21.163490471414242 24.222668004012036 33.42527582748245 21.188565697091274 10-14 22.826305220883533 28.95582329317269 27.279116465863453 20.938755020080322 15-19 23.363453815261046 28.23293172690763 27.786144578313255 20.617469879518072 20-24 22.83894905736061 28.770557561171277 27.60730044123546 20.78319294023265 25-29 23.17189460476788 28.53701380175659 28.02007528230866 20.271016311166875 30-34 23.030211783599317 29.358626919602532 27.155475258456292 20.455686038341863 35-39 22.97921478060046 28.56712521337484 27.783914047595136 20.669745958429562 40-44 23.77892676070478 27.493599718889616 28.74855679935746 19.97891672104814 45-49 23.211598274305207 28.45389786294773 28.167954249021772 20.166549613725294 50-54 23.135975915704968 28.299046663321626 27.94279979929754 20.622177621675867 55-59 23.42871485943775 28.0070281124498 27.931726907630523 20.632530120481928 60-64 23.43404938767316 27.49949809275246 28.7592852840795 20.30716723549488 65-69 23.15181932245922 28.316185696361355 27.909661229611043 20.62233375156838 70-74 23.356931264748706 28.156850931365163 27.885725761911935 20.600492041974192 75-79 23.48275688971437 28.30681190703278 27.493599718889616 20.716831484363237 80-84 23.771520353360437 28.208603122019777 27.88736636048788 20.132510164131908 85-89 23.974114578107756 27.831845088793017 27.7365305508177 20.45750978228153 90-94 23.811674948551925 28.1282939316368 28.273854339205943 19.78617678060533 95-99 23.95582329317269 28.99598393574297 27.776104417670684 19.272088353413654 100-104 24.854505318081475 28.306241220148504 26.80614087898856 20.033112582781456 105-109 24.058829434795705 28.270253990563198 27.81849211926513 19.852424455375967 110-114 24.337615415495783 27.724809313528702 27.93556804496186 20.00200722601365 115-119 24.775385233147617 28.499723937158063 27.992772172865532 18.732118656828792 120-124 24.535689187832546 28.686878827426966 27.31653448448951 19.46089750025098 125-129 25.247201726647596 28.670380966721883 27.259950810620893 18.82246649600964 130-134 25.452630523095443 28.54706855910527 26.982296002808564 19.018004914990723 135-139 25.827182808655923 27.996184164281768 26.981975197067833 19.194657829994476 140-144 25.75658720200753 28.516938519447933 26.66499372647428 19.061480552070265 145-149 26.00642505772513 28.616604758558378 26.423049894588896 18.9539202891276 150-151 26.3679718875502 28.237951807228917 27.03313253012048 18.360943775100402 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 3.5 2 5.0 3 2.0 4 0.5 5 0.0 6 1.0 7 1.0 8 0.0 9 0.0 10 0.0 11 0.5 12 1.5 13 1.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 1.0 22 2.0 23 3.0 24 4.5 25 6.0 26 5.0 27 4.0 28 7.0 29 9.5 30 12.5 31 20.5 32 31.0 33 40.0 34 54.0 35 69.5 36 94.5 37 118.0 38 134.0 39 177.0 40 206.0 41 226.5 42 259.0 43 282.0 44 286.0 45 280.5 46 288.0 47 269.5 48 216.0 49 184.5 50 162.5 51 132.0 52 105.0 53 71.0 54 52.0 55 48.0 56 36.0 57 22.5 58 16.5 59 10.0 60 5.0 61 4.5 62 4.5 63 5.5 64 6.0 65 2.0 66 0.5 67 1.5 68 2.0 69 1.5 70 1.0 71 1.5 72 1.0 73 0.0 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 0.0 2 0.44999999999999996 3 0.44999999999999996 4 0.44999999999999996 5 0.5 6 0.375 7 0.35000000000000003 8 0.375 9 0.3 10-14 0.4 15-19 0.4 20-24 0.27999999999999997 25-29 0.375 30-34 0.37 35-39 0.41000000000000003 40-44 0.395 45-49 0.33 50-54 0.35000000000000003 55-59 0.4 60-64 0.38 65-69 0.375 70-74 0.415 75-79 0.395 80-84 0.385 85-89 0.33 90-94 0.385 95-99 0.4 100-104 0.33999999999999997 105-109 0.38999999999999996 110-114 0.36 115-119 0.385 120-124 0.38999999999999996 125-129 0.385 130-134 0.305 135-139 0.415 140-144 0.375 145-149 0.38999999999999996 150-151 0.4 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.55000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.6735308890005 99.225 2 0.22601707684580613 0.44999999999999996 3 0.07533902561526871 0.22499999999999998 4 0.025113008538422906 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 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 0.0 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.3625 0.0 0.0 0.0 0.0 94-95 0.5249999999999999 0.0 0.0 0.0 0.0 96-97 0.8 0.0 0.0 0.0 0.0 98-99 1.0625 0.0 0.0 0.0 0.0 100-101 1.3624999999999998 0.0 0.0 0.0 0.0 102-103 1.7125 0.0 0.0 0.0 0.0 104-105 1.9875 0.0 0.0 0.0 0.0 106-107 2.2874999999999996 0.0 0.0 0.0 0.0 108-109 2.5875 0.0 0.0 0.0 0.0 110-111 2.9625000000000004 0.0 0.0 0.0 0.0 112-113 3.2625 0.0 0.0 0.0 0.0 114-115 3.675 0.0 0.0 0.0 0.0 116-117 4.05 0.0 0.0 0.0 0.0 118-119 4.5625 0.0 0.0 0.0 0.0 120-121 5.125 0.0 0.0 0.0 0.0 122-123 5.6375 0.0 0.0 0.0 0.0 124-125 6.375 0.0 0.0 0.0 0.0 126-127 6.875 0.0 0.0 0.0 0.0 128-129 7.5 0.0 0.0 0.0 0.0 130-131 8.1125 0.0 0.0 0.0 0.0 132-133 8.9 0.0 0.0 0.0 0.0 134-135 9.625 0.0 0.0 0.0 0.0 136-137 10.2625 0.0 0.0 0.0 0.0 138-139 11.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTTGAT 10 0.006830828 145.0 5 TTGATTA 10 0.006830828 145.0 2 >>END_MODULE Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232127 spots for SRR6053274.sra Written 3232127 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra Read 3232108 spots for SRR6053274.sra Written 3232108 spots for SRR6053274.sra SRR ids: ['SRR6053274.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hxu_g8w3 SRR6053274.sra spots: 64642179 blocks: [[1, 3232108], [3232109, 6464216], [6464217, 9696324], [9696325, 12928432], [12928433, 16160540], [16160541, 19392648], [19392649, 22624756], [22624757, 25856864], [25856865, 29088972], [29088973, 32321080], [32321081, 35553188], [35553189, 38785296], [38785297, 42017404], [42017405, 45249512], [45249513, 48481620], [48481621, 51713728], [51713729, 54945836], [54945837, 58177944], [58177945, 61410052], [61410053, 64642179]] SRR6053274 file size 21883413 SRR6053274 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 SRR6053274 SRR6053274_1.fastq SRR6053274_2.fastq Input file: SRR6053274_1.fastq Paired file: SRR6053274_2.fastq trimmed: SRR6053274-trimmed-pair1.fastq, SRR6053274-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 Tue Feb 11 15:54:44 2025 >> started Tue Feb 11 15:56:10 2025 >> done (86.164s) 64642179 read pairs processed; of these: 106300 ( 0.16%) short read pairs filtered out after trimming by size control 191738 ( 0.30%) empty read pairs filtered out after trimming by size control 64344141 (99.54%) read pairs available; of these: 29210857 (45.40%) trimmed read pairs available after processing 35133284 (54.60%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 25 0.00% 19 20 0.00% 20 29 0.00% 21 14 0.00% 22 24 0.00% 23 14 0.00% 24 11 0.00% 25 20 0.00% 26 29 0.00% 27 21 0.00% 28 20 0.00% 29 15 0.00% 30 29 0.00% 31 30 0.00% 32 23 0.00% 33 37 0.00% 34 38 0.00% 35 53 0.00% 36 45 0.00% 37 54 0.00% 38 55 0.00% 39 84 0.00% 40 113 0.00% 41 117 0.00% 42 127 0.00% 43 160 0.00% 44 174 0.00% 45 202 0.00% 46 217 0.00% 47 242 0.00% 48 351 0.00% 49 385 0.00% 50 461 0.00% 51 525 0.00% 52 615 0.00% 53 614 0.00% 54 734 0.00% 55 800 0.00% 56 935 0.00% 57 1050 0.00% 58 1172 0.00% 59 1418 0.00% 60 1640 0.00% 61 1863 0.00% 62 2158 0.00% 63 2276 0.00% 64 2730 0.00% 65 2960 0.00% 66 3125 0.00% 67 3640 0.01% 68 3897 0.01% 69 4437 0.01% 70 5277 0.01% 71 6025 0.01% 72 6564 0.01% 73 7605 0.01% 74 8218 0.01% 75 8900 0.01% 76 10034 0.02% 77 10942 0.02% 78 11884 0.02% 79 13172 0.02% 80 14582 0.02% 81 16312 0.03% 82 18412 0.03% 83 20732 0.03% 84 25118 0.04% 85 29265 0.05% 86 31444 0.05% 87 34381 0.05% 88 35721 0.06% 89 38671 0.06% 90 40155 0.06% 91 43883 0.07% 92 47866 0.07% 93 51188 0.08% 94 56033 0.09% 95 60363 0.09% 96 65355 0.10% 97 69553 0.11% 98 72668 0.11% 99 77219 0.12% 100 81944 0.13% 101 87466 0.14% 102 92651 0.14% 103 100616 0.16% 104 107037 0.17% 105 113758 0.18% 106 122158 0.19% 107 127234 0.20% 108 132342 0.21% 109 138109 0.21% 110 142800 0.22% 111 149284 0.23% 112 156913 0.24% 113 163569 0.25% 114 171963 0.27% 115 181261 0.28% 116 189404 0.29% 117 197186 0.31% 118 203646 0.32% 119 208678 0.32% 120 215571 0.34% 121 220720 0.34% 122 225871 0.35% 123 233170 0.36% 124 241603 0.38% 125 250025 0.39% 126 260358 0.40% 127 266493 0.41% 128 273838 0.43% 129 278770 0.43% 130 286137 0.44% 131 290969 0.45% 132 298446 0.46% 133 308985 0.48% 134 319660 0.50% 135 331823 0.52% 136 343593 0.53% 137 356709 0.55% 138 372396 0.58% 139 388565 0.60% 140 403350 0.63% 141 425485 0.66% 142 453800 0.71% 143 485902 0.76% 144 537933 0.84% 145 607374 0.94% 146 710464 1.10% 147 889662 1.38% 148 1236029 1.92% 149 2174375 3.38% 150 11677392 18.15% 151 35133284 54.60% 64344141 reads passed initial QC criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=9.46 fanout-score-rank=8 prefix-density=0.42 prefix-fanout=5.4 sequence=ACACCAGCAATGATTGTCTGACTTGTGGTGGTCTCGGAGAAACTCAAGTCTGGGTACATGCTGCATCCATTGCAGCCACTGCCGCACTTGCATCCAGAGCCGCAGCCACAGTTTCCTCCACAGCAAGACATTTTCTGTTGGAAAAGAAGGAAAGTGTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=199.85 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=16.6 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=34 prefix-density=0.33 prefix-fanout=2.0 sequence=CACACTTTCCTTCTTTTCCAACAGAAAATGTCTTGCTGTGGAGGAAACTGTGGCTGCGGCTCTGGATGCAAGTGCGGCAGTGGCTGCAATGGATGCAGCATGTACCCAGACTTGAGTTTCTCCGAGACCACCACAAGTCAGACAATCATTGCTGGTGT criterion=fanout-score sequence-density=0.05 sequence-density-rank=32 fanout-score=52.15 fanout-score-rank=1 prefix-density=0.42 prefix-fanout=6.1 sequence=TGATTTTGATCTTTTCTTGATTA SRR6053274 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 15:56:58 Started mapping on | Feb 11 15:56:59 Finished on | Feb 11 16:05:31 Mapping speed, Million of reads per hour | 452.42 Number of input reads | 64344141 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 60052730 Uniquely mapped reads % | 93.33% Average mapped length | 289.54 Number of splices: Total | 53791583 Number of splices: Annotated (sjdb) | 52432884 Number of splices: GT/AG | 52784105 Number of splices: GC/AG | 702213 Number of splices: AT/AC | 51242 Number of splices: Non-canonical | 254023 Mismatch rate per base, % | 0.78% Deletion rate per base | 0.07% Deletion average length | 2.93 Insertion rate per base | 0.05% Insertion average length | 2.72 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2112754 % of reads mapped to multiple loci | 3.28% Number of reads mapped to too many loci | 402735 % of reads mapped to too many loci | 0.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.60% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2242249 2242249 2242249 N_multimapping 2112754 2112754 2112754 N_noFeature 2234278 59164617 2718370 N_ambiguous 878454 4931 471871 UnstrandedReadsAssigned:56939998 PositiveStrandReadsAssigned:883182 NegativeStrandReadsAssigned:56862489 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=147 echo kmer=143 SRR6053274 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: SRR6053274-trimmed-pair1.fastq SRR6053274-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 64,344,141 reads, 56,149,601 reads pseudoaligned [quant] estimated average fragment length: 220.051 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,206 rounds 52401 SRR6053274.ke.tsv 34699 SRR6053274.se.tsv 87100 total ==> SRR6053274.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1798.95 5183 45.187 Potri.005G024800.1.v4.1 1035 815.949 5380 103.412 Potri.004G059700.1.v4.1 961 741.954 86 1.81791 Potri.007G009000.2.v4.1 1416 1196.95 0 0 Potri.003G141000.2.v4.1 2943 2723.95 2545.06 14.6538 Potri.016G087400.1.v4.1 270 92.9591 5804.54 979.326 Potri.015G069301.1.v4.1 564 347.334 0 0 Potri.010G195200.1.v4.1 1773 1553.95 313 3.15906 Potri.012G127500.1.v4.1 977 757.949 22064 456.557 ==> SRR6053274.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1371 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 1313 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 48 SRR6053274 completed mapping pipeline successfully