Starting /dee2/code/volunteer_pipeline.sh SRR8096898 current disk space = 1542194331648 free memory = 1601387292 SRR8096898 SRAfilesize 6edf0167c14007ce6c28ff5760aff4b7 SRR8096898.sra SRR8096898.sra file validated SRR8096898 is paired end SRR8096898 is conventional basespace SRR8096898 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096898_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.87875 34.0 33.0 34.0 32.0 34.0 2 33.04725 34.0 33.0 34.0 31.0 34.0 3 33.2115 34.0 33.0 34.0 32.0 34.0 4 33.27175 34.0 33.0 34.0 32.0 34.0 5 33.37325 34.0 33.0 34.0 33.0 34.0 6 37.119 38.0 38.0 38.0 36.0 38.0 7 37.43175 38.0 38.0 38.0 37.0 38.0 8 37.509 38.0 38.0 38.0 37.0 38.0 9 37.603 38.0 38.0 38.0 38.0 38.0 10-14 37.4409 38.0 38.0 38.0 37.4 38.0 15-19 37.44735000000001 38.0 38.0 38.0 37.4 38.0 20-24 37.458999999999996 38.0 38.0 38.0 38.0 38.0 25-29 37.44615 38.0 38.0 38.0 38.0 38.0 30-34 37.335899999999995 38.0 38.0 38.0 37.4 38.0 35-39 37.31585 38.0 38.0 38.0 37.0 38.0 40-44 37.2202 38.0 38.0 38.0 37.0 38.0 45-49 37.206100000000006 38.0 38.0 38.0 37.0 38.0 50-54 37.1586 38.0 38.0 38.0 36.8 38.0 55-59 37.20490000000001 38.0 38.0 38.0 37.0 38.0 60-64 37.10365 38.0 38.0 38.0 36.6 38.0 65-69 36.98285 38.0 38.0 38.0 36.0 38.0 70-74 36.809799999999996 38.0 38.0 38.0 36.0 38.0 75-79 36.59275 38.0 38.0 38.0 35.8 38.0 80-84 36.450649999999996 38.0 38.0 38.0 35.4 38.0 85-89 36.50815 38.0 38.0 38.0 35.2 38.0 90-94 36.33364999999999 38.0 38.0 38.0 34.4 38.0 95-99 36.3222 38.0 38.0 38.0 34.8 38.0 100-104 35.97585 38.0 37.8 38.0 33.4 38.0 105-109 35.734500000000004 38.0 37.8 38.0 32.6 38.0 110-114 35.84015000000001 38.0 38.0 38.0 33.4 38.0 115-119 35.73145 38.0 38.0 38.0 32.8 38.0 120-124 35.44435 38.0 38.0 38.0 31.0 38.0 125-129 35.34455 38.0 37.2 38.0 31.2 38.0 130-134 34.869099999999996 38.0 36.2 38.0 29.2 38.0 135-139 34.539699999999996 38.0 36.0 38.0 27.2 38.0 140-144 33.97355 38.0 35.6 38.0 23.6 38.0 145-149 32.8206 38.0 33.4 38.0 11.8 38.0 150 23.835 31.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 2.0 5 1.0 6 1.0 7 1.0 8 1.0 9 1.0 10 1.0 11 3.0 12 2.0 13 2.0 14 4.0 15 7.0 16 4.0 17 7.0 18 19.0 19 18.0 20 4.0 21 8.0 22 2.0 23 7.0 24 8.0 25 16.0 26 14.0 27 27.0 28 21.0 29 28.0 30 38.0 31 56.0 32 68.0 33 78.0 34 124.0 35 204.0 36 559.0 37 2663.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.74625689519306 11.452587339112162 6.882059364328868 43.919096401365906 2 21.8 17.275 37.05 23.875 3 21.95 19.575 26.924999999999997 31.55 4 26.650000000000002 26.375 20.775 26.200000000000003 5 28.61430715357679 30.515257628814407 22.26113056528264 18.609304652326163 6 20.65 32.85 24.925 21.575 7 16.075 23.075000000000003 41.5 19.35 8 19.400000000000002 22.225 32.074999999999996 26.3 9 19.275000000000002 20.75 33.775 26.200000000000003 10-14 22.75 26.650000000000002 25.074999999999996 25.525 15-19 22.535 26.025 25.885 25.555 20-24 22.725 26.125 25.974999999999998 25.174999999999997 25-29 22.8 26.055 25.180000000000003 25.965 30-34 22.66 25.585 25.979999999999997 25.775 35-39 23.435 25.735000000000003 25.405 25.424999999999997 40-44 22.905 25.814999999999998 25.83 25.45 45-49 23.885 25.669999999999998 25.595000000000002 24.85 50-54 23.294999999999998 25.405 25.05 26.25 55-59 22.825 24.905 26.68 25.590000000000003 60-64 23.51 24.545 26.1 25.845000000000002 65-69 22.555 26.540000000000003 25.83 25.074999999999996 70-74 23.355 25.919999999999998 25.45 25.275 75-79 23.07 26.245 25.035 25.650000000000002 80-84 23.53 25.4 25.419999999999998 25.650000000000002 85-89 23.82 25.474999999999998 25.4 25.305 90-94 23.169999999999998 25.569999999999997 25.61 25.650000000000002 95-99 23.474999999999998 25.419999999999998 24.735 26.369999999999997 100-104 23.785 26.195 24.645 25.374999999999996 105-109 23.44 25.495 25.555 25.509999999999998 110-114 24.11 25.15 24.92 25.82 115-119 23.7 25.55 24.709999999999997 26.040000000000003 120-124 23.544999999999998 25.4 25.35 25.705 125-129 23.69 25.295 25.06 25.955000000000002 130-134 24.37 25.495 24.715 25.419999999999998 135-139 24.015 25.374999999999996 24.57 26.040000000000003 140-144 24.22 25.205 24.745 25.83 145-149 24.43 24.91 24.555 26.105 150 23.849999999999998 25.1 25.95 25.1 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 4.0 1 3.5 2 1.5 3 1.0 4 2.0 5 2.5 6 3.5 7 2.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 1.0 15 1.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 1.0 23 0.0 24 0.5 25 2.0 26 3.0 27 5.0 28 7.0 29 6.0 30 11.0 31 17.5 32 16.0 33 19.5 34 33.5 35 48.0 36 58.0 37 74.0 38 87.0 39 97.0 40 114.0 41 142.0 42 175.5 43 191.0 44 197.5 45 195.0 46 189.0 47 192.5 48 171.0 49 152.0 50 147.5 51 138.0 52 132.0 53 120.0 54 108.0 55 94.5 56 98.0 57 96.5 58 87.5 59 78.5 60 76.5 61 80.5 62 78.5 63 74.5 64 64.0 65 61.0 66 55.0 67 42.5 68 34.0 69 28.5 70 23.5 71 18.0 72 12.5 73 9.5 74 4.5 75 2.5 76 2.5 77 1.5 78 0.5 79 0.5 80 0.5 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 4.825 2 0.0 3 0.0 4 0.0 5 0.05 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.2 #Duplication Level Percentage of deduplicated Percentage of total 1 98.63683127572016 95.875 2 1.1574074074074074 2.25 3 0.102880658436214 0.3 4 0.0257201646090535 0.1 5 0.0257201646090535 0.125 6 0.0 0.0 7 0.0257201646090535 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.0257201646090535 1.175 >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 fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCATCTCGTATGC 47 1.175 TruSeq Adapter, Index 20 (98% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 7 0.17500000000000002 No Hit CCGGAGTTTATATTACATGCCCCTCTCCCAACGATAGTTGTAGTACTCTT 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.037500000000000006 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.1875 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.2875 0.0 0.0 0.0 0.0 86-87 0.3125 0.0 0.0 0.0 0.0 88-89 0.325 0.0 0.0 0.0 0.0 90-91 0.3625 0.0 0.0 0.0 0.0 92-93 0.375 0.0 0.0 0.0 0.0 94-95 0.4375 0.0 0.0 0.0 0.0 96-97 0.5 0.0 0.0 0.0 0.0 98-99 0.5375000000000001 0.0 0.0 0.0 0.0 100-101 0.6625 0.0 0.0 0.0 0.0 102-103 0.725 0.0 0.0 0.0 0.0 104-105 0.8375 0.0 0.0 0.0 0.0 106-107 0.9874999999999999 0.0 0.0 0.0 0.0 108-109 1.1125 0.0 0.0 0.0 0.0 110-111 1.2 0.0 0.0 0.0 0.0 112-113 1.4125 0.0 0.0 0.0 0.0 114-115 1.575 0.0 0.0 0.0 0.0 116-117 1.7875 0.0 0.0 0.0 0.0 118-119 1.95 0.0 0.0 0.0 0.0 120-121 2.1125 0.0 0.0 0.0 0.0 122-123 2.4 0.0 0.0 0.0 0.0 124-125 2.5875 0.0 0.0 0.0 0.0 126-127 2.8125 0.0 0.0 0.0 0.0 128-129 3.0875 0.0 0.0 0.0 0.0 130-131 3.3499999999999996 0.0 0.0 0.0 0.0 132-133 3.625 0.0 0.0 0.0 0.0 134-135 3.95 0.0 0.0 0.0 0.0 136-137 4.3 0.0 0.0 0.0 0.0 138 4.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGATGAC 10 0.0069754543 143.9875 8 TTCACGA 10 0.0069754543 143.9875 3 GATCGGA 30 1.3710764E-5 97.20676 1 GAGCACA 30 1.4618472E-5 95.99167 9 AGAGCAC 30 1.4618472E-5 95.99167 8 GGAAGAG 30 1.4618472E-5 95.99167 5 AAGAGCA 35 3.1425407E-5 82.27857 7 TCGGAAG 35 3.1425407E-5 82.27857 3 GAAGAGC 40 6.093763E-5 71.99375 6 ATCGGAA 40 6.093763E-5 71.99375 2 CGGAAGA 45 1.0921781E-4 63.994446 4 TCTCGTA 20 0.006141849 28.797503 40-44 CCATCTC 20 0.006141849 28.797503 35-39 GCCATCT 20 0.006141849 28.797503 35-39 CTCGTAT 20 0.006141849 28.797503 40-44 GCTTGAA 40 0.007970727 17.99844 55-59 AAAAAAA 245 4.5474735E-10 10.578673 65-69 >>END_MODULE SRR8096898 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096898_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 50 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.75175 33.0 32.0 33.0 27.0 34.0 2 30.95575 33.0 32.0 33.0 27.0 34.0 3 31.23525 33.0 32.0 33.0 27.0 34.0 4 31.182 33.0 31.0 34.0 28.0 34.0 5 28.185 31.0 27.0 33.0 15.0 34.0 6 34.089 38.0 33.0 38.0 27.0 38.0 7 34.72175 38.0 36.0 38.0 28.0 38.0 8 35.22625 38.0 37.0 38.0 29.0 38.0 9 35.188 38.0 37.0 38.0 29.0 38.0 10-14 35.2952 38.0 37.0 38.0 29.0 38.0 15-19 35.14675 38.0 37.0 38.0 28.6 38.0 20-24 35.09495 38.0 37.0 38.0 28.0 38.0 25-29 34.89325 38.0 36.8 38.0 27.2 38.0 30-34 34.68495 38.0 36.2 38.0 26.2 38.0 35-39 34.60385 38.0 36.0 38.0 26.2 38.0 40-44 34.4947 38.0 36.0 38.0 26.2 38.0 45-49 34.3429 38.0 36.0 38.0 25.0 38.0 50-54 34.2517 38.0 36.0 38.0 24.4 38.0 55-59 33.8336 38.0 34.8 38.0 16.0 38.0 60-64 33.54835 38.0 34.0 38.0 16.0 38.0 65-69 33.173199999999994 38.0 34.0 38.0 15.8 38.0 70-74 32.65385 38.0 33.2 38.0 15.2 38.0 75-79 32.20765 37.8 32.2 38.0 15.0 38.0 80-84 31.944550000000003 37.8 31.8 38.0 15.0 38.0 85-89 31.38565 37.0 30.0 38.0 14.2 38.0 90-94 31.140050000000002 37.0 29.0 38.0 13.6 38.0 95-99 30.178449999999998 36.4 26.6 38.0 13.0 38.0 100-104 29.639750000000003 36.0 24.6 38.0 10.8 38.0 105-109 28.99385 35.0 23.0 38.0 2.0 38.0 110-114 28.498 35.0 21.8 38.0 2.0 38.0 115-119 27.42215 34.0 15.0 38.0 2.0 38.0 120-124 26.445999999999998 33.4 14.4 38.0 2.0 38.0 125-129 25.3635 31.8 13.2 38.0 2.0 38.0 130-134 24.01185 31.0 13.0 37.0 2.0 38.0 135-139 22.022799999999997 28.2 2.0 36.2 2.0 38.0 140-144 20.10685 22.8 2.0 34.4 2.0 38.0 145-149 16.9648 10.2 2.0 33.2 2.0 38.0 150 11.49325 2.0 2.0 28.0 2.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 77.0 3 10.0 4 8.0 5 6.0 6 9.0 7 5.0 8 10.0 9 14.0 10 11.0 11 15.0 12 18.0 13 19.0 14 33.0 15 31.0 16 28.0 17 49.0 18 44.0 19 33.0 20 43.0 21 41.0 22 57.0 23 47.0 24 70.0 25 79.0 26 88.0 27 116.0 28 133.0 29 146.0 30 188.0 31 225.0 32 284.0 33 320.0 34 448.0 35 538.0 36 544.0 37 213.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 34.42047165077772 17.486201705970895 8.70546914199699 39.387857501254395 2 25.496106505903036 24.541572469228836 32.27832202964079 17.68399899522733 3 23.560472718129244 24.64168971586623 26.301232084485793 25.49660548151873 4 25.553319919517104 30.985915492957744 19.26559356136821 24.19517102615694 5 29.275653923541245 33.47585513078471 19.718309859154928 17.530181086519114 6 22.95905551369003 35.11680482290881 19.66842501883949 22.255714644561667 7 22.30035158211954 17.9809141135108 34.053239578101454 25.665494726268207 8 22.30035158211954 22.22501255650427 25.213460572576597 30.261175288799596 9 24.937217478653942 21.97388247112004 27.59919638372677 25.489703666499246 10-14 26.760421898543445 24.434957307885487 22.933199397287794 25.871421396283274 15-19 26.507960423886296 24.574355883682387 23.750690573050072 25.16699311938125 20-24 26.302044096228215 25.463311737230676 23.233388579177337 25.00125558736377 25-29 25.866224766495932 25.017575574972383 23.857587626795222 25.258612031736465 30-34 26.339308128734245 25.008786463824872 24.330973540191795 24.320931867249087 35-39 25.621328513330322 25.24476577797861 23.889139930712457 25.24476577797861 40-44 26.63420022090571 25.082839642534395 24.154031529270007 24.128928607289886 45-49 26.022995431038808 24.250640156650096 23.929306622483306 25.797057789827786 50-54 26.114905584572117 25.60265166733628 24.643431096826035 23.63901165126557 55-59 26.71889910099945 25.4783787855959 23.479483702476017 24.32323841092863 60-64 25.286317058468953 26.265822784810126 23.724131002612015 24.723729154108902 65-69 25.371709865380755 25.708257986738996 24.45750452079566 24.46252762708459 70-74 26.14897784921392 25.30011552564167 23.788236475965643 24.762670149178764 75-79 25.81374321880651 25.48221820373719 23.734177215189874 24.96986136226643 80-84 26.031044356256594 25.825086652936154 23.564575275028883 24.57929371577837 85-89 25.566440592815876 25.55639286611404 24.29540316503391 24.58176337603617 90-94 26.08258816437255 25.283834019893497 24.329347935295893 24.304229880438058 95-99 26.000904204551162 25.20721354297483 24.16737830913749 24.624503943336514 100-104 26.479156202913106 25.148166750376692 23.832245102963334 24.54043194374686 105-109 25.78117150607857 26.188083994775447 23.480357681101175 24.55038681804481 110-114 25.330319015322782 25.787490580256218 24.079377040944486 24.802813363476513 115-119 26.037375665628453 26.173013161860748 23.631066010248166 24.158545162262634 120-124 26.01225761077062 25.967045112026526 23.425097960413947 24.595599316788906 125-129 26.117753441173512 25.86154928162363 23.927459057570584 24.09323821963227 130-134 26.5370705244123 26.30600763512156 23.33735181836448 23.81957002210167 135-139 26.31473203073987 26.06861218544377 23.15535687377568 24.461298910040686 140-144 26.92114515318935 26.167754897036666 23.375188347564038 23.535911602209943 145-149 27.246625025186376 25.967156961515215 23.307475317348377 23.478742695950032 150 28.37057494350992 24.956063268892795 22.94752698970625 23.72583479789104 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 14.0 1 8.0 2 1.5 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.5 19 1.0 20 0.5 21 1.0 22 1.0 23 1.5 24 2.5 25 2.5 26 2.0 27 2.0 28 4.5 29 5.0 30 5.0 31 11.0 32 18.5 33 20.0 34 25.5 35 39.5 36 46.5 37 47.5 38 61.0 39 80.0 40 95.5 41 125.0 42 143.0 43 140.5 44 160.0 45 173.0 46 155.0 47 164.0 48 169.0 49 160.0 50 152.0 51 143.0 52 135.5 53 122.5 54 116.0 55 102.5 56 98.5 57 99.5 58 108.5 59 121.0 60 120.0 61 109.5 62 98.0 63 85.0 64 74.5 65 74.0 66 73.0 67 59.0 68 49.5 69 51.0 70 42.0 71 28.0 72 20.0 73 12.0 74 6.5 75 5.5 76 3.0 77 2.0 78 2.5 79 1.5 80 0.5 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 0.35000000000000003 2 0.475 3 0.575 4 0.6 5 0.6 6 0.475 7 0.44999999999999996 8 0.44999999999999996 9 0.44999999999999996 10-14 0.44999999999999996 15-19 0.445 20-24 0.445 25-29 0.43 30-34 0.415 35-39 0.415 40-44 0.41000000000000003 45-49 0.415 50-54 0.44 55-59 0.445 60-64 0.45999999999999996 65-69 0.45999999999999996 70-74 0.455 75-79 0.45999999999999996 80-84 0.46499999999999997 85-89 0.475 90-94 0.47000000000000003 95-99 0.46499999999999997 100-104 0.44999999999999996 105-109 0.47000000000000003 110-114 0.475 115-119 0.47000000000000003 120-124 0.47000000000000003 125-129 0.47000000000000003 130-134 0.45999999999999996 135-139 0.455 140-144 0.44999999999999996 145-149 0.74 150 0.42500000000000004 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.175 #Duplication Level Percentage of deduplicated Percentage of total 1 98.55930023154103 95.775 2 1.1062516079238487 2.15 3 0.20581425263699513 0.6 4 0.02572678157962439 0.1 5 0.0 0.0 6 0.05145356315924878 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.05145356315924878 1.075 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 29 0.7250000000000001 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 14 0.35000000000000003 No Hit CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 6 0.15 No Hit CTCTTGTTAGCTATCTACGTACGTGTACGATGGCTCCCACAGTGATGTCG 6 0.15 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 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.16249999999999998 0.0 0.0 0.0 0.0 86-87 0.1875 0.0 0.0 0.0 0.0 88-89 0.2 0.0 0.0 0.0 0.0 90-91 0.2375 0.0 0.0 0.0 0.0 92-93 0.25 0.0 0.0 0.0 0.0 94-95 0.275 0.0 0.0 0.0 0.0 96-97 0.325 0.0 0.0 0.0 0.0 98-99 0.3625 0.0 0.0 0.0 0.0 100-101 0.48750000000000004 0.0 0.0 0.0 0.0 102-103 0.5375000000000001 0.0 0.0 0.0 0.0 104-105 0.575 0.0 0.0 0.0 0.0 106-107 0.65 0.0 0.0 0.0 0.0 108-109 0.7375 0.0 0.0 0.0 0.0 110-111 0.775 0.0 0.0 0.0 0.0 112-113 0.9 0.0 0.0 0.0 0.0 114-115 1.0 0.0 0.0 0.0 0.0 116-117 1.1625 0.0 0.0 0.0 0.0 118-119 1.2875 0.0 0.0 0.0 0.0 120-121 1.3875 0.0 0.0 0.0 0.0 122-123 1.5125 0.0 0.0 0.0 0.0 124-125 1.6124999999999998 0.0 0.0 0.0 0.0 126-127 1.725 0.0 0.0 0.0 0.0 128-129 1.85 0.0 0.0 0.0 0.0 130-131 1.9249999999999998 0.0 0.0 0.0 0.0 132-133 2.0625 0.0 0.0 0.0 0.0 134-135 2.2375 0.0 0.0 0.0 0.0 136-137 2.4375 0.0 0.0 0.0 0.0 138 2.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTC 15 1.17425385E-4 143.96251 9 TCAAGCT 10 0.0069790767 143.96251 9 AAGAGCG 20 1.9477447E-6 143.96251 7 ACCAAGG 10 0.0069790767 143.96251 6 AGAGCGT 15 1.17425385E-4 143.96251 8 CTCAAGC 10 0.0069790767 143.96251 8 GATCGGA 25 5.9118884E-6 115.16999 1 CGGAAGA 25 5.9118884E-6 115.16999 4 ATCGGAA 25 5.9118884E-6 115.16999 2 GAAGAGC 30 1.4631087E-5 95.975 6 TCGGAAG 30 1.4631087E-5 95.975 3 GGAAGAG 30 1.4631087E-5 95.975 5 AAAAAAA 315 3.1705895E-7 7.769405 60-64 >>END_MODULE Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549915 spots for SRR8096898.sra Written 1549915 spots for SRR8096898.sra Read 1549921 spots for SRR8096898.sra Written 1549921 spots for SRR8096898.sra SRR ids: ['SRR8096898.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ucp4pj7p SRR8096898.sra spots: 30998306 blocks: [[1, 1549915], [1549916, 3099830], [3099831, 4649745], [4649746, 6199660], [6199661, 7749575], [7749576, 9299490], [9299491, 10849405], [10849406, 12399320], [12399321, 13949235], [13949236, 15499150], [15499151, 17049065], [17049066, 18598980], [18598981, 20148895], [20148896, 21698810], [21698811, 23248725], [23248726, 24798640], [24798641, 26348555], [26348556, 27898470], [27898471, 29448385], [29448386, 30998306]] SRR8096898 file size 10422064 SRR8096898 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 SRR8096898 SRR8096898_1.fastq SRR8096898_2.fastq Input file: SRR8096898_1.fastq Paired file: SRR8096898_2.fastq trimmed: SRR8096898-trimmed-pair1.fastq, SRR8096898-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 Sat Dec 7 15:58:50 2024 >> started Sat Dec 7 15:59:24 2024 >> done (33.730s) 30998306 read pairs processed; of these: 113905 ( 0.37%) short read pairs filtered out after trimming by size control 757817 ( 2.44%) empty read pairs filtered out after trimming by size control 30126584 (97.19%) read pairs available; of these: 18051217 (59.92%) trimmed read pairs available after processing 12075367 (40.08%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 63 0.00% 19 101 0.00% 20 59 0.00% 21 102 0.00% 22 134 0.00% 23 209 0.00% 24 267 0.00% 25 226 0.00% 26 286 0.00% 27 385 0.00% 28 210 0.00% 29 191 0.00% 30 759 0.00% 31 318 0.00% 32 505 0.00% 33 217 0.00% 34 600 0.00% 35 899 0.00% 36 636 0.00% 37 385 0.00% 38 442 0.00% 39 475 0.00% 40 890 0.00% 41 1044 0.00% 42 693 0.00% 43 981 0.00% 44 680 0.00% 45 885 0.00% 46 1074 0.00% 47 1421 0.00% 48 1088 0.00% 49 989 0.00% 50 1102 0.00% 51 1157 0.00% 52 1296 0.00% 53 1329 0.00% 54 1444 0.00% 55 1380 0.00% 56 1654 0.01% 57 1369 0.00% 58 1555 0.01% 59 1522 0.01% 60 1245 0.00% 61 2391 0.01% 62 1743 0.01% 63 1247 0.00% 64 1274 0.00% 65 1423 0.00% 66 1492 0.00% 67 1640 0.01% 68 1861 0.01% 69 2286 0.01% 70 2336 0.01% 71 2423 0.01% 72 2451 0.01% 73 2720 0.01% 74 2969 0.01% 75 3261 0.01% 76 3662 0.01% 77 3949 0.01% 78 4344 0.01% 79 4885 0.02% 80 5571 0.02% 81 5995 0.02% 82 7027 0.02% 83 8926 0.03% 84 15460 0.05% 85 16858 0.06% 86 18557 0.06% 87 20074 0.07% 88 20510 0.07% 89 20801 0.07% 90 20841 0.07% 91 21022 0.07% 92 21233 0.07% 93 21710 0.07% 94 23294 0.08% 95 24705 0.08% 96 26181 0.09% 97 28379 0.09% 98 30610 0.10% 99 32139 0.11% 100 33223 0.11% 101 35322 0.12% 102 37576 0.12% 103 40161 0.13% 104 42804 0.14% 105 46269 0.15% 106 46615 0.15% 107 47946 0.16% 108 52512 0.17% 109 51614 0.17% 110 53343 0.18% 111 54544 0.18% 112 57024 0.19% 113 58857 0.20% 114 61733 0.20% 115 65089 0.22% 116 67093 0.22% 117 70822 0.24% 118 73731 0.24% 119 76862 0.26% 120 79908 0.27% 121 84869 0.28% 122 89737 0.30% 123 93166 0.31% 124 98438 0.33% 125 103341 0.34% 126 110896 0.37% 127 114866 0.38% 128 121755 0.40% 129 128075 0.43% 130 135611 0.45% 131 144379 0.48% 132 152687 0.51% 133 162274 0.54% 134 173780 0.58% 135 184166 0.61% 136 199959 0.66% 137 214469 0.71% 138 231287 0.77% 139 251180 0.83% 140 272317 0.90% 141 305327 1.01% 142 337397 1.12% 143 378558 1.26% 144 447422 1.49% 145 542899 1.80% 146 717655 2.38% 147 1041263 3.46% 148 1983022 6.58% 149 7606857 25.25% 150 12075367 40.08% 30126584 reads passed initial QC criterion=sequence-density sequence-density=1.24 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=31 prefix-density=1.26 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=31.48 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=3.1 sequence=TATATATTACTGTTCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTT criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=3.18 fanout-score-rank=11 prefix-density=1.02 prefix-fanout=2.8 sequence=GAGTTCAGCAAGGTCGG criterion=fanout-score sequence-density=0.05 sequence-density-rank=28 fanout-score=19.80 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=3.9 sequence=GCAAGAACAAGTACGCCGGTGTTGGGTCGGCCATCGAGTACGCCGTGTGTGCCCTCAAGGTTGAGGTCATCGTGGTGATTGGCCACAGCCGCTGCGGTGGAATCAAGGCACTCCTCTCGCTCAAGGATGGTGCAGATGACAGCTTCCACTTCGTCGAGGACTGGGTCAGGATCGGGTTCCCGGCCAAGAAGAAGGTGCAGACCGAGTGCGCCTCCATGCCTTTCGATGACCAATGCGCCGTCTTGGAAAAGGAGGCCGTGAACGTGTCCCTCGAGAAC SRR8096898 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 16:00:07 Started mapping on | Dec 07 16:00:07 Finished on | Dec 07 16:02:58 Mapping speed, Million of reads per hour | 634.24 Number of input reads | 30126584 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 29228566 Uniquely mapped reads % | 97.02% Average mapped length | 289.56 Number of splices: Total | 28706597 Number of splices: Annotated (sjdb) | 27094066 Number of splices: GT/AG | 28325246 Number of splices: GC/AG | 329564 Number of splices: AT/AC | 8293 Number of splices: Non-canonical | 43494 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.01% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 344575 % of reads mapped to multiple loci | 1.14% Number of reads mapped to too many loci | 12392 % of reads mapped to too many loci | 0.04% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.52% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 685687 685687 685687 N_multimapping 344575 344575 344575 N_noFeature 953130 28254236 1172431 N_ambiguous 880497 3181 128074 UnstrandedReadsAssigned:27394939 PositiveStrandReadsAssigned:971149 NegativeStrandReadsAssigned:27928061 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR8096898 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: SRR8096898-trimmed-pair1.fastq SRR8096898-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 30,126,584 reads, 27,930,242 reads pseudoaligned [quant] estimated average fragment length: 266.887 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,142 rounds 52973 SRR8096898.ke.tsv 35125 SRR8096898.se.tsv 88098 total ==> SRR8096898.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 670.562 0 0 PNS24247 1044 778.113 64.1624 3.87956 PNS24249 1928 1662.11 39.1352 1.10778 PNS24246 1044 778.113 64.1624 3.87956 PNS24248 1044 778.113 64.1624 3.87956 PNS24244 1471 1205.11 253.378 9.89203 PNS24243 293 85.1416 0 0 KQK14069 1603 1337.11 9342.25 328.722 KQK14071 474 225.153 181.982 38.0274 ==> SRR8096898.se.tsv <== BRADI_1g14170v3 11010 BRADI_1g53295v3 56 BRADI_1g59795v3 1434 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 165 BRADI_1g74790v3 98 BRADI_1g09890v3 0 BRADI_1g77505v3 447 BRADI_1g48960v3 0 SRR8096898 completed mapping pipeline successfully