Starting /dee2/code/volunteer_pipeline.sh SRR6958249 current disk space = 1550640476160 free memory = 1601811848 SRR6958249 SRAfilesize 52fd48fa1945182f5ecaedb484e83695 SRR6958249.sra SRR6958249.sra file validated SRR6958249 is paired end SRR6958249 is conventional basespace SRR6958249 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958249_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 51 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 20.1565 18.0 18.0 18.0 18.0 32.0 2 21.32075 18.0 18.0 25.0 18.0 28.0 3 25.791 27.0 25.0 29.0 18.0 31.0 4 28.651 29.0 27.0 31.0 25.0 33.0 5 31.8455 32.0 32.0 33.0 31.0 33.0 6 35.76775 37.0 36.0 38.0 33.0 38.0 7 36.2455 38.0 36.0 38.0 33.0 38.0 8 37.13625 38.0 38.0 38.0 36.0 38.0 9 37.34275 38.0 38.0 38.0 37.0 38.0 10-14 37.416549999999994 38.0 38.0 38.0 37.0 38.0 15-19 37.485 38.0 38.0 38.0 37.4 38.0 20-24 37.52345 38.0 38.0 38.0 37.4 38.0 25-29 37.43715 38.0 38.0 38.0 37.0 38.0 30-34 37.42530000000001 38.0 38.0 38.0 37.0 38.0 35-39 37.362899999999996 38.0 38.0 38.0 37.0 38.0 40-44 37.4316 38.0 38.0 38.0 37.0 38.0 45-49 37.350049999999996 38.0 38.0 38.0 37.0 38.0 50-54 37.322250000000004 38.0 38.0 38.0 37.0 38.0 55-59 37.1969 38.0 38.0 38.0 36.6 38.0 60-64 37.0129 38.0 38.0 38.0 36.0 38.0 65-69 37.18339999999999 38.0 38.0 38.0 36.0 38.0 70-74 37.125350000000005 38.0 38.0 38.0 36.0 38.0 75-79 37.057 38.0 38.0 38.0 36.0 38.0 80-84 36.94885000000001 38.0 38.0 38.0 35.2 38.0 85-89 36.8907 38.0 38.0 38.0 35.0 38.0 90-94 36.77325 38.0 38.0 38.0 34.6 38.0 95-99 36.70915 38.0 38.0 38.0 34.4 38.0 100-104 36.64534999999999 38.0 38.0 38.0 34.2 38.0 105-109 36.53035 38.0 38.0 38.0 34.0 38.0 110-114 36.234899999999996 38.0 37.6 38.0 33.6 38.0 115-119 36.0603 38.0 37.4 38.0 32.8 38.0 120-124 35.83755 38.0 36.8 38.0 31.2 38.0 125-129 35.5599 38.0 36.0 38.0 30.4 38.0 130-134 35.128949999999996 38.0 35.8 38.0 28.6 38.0 135-139 34.5782 38.0 35.0 38.0 27.0 38.0 140-144 34.50715 38.0 35.0 38.0 27.0 38.0 145-149 33.28825 38.0 33.0 38.0 19.6 38.0 150-151 27.66175 33.5 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 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 1.0 16 0.0 17 1.0 18 4.0 19 1.0 20 2.0 21 2.0 22 6.0 23 4.0 24 10.0 25 17.0 26 17.0 27 18.0 28 25.0 29 32.0 30 43.0 31 57.0 32 81.0 33 102.0 34 206.0 35 385.0 36 1034.0 37 1951.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 16.475 31.825 8.575000000000001 43.125 2 16.525000000000002 14.249999999999998 29.2 40.025 3 20.549999999999997 14.224999999999998 24.75 40.475 4 25.474999999999998 20.674999999999997 23.125 30.725 5 28.1 24.5 22.475 24.925 6 26.6 28.449999999999996 22.175 22.775000000000002 7 18.425 24.15 37.375 20.05 8 22.75 23.35 26.5 27.400000000000002 9 21.625 22.125 31.5 24.75 10-14 23.905 24.775 25.71 25.61 15-19 24.205 23.79 25.45 26.555 20-24 24.165 23.68 25.074999999999996 27.08 25-29 23.825 24.79 25.195 26.19 30-34 24.34 24.07 24.990000000000002 26.6 35-39 24.425 23.565 25.040000000000003 26.97 40-44 24.575 23.49 25.380000000000003 26.555 45-49 24.355 24.154999999999998 24.55 26.939999999999998 50-54 24.03 24.365000000000002 24.715 26.889999999999997 55-59 24.819530780028074 23.51614196911971 25.00501303388811 26.65931421696411 60-64 24.7215253386854 23.878575012543905 25.288509784244855 26.11138986452584 65-69 24.39 24.09 24.705 26.815 70-74 24.715 24.305 24.595 26.384999999999998 75-79 25.215 23.474999999999998 24.834999999999997 26.474999999999998 80-84 25.0 23.66 24.38 26.96 85-89 24.325 23.24 25.380000000000003 27.055 90-94 24.445 23.165 25.11 27.279999999999998 95-99 24.525 23.75 24.605 27.12 100-104 24.685000000000002 23.400000000000002 24.875 27.04 105-109 24.535 23.69 24.67 27.105 110-114 25.305 23.525 24.64 26.529999999999998 115-119 25.28 23.73 24.575 26.415 120-124 25.4 23.625 24.12 26.855 125-129 25.174999999999997 22.75 24.825 27.250000000000004 130-134 24.86 24.065 24.52 26.555 135-139 25.035 23.59 24.705 26.669999999999998 140-144 25.785000000000004 23.46 24.565 26.19 145-149 25.180000000000003 23.395 24.42 27.005000000000003 150-151 25.275 24.3625 23.9875 26.375 >>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 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 0.5 27 0.5 28 2.0 29 4.0 30 5.0 31 6.5 32 10.0 33 12.5 34 14.5 35 24.5 36 37.0 37 40.5 38 59.0 39 82.5 40 93.0 41 119.5 42 139.5 43 154.5 44 184.5 45 197.0 46 200.0 47 185.5 48 171.0 49 167.5 50 158.0 51 157.5 52 138.5 53 117.0 54 116.0 55 116.5 56 106.0 57 92.0 58 86.0 59 87.0 60 87.5 61 80.0 62 83.5 63 86.5 64 80.0 65 77.0 66 70.5 67 64.0 68 53.0 69 43.5 70 35.5 71 27.5 72 25.0 73 28.5 74 24.5 75 13.5 76 11.5 77 9.5 78 6.0 79 2.5 80 2.5 81 2.0 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 0.0 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 0.26 60-64 0.35000000000000003 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 99.325 #Duplication Level Percentage of deduplicated Percentage of total 1 99.345582683111 98.675 2 0.6292474200855777 1.25 3 0.025169896803423106 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 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 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 90-91 0.0625 0.0 0.0 0.0 0.0 92-93 0.0875 0.0 0.0 0.0 0.0 94-95 0.15 0.0 0.0 0.0 0.0 96-97 0.1875 0.0 0.0 0.0 0.0 98-99 0.225 0.0 0.0 0.0 0.0 100-101 0.2875 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.4375 0.0 0.0 0.0 0.0 106-107 0.5375000000000001 0.0 0.0 0.0 0.0 108-109 0.6 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.85 0.0 0.0 0.0 0.0 114-115 0.9875 0.0 0.0 0.0 0.0 116-117 1.1125 0.0 0.0 0.0 0.0 118-119 1.1875 0.0 0.0 0.0 0.0 120-121 1.375 0.0 0.0 0.0 0.0 122-123 1.525 0.0 0.0 0.0 0.0 124-125 1.7625000000000002 0.0 0.0 0.0 0.0 126-127 2.0375 0.0 0.0 0.0 0.0 128-129 2.3875 0.0 0.0 0.0 0.0 130-131 2.675 0.0 0.0 0.0 0.0 132-133 2.8375 0.0 0.0 0.0 0.0 134-135 3.1875 0.0 0.0 0.0 0.0 136-137 3.6375 0.0 0.0 0.0 0.0 138-139 4.0125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6958249 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958249_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.783 33.0 33.0 34.0 32.0 34.0 2 32.846 33.0 33.0 34.0 32.0 34.0 3 32.932 34.0 33.0 34.0 32.0 34.0 4 32.8625 34.0 33.0 34.0 32.0 34.0 5 32.889 34.0 33.0 34.0 32.0 34.0 6 37.00875 38.0 38.0 38.0 36.0 38.0 7 37.015 38.0 38.0 38.0 36.0 38.0 8 37.11175 38.0 38.0 38.0 37.0 38.0 9 37.06 38.0 38.0 38.0 37.0 38.0 10-14 37.0089 38.0 38.0 38.0 36.8 38.0 15-19 37.0397 38.0 38.0 38.0 37.0 38.0 20-24 36.91755 38.0 38.0 38.0 36.2 38.0 25-29 36.933749999999996 38.0 38.0 38.0 36.4 38.0 30-34 36.8899 38.0 38.0 38.0 36.2 38.0 35-39 36.890499999999996 38.0 38.0 38.0 36.0 38.0 40-44 36.89035 38.0 38.0 38.0 36.0 38.0 45-49 36.8418 38.0 38.0 38.0 36.0 38.0 50-54 36.74444999999999 38.0 38.0 38.0 36.0 38.0 55-59 36.6915 38.0 38.0 38.0 35.4 38.0 60-64 36.72145 38.0 38.0 38.0 35.6 38.0 65-69 36.5673 38.0 38.0 38.0 34.8 38.0 70-74 36.6118 38.0 38.0 38.0 35.0 38.0 75-79 36.5046 38.0 38.0 38.0 34.8 38.0 80-84 36.505100000000006 38.0 38.0 38.0 34.6 38.0 85-89 36.4034 38.0 38.0 38.0 34.4 38.0 90-94 36.230650000000004 38.0 38.0 38.0 34.2 38.0 95-99 36.1439 38.0 38.0 38.0 33.8 38.0 100-104 36.0866 38.0 38.0 38.0 34.0 38.0 105-109 36.01535 38.0 38.0 38.0 33.8 38.0 110-114 35.678700000000006 38.0 37.8 38.0 32.2 38.0 115-119 35.609350000000006 38.0 37.2 38.0 32.0 38.0 120-124 35.53830000000001 38.0 37.0 38.0 31.6 38.0 125-129 35.4733 38.0 36.4 38.0 31.6 38.0 130-134 35.10005 38.0 36.0 38.0 30.2 38.0 135-139 34.962849999999996 38.0 36.0 38.0 29.4 38.0 140-144 34.522800000000004 38.0 35.2 38.0 27.4 38.0 145-149 33.83364999999999 38.0 34.2 38.0 23.6 38.0 150-151 29.76025 35.5 27.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 19.0 3 6.0 4 2.0 5 1.0 6 4.0 7 4.0 8 1.0 9 0.0 10 2.0 11 0.0 12 2.0 13 1.0 14 5.0 15 2.0 16 6.0 17 4.0 18 4.0 19 6.0 20 3.0 21 7.0 22 5.0 23 10.0 24 14.0 25 11.0 26 13.0 27 20.0 28 18.0 29 31.0 30 50.0 31 52.0 32 71.0 33 91.0 34 157.0 35 208.0 36 549.0 37 2621.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.300000000000004 18.7 11.675 29.325000000000003 2 30.200501253132835 22.982456140350877 23.809523809523807 23.007518796992482 3 23.959899749373434 24.711779448621556 26.516290726817044 24.81203007518797 4 26.71679197994987 30.250626566416038 19.774436090225564 23.258145363408524 5 26.95390781563126 31.688376753507015 18.912825651302605 22.44488977955912 6 23.103879849812266 34.81852315394243 19.39924906132666 22.678347934918648 7 24.536340852130326 19.62406015037594 31.403508771929822 24.43609022556391 8 25.6390977443609 21.704260651629074 23.283208020050125 29.3734335839599 9 23.93483709273183 23.55889724310777 24.586466165413533 27.919799498746865 10-14 26.377755511022045 25.30060120240481 22.11422845691383 26.20741482965932 15-19 26.185463659147867 24.421052631578945 23.51378446115288 25.879699248120303 20-24 26.536340852130323 25.343358395989974 22.962406015037594 25.157894736842106 25-29 26.71644783000902 24.792021649794528 22.63706525007517 25.85446527012128 30-34 25.533834586466163 24.927318295739347 23.659147869674186 25.879699248120303 35-39 26.137274549098194 24.76452905811623 22.84068136272545 26.25751503006012 40-44 26.364593253471003 24.65540574407298 22.59535862864017 26.384642373815847 45-49 26.607250150210294 24.579411175645905 23.22251151612257 25.590827158021227 50-54 26.22228894560376 24.31566831807036 23.68012810889256 25.781914627433316 55-59 27.131122908945205 23.91565661624762 22.753681258138837 26.199539216668338 60-64 26.879727495867357 24.525371938085456 23.132795671993186 25.462104894054 65-69 27.06235912847483 24.728274480340595 22.609566741798144 25.59979964938643 70-74 26.95813301282051 24.43409455128205 23.24719551282051 25.360576923076923 75-79 26.449511400651467 24.299674267100976 23.56802806314207 25.68278626910549 80-84 27.454709238314486 23.70133119807827 23.160844760284256 25.683114803322994 85-89 26.801080648389032 24.359615769461676 23.16890134080448 25.67040224134481 90-94 26.71973565635326 24.316611595073596 23.86101932512266 25.102633423450488 95-99 26.44098352446292 24.783414292152838 23.426310781711653 25.34929140167259 100-104 27.086149071432146 24.45312108925264 23.051509235620966 25.409220603694248 105-109 27.207207207207208 24.64964964964965 23.06806806806807 25.075075075075077 110-114 27.210373485531193 24.882347051166516 22.979873835986783 24.927405627315512 115-119 27.571006361769275 25.051344988228223 22.47157240895657 24.906076241045934 120-124 27.874267981380452 24.876119925922218 22.313429100555584 24.93618299214175 125-129 27.62367314239936 24.909873823352694 22.84698578009213 24.61946725415582 130-134 27.56067050287716 24.818613960470355 22.952214160620464 24.668501376032022 135-139 27.090217282467204 25.778512065685387 22.69450285370982 24.43676779813758 140-144 28.13876651982379 24.984981978374048 23.192831397677214 23.68342010412495 145-149 27.655420963059363 25.367904695164682 22.830113124436878 24.146561217339073 150-151 27.388854101440202 25.62304320601127 23.180964308077645 23.807138384470882 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 1.0 4 1.5 5 0.5 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 13 0.5 14 0.5 15 1.0 16 1.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 0.5 26 0.0 27 1.0 28 2.5 29 4.5 30 5.0 31 5.5 32 7.0 33 6.5 34 8.0 35 17.5 36 26.5 37 39.0 38 51.0 39 71.0 40 97.0 41 124.0 42 129.5 43 130.5 44 154.0 45 166.0 46 171.0 47 162.5 48 166.0 49 182.0 50 161.0 51 140.5 52 133.5 53 123.5 54 115.5 55 103.5 56 103.0 57 101.5 58 103.0 59 112.0 60 101.0 61 83.0 62 90.0 63 96.0 64 88.0 65 79.5 66 73.5 67 74.0 68 67.5 69 58.0 70 56.5 71 50.0 72 37.0 73 31.5 74 33.0 75 23.0 76 8.0 77 3.0 78 3.0 79 3.5 80 2.5 81 1.0 82 0.0 83 0.5 84 0.5 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 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 0.25 3 0.25 4 0.25 5 0.2 6 0.125 7 0.25 8 0.25 9 0.25 10-14 0.2 15-19 0.25 20-24 0.25 25-29 0.22999999999999998 30-34 0.25 35-39 0.2 40-44 0.245 45-49 0.13999999999999999 50-54 0.08499999999999999 55-59 0.16999999999999998 60-64 0.185 65-69 0.17500000000000002 70-74 0.16 75-79 0.22499999999999998 80-84 0.09 85-89 0.06 90-94 0.13 95-99 0.155 100-104 0.11499999999999999 105-109 0.1 110-114 0.13 115-119 0.185 120-124 0.105 125-129 0.13999999999999999 130-134 0.075 135-139 0.13 140-144 0.12 145-149 0.11 150-151 0.1875 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.075 #Duplication Level Percentage of deduplicated Percentage of total 1 98.52153963803212 96.625 2 1.2235534030079023 2.4 3 0.10196278358399186 0.3 4 0.10196278358399186 0.4 5 0.025490695895997964 0.125 6 0.025490695895997964 0.15 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 CTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGA 6 0.15 No Hit GCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAG 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 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.07500000000000001 0.0 0.0 0.0 0.0 90-91 0.1125 0.0 0.0 0.0 0.0 92-93 0.1375 0.0 0.0 0.0 0.0 94-95 0.2 0.0 0.0 0.0 0.0 96-97 0.2375 0.0 0.0 0.0 0.0 98-99 0.2625 0.0 0.0 0.0 0.0 100-101 0.3125 0.0 0.0 0.0 0.0 102-103 0.4125 0.0 0.0 0.0 0.0 104-105 0.44999999999999996 0.0 0.0 0.0 0.0 106-107 0.5375000000000001 0.0 0.0 0.0 0.0 108-109 0.575 0.0 0.0 0.0 0.0 110-111 0.675 0.0 0.0 0.0 0.0 112-113 0.825 0.0 0.0 0.0 0.0 114-115 0.9750000000000001 0.0 0.0 0.0 0.0 116-117 1.1375 0.0 0.0 0.0 0.0 118-119 1.2125 0.0 0.0 0.0 0.0 120-121 1.4 0.0 0.0 0.0 0.0 122-123 1.55 0.0 0.0 0.0 0.0 124-125 1.7875 0.0 0.0 0.0 0.0 126-127 2.0625 0.0 0.0 0.0 0.0 128-129 2.4 0.0 0.0 0.0 0.0 130-131 2.7 0.0 0.0 0.0 0.0 132-133 2.8625 0.0 0.0 0.0 0.0 134-135 3.2249999999999996 0.0 0.0 0.0 0.0 136-137 3.625 0.0 0.0 0.0 0.0 138-139 3.9875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra Read 1018997 spots for SRR6958249.sra Written 1018997 spots for SRR6958249.sra Read 1018978 spots for SRR6958249.sra Written 1018978 spots for SRR6958249.sra SRR ids: ['SRR6958249.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8xlj6hjm SRR6958249.sra spots: 20379579 blocks: [[1, 1018978], [1018979, 2037956], [2037957, 3056934], [3056935, 4075912], [4075913, 5094890], [5094891, 6113868], [6113869, 7132846], [7132847, 8151824], [8151825, 9170802], [9170803, 10189780], [10189781, 11208758], [11208759, 12227736], [12227737, 13246714], [13246715, 14265692], [14265693, 15284670], [15284671, 16303648], [16303649, 17322626], [17322627, 18341604], [18341605, 19360582], [19360583, 20379579]] SRR6958249 file size 6884270 SRR6958249 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 SRR6958249 SRR6958249_1.fastq SRR6958249_2.fastq Input file: SRR6958249_1.fastq Paired file: SRR6958249_2.fastq trimmed: SRR6958249-trimmed-pair1.fastq, SRR6958249-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Fri Dec 6 17:34:58 2024 >> started Fri Dec 6 17:35:21 2024 >> done (22.554s) 20379579 read pairs processed; of these: 43604 ( 0.21%) short read pairs filtered out after trimming by size control 54188 ( 0.27%) empty read pairs filtered out after trimming by size control 20281787 (99.52%) read pairs available; of these: 8820164 (43.49%) trimmed read pairs available after processing 11461623 (56.51%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 2 0.00% 20 3 0.00% 21 10 0.00% 22 6 0.00% 23 7 0.00% 24 5 0.00% 25 11 0.00% 26 8 0.00% 27 11 0.00% 28 7 0.00% 29 11 0.00% 30 11 0.00% 31 12 0.00% 32 9 0.00% 33 7 0.00% 34 13 0.00% 35 10 0.00% 36 9 0.00% 37 7 0.00% 38 15 0.00% 39 13 0.00% 40 18 0.00% 41 23 0.00% 42 18 0.00% 43 15 0.00% 44 22 0.00% 45 27 0.00% 46 19 0.00% 47 39 0.00% 48 39 0.00% 49 42 0.00% 50 40 0.00% 51 45 0.00% 52 62 0.00% 53 60 0.00% 54 71 0.00% 55 58 0.00% 56 71 0.00% 57 96 0.00% 58 98 0.00% 59 128 0.00% 60 124 0.00% 61 147 0.00% 62 150 0.00% 63 174 0.00% 64 204 0.00% 65 211 0.00% 66 224 0.00% 67 250 0.00% 68 276 0.00% 69 326 0.00% 70 369 0.00% 71 407 0.00% 72 506 0.00% 73 530 0.00% 74 587 0.00% 75 695 0.00% 76 800 0.00% 77 887 0.00% 78 990 0.00% 79 1112 0.01% 80 1219 0.01% 81 1442 0.01% 82 1658 0.01% 83 1939 0.01% 84 3351 0.02% 85 4154 0.02% 86 4359 0.02% 87 4478 0.02% 88 4772 0.02% 89 4735 0.02% 90 4949 0.02% 91 5350 0.03% 92 5523 0.03% 93 5737 0.03% 94 6193 0.03% 95 6508 0.03% 96 7042 0.03% 97 7568 0.04% 98 7987 0.04% 99 8358 0.04% 100 8923 0.04% 101 9638 0.05% 102 10320 0.05% 103 10966 0.05% 104 11863 0.06% 105 12510 0.06% 106 13298 0.07% 107 13729 0.07% 108 14688 0.07% 109 15879 0.08% 110 16338 0.08% 111 17193 0.08% 112 18573 0.09% 113 19463 0.10% 114 20759 0.10% 115 22066 0.11% 116 23343 0.12% 117 24245 0.12% 118 25072 0.12% 119 26094 0.13% 120 27327 0.13% 121 28648 0.14% 122 30094 0.15% 123 31617 0.16% 124 33272 0.16% 125 35090 0.17% 126 36560 0.18% 127 38763 0.19% 128 39740 0.20% 129 41444 0.20% 130 43494 0.21% 131 45591 0.22% 132 47800 0.24% 133 50886 0.25% 134 53440 0.26% 135 56575 0.28% 136 59562 0.29% 137 62635 0.31% 138 66178 0.33% 139 70929 0.35% 140 76005 0.37% 141 82553 0.41% 142 92171 0.45% 143 101724 0.50% 144 117379 0.58% 145 138973 0.69% 146 172069 0.85% 147 233538 1.15% 148 365509 1.80% 149 774959 3.82% 150 5323206 26.25% 151 11461623 56.51% 20281787 reads passed initial QC criterion=sequence-density sequence-density=0.74 sequence-density-rank=1 fanout-score=3.27 fanout-score-rank=21 prefix-density=0.79 prefix-fanout=3.1 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTCCGG criterion=fanout-score sequence-density=0.06 sequence-density-rank=29 fanout-score=119.15 fanout-score-rank=1 prefix-density=0.58 prefix-fanout=12.9 sequence=CGGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAA criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=3.10 fanout-score-rank=24 prefix-density=0.59 prefix-fanout=2.6 sequence=CTTCGACAACACCATGGGAGGCTTCTACATCGCCCCAGCCTTCATGGACAAGCTCGTCGTCCACCTCTCCAAGAACTTCATGACCCTGCCCAACATCAAGGTGCCACTCATCTTGGGTATCTGGGGAGGCAAGGGTCAAGGAAAATCCTTCCAATGTGAGCTTGTCTTCGCCAAGATGGGCATCAACCCAATCATGATGAGTGCCGGAGAGCTGGAGAGCGGAAACGCCGGAGAGCCAGCCAAGCTGATCAGGCAGCGGTACCGTGAGGCCGCAGACTTGATCAAGAAGGGTAAGATGTGCTGCCTCTTCATCAACGATCTCGACGCTGGTGCGGGTCGGATGGGCGGGACCACCCAGTACACTGTCAACAACCAGATGGTTAACGCCACCCTGATGAACATCGCGGATGCCCCCACCAACGTGCAGCTCCCTGGGATGTACAACAAGGAGGAAAACCCCCGTGTGCCCATCATCGTCACTGGTAACGATTTCTCCACGCTCTACGCGCCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=172.81 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=11.6 sequence=AGAACAAGGAGTGCAAGAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGTTCGAGCACTCGACCGAAGATGTCTTGCTGCGGAGGAAACTGCAACTGCGGGTCATCCTGCAAGTGCGGCA SRR6958249 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 17:36:10 Started mapping on | Dec 06 17:36:10 Finished on | Dec 06 17:37:47 Mapping speed, Million of reads per hour | 752.73 Number of input reads | 20281787 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 19484584 Uniquely mapped reads % | 96.07% Average mapped length | 296.53 Number of splices: Total | 21865228 Number of splices: Annotated (sjdb) | 20588031 Number of splices: GT/AG | 21583500 Number of splices: GC/AG | 257876 Number of splices: AT/AC | 8384 Number of splices: Non-canonical | 15468 Mismatch rate per base, % | 0.08% Deletion rate per base | 0.00% Deletion average length | 1.38 Insertion rate per base | 0.00% Insertion average length | 1.18 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 171461 % of reads mapped to multiple loci | 0.85% Number of reads mapped to too many loci | 40347 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.75% % of reads unmapped: other | 1.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 646069 646069 646069 N_multimapping 171461 171461 171461 N_noFeature 534207 18968879 664651 N_ambiguous 458952 2352 74948 UnstrandedReadsAssigned:18491425 PositiveStrandReadsAssigned:513353 NegativeStrandReadsAssigned:18744985 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958249 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: SRR6958249-trimmed-pair1.fastq SRR6958249-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,281,787 reads, 18,754,721 reads pseudoaligned [quant] estimated average fragment length: 263.014 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,180 rounds 52973 SRR6958249.ke.tsv 35125 SRR6958249.se.tsv 88098 total ==> SRR6958249.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 674.503 25.0078 2.75891 PNS24247 1044 781.986 55.1654 5.24944 PNS24249 1928 1665.99 72.997 3.26046 PNS24246 1044 781.986 55.1654 5.24944 PNS24248 1044 781.986 55.1654 5.24944 PNS24244 1471 1208.99 33.4989 2.06184 PNS24243 293 84.7158 0 0 KQK14069 1603 1340.99 5418.13 300.657 KQK14071 474 226.614 135.859 44.6115 ==> SRR6958249.se.tsv <== BRADI_1g14170v3 6086 BRADI_1g53295v3 184 BRADI_1g59795v3 176 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 213 BRADI_1g74790v3 134 BRADI_1g09890v3 0 BRADI_1g77505v3 253 BRADI_1g48960v3 0 SRR6958249 completed mapping pipeline successfully