Starting /dee2/code/volunteer_pipeline.sh SRR6958427 current disk space = 1548359761920 free memory = 1603530004 SRR6958427 SRAfilesize 426ec1400592204d99e2ee6dfab6dc0f SRR6958427.sra SRR6958427.sra file validated SRR6958427 is paired end SRR6958427 is conventional basespace SRR6958427 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958427_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 26.137 30.0 18.0 33.0 18.0 34.0 2 31.10775 31.0 30.0 33.0 27.0 34.0 3 32.29225 33.0 33.0 33.0 30.0 34.0 4 32.63925 33.0 33.0 34.0 31.0 34.0 5 32.17675 33.0 33.0 33.0 31.0 34.0 6 36.348 38.0 36.0 38.0 34.0 38.0 7 36.8755 38.0 37.0 38.0 35.0 38.0 8 37.33075 38.0 38.0 38.0 36.0 38.0 9 37.558 38.0 38.0 38.0 37.0 38.0 10-14 37.49915 38.0 38.0 38.0 37.2 38.0 15-19 37.584799999999994 38.0 38.0 38.0 38.0 38.0 20-24 37.5751 38.0 38.0 38.0 38.0 38.0 25-29 37.52720000000001 38.0 38.0 38.0 38.0 38.0 30-34 37.55405 38.0 38.0 38.0 38.0 38.0 35-39 37.507799999999996 38.0 38.0 38.0 38.0 38.0 40-44 37.462399999999995 38.0 38.0 38.0 37.2 38.0 45-49 37.43405 38.0 38.0 38.0 37.0 38.0 50-54 37.33295 38.0 38.0 38.0 37.0 38.0 55-59 36.8594 38.0 38.0 38.0 36.2 38.0 60-64 36.63925 38.0 38.0 38.0 36.0 38.0 65-69 36.96455 38.0 38.0 38.0 36.0 38.0 70-74 37.160000000000004 38.0 38.0 38.0 36.0 38.0 75-79 37.16175 38.0 38.0 38.0 36.0 38.0 80-84 37.0417 38.0 38.0 38.0 36.0 38.0 85-89 36.895799999999994 38.0 38.0 38.0 35.2 38.0 90-94 36.898 38.0 38.0 38.0 35.0 38.0 95-99 36.850350000000006 38.0 38.0 38.0 35.0 38.0 100-104 36.665350000000004 38.0 38.0 38.0 34.4 38.0 105-109 36.53545 38.0 38.0 38.0 34.0 38.0 110-114 36.351299999999995 38.0 37.8 38.0 33.8 38.0 115-119 36.21785 38.0 38.0 38.0 33.4 38.0 120-124 35.8754 38.0 36.8 38.0 31.8 38.0 125-129 35.4243 38.0 36.0 38.0 31.0 38.0 130-134 35.22905 38.0 36.0 38.0 29.2 38.0 135-139 34.652699999999996 38.0 35.6 38.0 27.4 38.0 140-144 34.2649 38.0 34.4 38.0 26.2 38.0 145-149 33.55265 38.0 33.2 38.0 22.6 38.0 150-151 28.657 34.5 18.0 38.0 6.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 2.0 9 2.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 0.0 18 2.0 19 2.0 20 3.0 21 7.0 22 5.0 23 6.0 24 11.0 25 16.0 26 14.0 27 14.0 28 24.0 29 27.0 30 26.0 31 47.0 32 66.0 33 110.0 34 190.0 35 302.0 36 738.0 37 2385.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.475 13.5 8.4 35.625 2 23.055763940985248 12.10302575643911 33.4333583395849 31.407851962990748 3 18.9 16.7 26.200000000000003 38.2 4 24.3 21.65 22.6 31.45 5 24.6 26.200000000000003 24.2 25.0 6 24.4 30.325000000000003 23.9 21.375 7 18.425 23.375 37.974999999999994 20.225 8 20.275000000000002 24.224999999999998 27.900000000000002 27.6 9 19.05 21.65 33.475 25.825 10-14 22.606303151575787 26.67333666833417 25.56778389194597 25.152576288144076 15-19 22.605 24.709999999999997 26.105 26.58 20-24 23.18 25.180000000000003 25.56 26.08 25-29 22.89 25.650000000000002 24.725 26.735 30-34 22.770000000000003 25.165 25.05 27.015 35-39 23.035 25.21 25.34 26.415 40-44 23.415 24.82 25.130000000000003 26.634999999999998 45-49 23.31 24.62 25.380000000000003 26.69 50-54 23.064999999999998 24.89 25.19 26.855 55-59 23.69980250164582 25.381070542360867 24.77338329872892 26.145743657264394 60-64 23.288716983052574 25.136139243727417 25.293908086925544 26.28123568629447 65-69 23.466880609737753 24.971167828310687 25.176753748182318 26.38519781376924 70-74 23.13 24.995 25.525 26.35 75-79 24.015 24.6 24.8 26.584999999999997 80-84 23.505000000000003 24.39 25.705 26.400000000000002 85-89 23.73 25.235000000000003 24.695 26.340000000000003 90-94 24.169999999999998 24.6 24.58 26.650000000000002 95-99 23.895 24.415 25.095 26.595000000000002 100-104 23.385 24.205 25.685000000000002 26.724999999999998 105-109 24.245 24.67 24.875 26.21 110-114 23.39 24.68 24.985 26.945000000000004 115-119 23.74 24.575 25.31 26.375 120-124 23.71 24.58 25.06 26.650000000000002 125-129 23.89 24.825 24.455 26.83 130-134 24.4 24.775 24.355 26.47 135-139 24.445 25.1 24.51 25.945 140-144 24.135 25.115 24.135 26.615 145-149 24.615000000000002 24.5 24.42 26.465 150-151 24.3 25.324999999999996 24.425 25.95 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 0.5 12 0.5 13 0.0 14 0.5 15 0.5 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 0.5 25 1.0 26 2.0 27 2.5 28 2.5 29 3.5 30 5.0 31 9.0 32 14.0 33 16.0 34 27.5 35 34.0 36 44.0 37 72.5 38 89.5 39 103.0 40 123.0 41 133.5 42 141.5 43 168.5 44 197.5 45 204.0 46 179.5 47 176.0 48 190.5 49 174.5 50 151.5 51 147.5 52 146.5 53 139.5 54 119.0 55 105.0 56 96.0 57 82.0 58 77.0 59 69.5 60 70.0 61 74.5 62 74.0 63 65.0 64 60.0 65 51.0 66 45.5 67 43.5 68 37.5 69 39.0 70 32.0 71 24.5 72 26.5 73 27.0 74 21.0 75 18.0 76 18.5 77 11.0 78 4.5 79 2.0 80 0.5 81 0.5 82 1.0 83 0.5 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 0.5 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 0.025 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.05 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 1.265 60-64 1.755 65-69 0.28500000000000003 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 99.275 #Duplication Level Percentage of deduplicated Percentage of total 1 99.5467136741375 98.825 2 0.2518257365902795 0.5 3 0.12591286829513976 0.375 4 0.07554772097708386 0.3 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 0.025 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 0.025 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.0875 0.0 0.0 0.0 0.0 92-93 0.1 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.2875 0.0 0.0 0.0 0.0 100-101 0.3125 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.42500000000000004 0.0 0.0 0.0 0.0 106-107 0.5125 0.0 0.0 0.0 0.0 108-109 0.5874999999999999 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.8 0.0 0.0 0.0 0.0 114-115 1.0125 0.0 0.0 0.0 0.0 116-117 1.15 0.0 0.0 0.0 0.0 118-119 1.3 0.0 0.0 0.0 0.0 120-121 1.475 0.0 0.0 0.0 0.0 122-123 1.7 0.0 0.0 0.0 0.0 124-125 1.95 0.0 0.0 0.0 0.0 126-127 2.2 0.0 0.0 0.0 0.0 128-129 2.6125 0.0 0.0 0.0 0.0 130-131 3.0125 0.0 0.0 0.0 0.0 132-133 3.3499999999999996 0.0 0.0 0.0 0.0 134-135 3.5625 0.0 0.0 0.0 0.0 136-137 3.95 0.0 0.0 0.0 0.0 138-139 4.4 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6958427 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958427_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.89675 33.0 33.0 34.0 32.0 34.0 2 32.971 34.0 33.0 34.0 32.0 34.0 3 33.005 34.0 33.0 34.0 32.0 34.0 4 33.005 34.0 33.0 34.0 33.0 34.0 5 32.99975 34.0 33.0 34.0 33.0 34.0 6 37.139 38.0 38.0 38.0 37.0 38.0 7 37.15425 38.0 38.0 38.0 37.0 38.0 8 37.21925 38.0 38.0 38.0 37.0 38.0 9 37.19825 38.0 38.0 38.0 37.0 38.0 10-14 37.091950000000004 38.0 38.0 38.0 36.8 38.0 15-19 37.072199999999995 38.0 38.0 38.0 36.8 38.0 20-24 37.08285 38.0 38.0 38.0 36.6 38.0 25-29 37.026 38.0 38.0 38.0 36.6 38.0 30-34 37.01115 38.0 38.0 38.0 36.2 38.0 35-39 36.97965 38.0 38.0 38.0 36.0 38.0 40-44 36.993 38.0 38.0 38.0 36.0 38.0 45-49 36.94725 38.0 38.0 38.0 36.0 38.0 50-54 36.899100000000004 38.0 38.0 38.0 36.0 38.0 55-59 36.838800000000006 38.0 38.0 38.0 35.6 38.0 60-64 36.7706 38.0 38.0 38.0 35.4 38.0 65-69 36.7311 38.0 38.0 38.0 35.4 38.0 70-74 36.693549999999995 38.0 38.0 38.0 35.2 38.0 75-79 36.626999999999995 38.0 38.0 38.0 35.0 38.0 80-84 36.6057 38.0 38.0 38.0 35.0 38.0 85-89 36.49145 38.0 38.0 38.0 34.4 38.0 90-94 36.4067 38.0 38.0 38.0 34.2 38.0 95-99 36.29975 38.0 38.0 38.0 34.0 38.0 100-104 36.212 38.0 38.0 38.0 34.0 38.0 105-109 35.9589 38.0 37.8 38.0 33.2 38.0 110-114 35.8218 38.0 37.6 38.0 32.4 38.0 115-119 35.61900000000001 38.0 36.6 38.0 31.6 38.0 120-124 35.44585 38.0 36.4 38.0 30.4 38.0 125-129 35.37115 38.0 36.2 38.0 31.0 38.0 130-134 35.2568 38.0 36.0 38.0 30.6 38.0 135-139 34.9059 38.0 35.6 38.0 28.8 38.0 140-144 34.511750000000006 38.0 35.0 38.0 27.6 38.0 145-149 34.033699999999996 38.0 34.2 38.0 25.2 38.0 150-151 29.66375 35.5 27.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 14.0 3 3.0 4 1.0 5 0.0 6 2.0 7 3.0 8 1.0 9 2.0 10 0.0 11 4.0 12 4.0 13 1.0 14 1.0 15 2.0 16 5.0 17 2.0 18 2.0 19 3.0 20 4.0 21 2.0 22 6.0 23 8.0 24 15.0 25 14.0 26 18.0 27 25.0 28 37.0 29 32.0 30 32.0 31 50.0 32 62.0 33 86.0 34 140.0 35 241.0 36 586.0 37 2592.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.9 19.15 11.025 27.925 2 30.375000000000004 24.425 23.5 21.7 3 24.175 25.4 27.525 22.900000000000002 4 27.224999999999998 30.8 20.3 21.675 5 26.575 30.85 20.575 22.0 6 24.05 34.575 19.325 22.05 7 23.549999999999997 20.599999999999998 32.9 22.95 8 24.175 23.724999999999998 22.375 29.725 9 25.05 23.425 26.5 25.025 10-14 26.895000000000003 25.575 22.145 25.385 15-19 26.565 25.215 24.060000000000002 24.16 20-24 26.295 25.195 23.64 24.87 25-29 27.07 24.525 23.175 25.230000000000004 30-34 26.805 24.88 23.68 24.635 35-39 25.645 25.0 24.26 25.095 40-44 26.939999999999998 24.935 23.419999999999998 24.705 45-49 26.240000000000002 24.95 23.974999999999998 24.834999999999997 50-54 26.14 25.205 24.275 24.38 55-59 27.189999999999998 24.04 24.654999999999998 24.115000000000002 60-64 26.955000000000002 24.445 24.474999999999998 24.125 65-69 26.840000000000003 25.005 23.905 24.25 70-74 27.07 24.54 24.224999999999998 24.165 75-79 26.615 24.4 24.385 24.6 80-84 26.515 25.169999999999998 24.605 23.71 85-89 26.97 24.515 24.610000000000003 23.905 90-94 26.69 25.88 23.79 23.64 95-99 27.185 25.1 23.925 23.79 100-104 27.07 24.779999999999998 23.59 24.560000000000002 105-109 27.084999999999997 24.990000000000002 23.919999999999998 24.005000000000003 110-114 26.810000000000002 25.259999999999998 23.885 24.044999999999998 115-119 27.11 25.485000000000003 23.380000000000003 24.025 120-124 26.91 24.735 24.55 23.805 125-129 27.279999999999998 25.515 23.845 23.36 130-134 26.884999999999998 25.185000000000002 24.404999999999998 23.525 135-139 27.265 25.03 24.595 23.11 140-144 27.32 25.295 24.11 23.275000000000002 145-149 27.55 25.61 24.05 22.79 150-151 27.5625 25.6125 23.2375 23.5875 >>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 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.5 18 0.5 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 0.0 25 0.5 26 0.5 27 0.5 28 1.5 29 2.0 30 5.0 31 9.0 32 9.0 33 11.5 34 21.5 35 26.0 36 35.5 37 50.0 38 62.0 39 82.0 40 101.0 41 117.0 42 140.5 43 145.0 44 153.5 45 187.0 46 204.0 47 200.0 48 180.0 49 172.0 50 168.5 51 149.5 52 135.5 53 133.0 54 122.5 55 108.0 56 97.0 57 90.0 58 90.0 59 86.5 60 84.5 61 85.5 62 85.5 63 75.0 64 59.5 65 60.0 66 64.0 67 60.5 68 53.0 69 50.5 70 45.5 71 39.5 72 40.0 73 29.0 74 22.0 75 20.5 76 11.5 77 5.0 78 2.0 79 0.5 80 1.0 81 1.0 82 0.5 83 0.5 84 1.0 85 0.5 86 0.5 87 0.5 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 0.0 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 98.65 #Duplication Level Percentage of deduplicated Percentage of total 1 99.06234161175874 97.725 2 0.7095793208312215 1.4000000000000001 3 0.15205271160669032 0.44999999999999996 4 0.025342118601115054 0.1 5 0.025342118601115054 0.125 6 0.0 0.0 7 0.0 0.0 8 0.025342118601115054 0.2 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 CAGACACAGCCACGAATTTGCAGTGTACGCAGTTCTAGTAAACAAGAACC 8 0.2 No Hit GACACAGCCACGAATTTGCAGTGTACGCAGTTCTAGTAAACAAGAACCAC 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 0.025 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 0.025 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.0875 0.0 0.0 0.0 0.0 92-93 0.1 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.2625 0.0 0.0 0.0 0.0 100-101 0.275 0.0 0.0 0.0 0.0 102-103 0.3375 0.0 0.0 0.0 0.0 104-105 0.375 0.0 0.0 0.0 0.0 106-107 0.475 0.0 0.0 0.0 0.0 108-109 0.5625 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.8 0.0 0.0 0.0 0.0 114-115 1.0125 0.0 0.0 0.0 0.0 116-117 1.15 0.0 0.0 0.0 0.0 118-119 1.2875 0.0 0.0 0.0 0.0 120-121 1.45 0.0 0.0 0.0 0.0 122-123 1.6625 0.0 0.0 0.0 0.0 124-125 1.8875000000000002 0.0 0.0 0.0 0.0 126-127 2.1625 0.0 0.0 0.0 0.0 128-129 2.5625 0.0 0.0 0.0 0.0 130-131 2.9625 0.0 0.0 0.0 0.0 132-133 3.3 0.0 0.0 0.0 0.0 134-135 3.5125 0.0 0.0 0.0 0.0 136-137 3.925 0.0 0.0 0.0 0.0 138-139 4.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235146 spots for SRR6958427.sra Written 1235146 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra Read 1235128 spots for SRR6958427.sra Written 1235128 spots for SRR6958427.sra SRR ids: ['SRR6958427.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mspqkhi2 SRR6958427.sra spots: 24702578 blocks: [[1, 1235128], [1235129, 2470256], [2470257, 3705384], [3705385, 4940512], [4940513, 6175640], [6175641, 7410768], [7410769, 8645896], [8645897, 9881024], [9881025, 11116152], [11116153, 12351280], [12351281, 13586408], [13586409, 14821536], [14821537, 16056664], [16056665, 17291792], [17291793, 18526920], [18526921, 19762048], [19762049, 20997176], [20997177, 22232304], [22232305, 23467432], [23467433, 24702578]] SRR6958427 file size 8349192 SRR6958427 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 SRR6958427 SRR6958427_1.fastq SRR6958427_2.fastq Input file: SRR6958427_1.fastq Paired file: SRR6958427_2.fastq trimmed: SRR6958427-trimmed-pair1.fastq, SRR6958427-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 22:54:57 2024 >> started Fri Dec 6 22:55:22 2024 >> done (24.775s) 24702578 read pairs processed; of these: 43797 ( 0.18%) short read pairs filtered out after trimming by size control 49594 ( 0.20%) empty read pairs filtered out after trimming by size control 24609187 (99.62%) read pairs available; of these: 9785104 (39.76%) trimmed read pairs available after processing 14824083 (60.24%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 13 0.00% 20 4 0.00% 21 7 0.00% 22 9 0.00% 23 6 0.00% 24 5 0.00% 25 8 0.00% 26 9 0.00% 27 8 0.00% 28 14 0.00% 29 10 0.00% 30 10 0.00% 31 14 0.00% 32 7 0.00% 33 11 0.00% 34 10 0.00% 35 20 0.00% 36 12 0.00% 37 12 0.00% 38 21 0.00% 39 15 0.00% 40 20 0.00% 41 18 0.00% 42 17 0.00% 43 21 0.00% 44 23 0.00% 45 30 0.00% 46 25 0.00% 47 37 0.00% 48 35 0.00% 49 36 0.00% 50 33 0.00% 51 40 0.00% 52 47 0.00% 53 49 0.00% 54 61 0.00% 55 67 0.00% 56 69 0.00% 57 92 0.00% 58 86 0.00% 59 104 0.00% 60 108 0.00% 61 147 0.00% 62 172 0.00% 63 175 0.00% 64 193 0.00% 65 213 0.00% 66 229 0.00% 67 243 0.00% 68 307 0.00% 69 363 0.00% 70 363 0.00% 71 447 0.00% 72 512 0.00% 73 625 0.00% 74 768 0.00% 75 768 0.00% 76 891 0.00% 77 1024 0.00% 78 1108 0.00% 79 1311 0.01% 80 1437 0.01% 81 1687 0.01% 82 1922 0.01% 83 2316 0.01% 84 3769 0.02% 85 4886 0.02% 86 4962 0.02% 87 5201 0.02% 88 5674 0.02% 89 5824 0.02% 90 6076 0.02% 91 6446 0.03% 92 6785 0.03% 93 7354 0.03% 94 7888 0.03% 95 8208 0.03% 96 8537 0.03% 97 9161 0.04% 98 9676 0.04% 99 10318 0.04% 100 10901 0.04% 101 11578 0.05% 102 12942 0.05% 103 13433 0.05% 104 14437 0.06% 105 15367 0.06% 106 16108 0.07% 107 16328 0.07% 108 17566 0.07% 109 18480 0.08% 110 19526 0.08% 111 20494 0.08% 112 22580 0.09% 113 23561 0.10% 114 24900 0.10% 115 26402 0.11% 116 27920 0.11% 117 29094 0.12% 118 30324 0.12% 119 30913 0.13% 120 32462 0.13% 121 33783 0.14% 122 36523 0.15% 123 38525 0.16% 124 40711 0.17% 125 42482 0.17% 126 43999 0.18% 127 46311 0.19% 128 46768 0.19% 129 48794 0.20% 130 50742 0.21% 131 53261 0.22% 132 55909 0.23% 133 59318 0.24% 134 62228 0.25% 135 66064 0.27% 136 70868 0.29% 137 75055 0.30% 138 78544 0.32% 139 82449 0.34% 140 89516 0.36% 141 96231 0.39% 142 105660 0.43% 143 116387 0.47% 144 133374 0.54% 145 156742 0.64% 146 193807 0.79% 147 268292 1.09% 148 394436 1.60% 149 805831 3.27% 150 5827945 23.68% 151 14824083 60.24% 24609187 reads passed initial QC criterion=sequence-density sequence-density=0.92 sequence-density-rank=1 fanout-score=2.45 fanout-score-rank=37 prefix-density=1.00 prefix-fanout=2.2 sequence=GAGCTGGAGCTG criterion=fanout-score sequence-density=0.04 sequence-density-rank=34 fanout-score=188.43 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=10.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.67 sequence-density-rank=1 fanout-score=10.30 fanout-score-rank=15 prefix-density=2.08 prefix-fanout=3.3 sequence=AAGGAGAAGCTGCCTGGCCAGCACTGAGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=54.22 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.5 sequence=GTGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCACCAGCAGCACCCAGGCCCAGGTGGTGGTTCTCGGCATGGCGCCGGAGAAGAAACAGGAGCAGTTCGAGATGGCCGGCGTGTCCGGCGAAGGGTGCAGCTGCGGCGACAACTGCAAGTGCAACCCTTGTAACTGTTAGTCCATTAATCATGATGAACTTGTGGTTAGTAAATAAGCGCCGAGTCAGAGCGTGTGGTGTGATTGTGTTGTTGTT SRR6958427 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:56:20 Started mapping on | Dec 06 22:56:20 Finished on | Dec 06 22:58:24 Mapping speed, Million of reads per hour | 714.46 Number of input reads | 24609187 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 23499260 Uniquely mapped reads % | 95.49% Average mapped length | 296.55 Number of splices: Total | 23172669 Number of splices: Annotated (sjdb) | 21659887 Number of splices: GT/AG | 22892465 Number of splices: GC/AG | 217107 Number of splices: AT/AC | 9372 Number of splices: Non-canonical | 53725 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.02% Deletion average length | 2.21 Insertion rate per base | 0.01% Insertion average length | 2.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 186314 % of reads mapped to multiple loci | 0.76% Number of reads mapped to too many loci | 64140 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.58% % of reads unmapped: other | 1.92% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 946175 946175 946175 N_multimapping 186314 186314 186314 N_noFeature 965246 22776601 1245105 N_ambiguous 513875 3616 73091 UnstrandedReadsAssigned:22020139 PositiveStrandReadsAssigned:719043 NegativeStrandReadsAssigned:22181064 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958427 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: SRR6958427-trimmed-pair1.fastq SRR6958427-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,609,187 reads, 22,124,941 reads pseudoaligned [quant] estimated average fragment length: 249.971 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,263 rounds 52973 SRR6958427.ke.tsv 35125 SRR6958427.se.tsv 88098 total ==> SRR6958427.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 687.365 322.903 27.6176 PNS24247 1044 795.029 53.5849 3.96243 PNS24249 1928 1679.03 227.049 7.94993 PNS24246 1044 795.029 53.5849 3.96243 PNS24248 1044 795.029 53.5849 3.96243 PNS24244 1471 1222.03 128.294 6.172 PNS24243 293 86.5412 0 0 KQK14069 1603 1354.03 280.722 12.1885 KQK14071 474 235.109 7.76121 1.94072 ==> SRR6958427.se.tsv <== BRADI_1g14170v3 308 BRADI_1g53295v3 274 BRADI_1g59795v3 70 BRADI_1g07683v3 0 BRADI_1g00485v3 18 BRADI_1g20270v3 1368 BRADI_1g74790v3 1247 BRADI_1g09890v3 0 BRADI_1g77505v3 80 BRADI_1g48960v3 0 SRR6958427 completed mapping pipeline successfully