Starting /dee2/code/volunteer_pipeline.sh SRR7171465 current disk space = 3087709442048 free memory = 1550526064 SRR7171465 SRAfilesize 7abb5b61952406b4f74f88a3f7dbe2df SRR7171465.sra SRR7171465.sra file validated SRR7171465 is paired end SRR7171465 is conventional basespace SRR7171465 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171465_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.8395 32.0 27.0 33.0 18.0 34.0 2 31.56475 33.0 31.0 33.0 27.0 34.0 3 31.874 33.0 32.0 33.0 28.0 34.0 4 31.834 33.0 31.0 33.0 29.0 34.0 5 32.45775 33.0 33.0 33.0 31.0 34.0 6 36.53075 38.0 37.0 38.0 34.0 38.0 7 37.0695 38.0 38.0 38.0 36.0 38.0 8 37.31975 38.0 38.0 38.0 37.0 38.0 9 37.43225 38.0 38.0 38.0 37.0 38.0 10-14 37.4394 38.0 38.0 38.0 37.2 38.0 15-19 37.4616 38.0 38.0 38.0 37.2 38.0 20-24 37.4795 38.0 38.0 38.0 37.0 38.0 25-29 37.3645 38.0 38.0 38.0 37.0 38.0 30-34 37.4216 38.0 38.0 38.0 37.0 38.0 35-39 37.318 38.0 38.0 38.0 37.0 38.0 40-44 37.27419999999999 38.0 38.0 38.0 37.0 38.0 45-49 37.2568 38.0 38.0 38.0 37.0 38.0 50-54 37.206399999999995 38.0 38.0 38.0 36.4 38.0 55-59 37.1356 38.0 38.0 38.0 36.0 38.0 60-64 37.0227 38.0 38.0 38.0 36.0 38.0 65-69 36.965700000000005 38.0 38.0 38.0 35.6 38.0 70-74 36.995549999999994 38.0 38.0 38.0 35.6 38.0 75-79 36.9286 38.0 38.0 38.0 35.2 38.0 80-84 36.7312 38.0 38.0 38.0 34.6 38.0 85-89 36.558550000000004 38.0 38.0 38.0 34.0 38.0 90-94 36.5388 38.0 38.0 38.0 34.0 38.0 95-99 36.576950000000004 38.0 38.0 38.0 34.4 38.0 100-104 36.30825 38.0 37.4 38.0 33.4 38.0 105-109 36.17274999999999 38.0 37.0 38.0 33.0 38.0 110-114 36.04595 38.0 37.0 38.0 32.6 38.0 115-119 35.81875 38.0 36.6 38.0 31.6 38.0 120-124 35.5786 38.0 36.0 38.0 30.2 38.0 125-129 35.49980000000001 38.0 36.0 38.0 29.8 38.0 130-134 35.518600000000006 38.0 36.0 38.0 29.8 38.0 135-139 35.22375 38.0 35.0 38.0 28.2 38.0 140-144 34.822500000000005 38.0 35.0 38.0 27.2 38.0 145-149 34.50855 38.0 34.8 38.0 24.6 38.0 150-151 32.191 36.0 28.5 38.0 18.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 3.0 22 2.0 23 7.0 24 7.0 25 10.0 26 14.0 27 14.0 28 23.0 29 30.0 30 50.0 31 64.0 32 79.0 33 132.0 34 187.0 35 343.0 36 750.0 37 2284.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.312706900942196 12.859689330277565 10.16042780748663 40.66717596129361 2 19.409704852426213 13.531765882941471 33.21660830415208 33.84192096048024 3 18.875 17.599999999999998 25.2 38.324999999999996 4 25.174999999999997 24.5 21.95 28.375 5 23.875 28.325 24.175 23.625 6 19.575 32.175 26.224999999999998 22.025 7 14.374999999999998 25.8 40.65 19.175 8 18.05 25.174999999999997 31.0 25.775 9 16.900000000000002 25.15 32.975 24.975 10-14 19.77 28.32 27.189999999999998 24.72 15-19 19.869999999999997 27.63 27.445000000000004 25.055 20-24 20.125 27.365000000000002 28.139999999999997 24.37 25-29 20.21 27.195000000000004 27.51 25.085 30-34 20.31 27.800000000000004 27.72 24.169999999999998 35-39 20.5 27.465 27.315 24.72 40-44 20.615 27.415 27.975 23.995 45-49 20.544999999999998 27.045 27.435 24.975 50-54 20.27 27.560000000000002 27.450000000000003 24.72 55-59 20.51 27.71 27.555000000000003 24.224999999999998 60-64 20.200000000000003 27.41 27.555000000000003 24.834999999999997 65-69 20.474999999999998 27.24 27.725 24.560000000000002 70-74 20.11201120112011 27.30773077307731 27.63776377637764 24.942494249424943 75-79 20.685000000000002 26.86 27.91 24.545 80-84 20.349999999999998 26.974999999999998 27.845 24.83 85-89 20.665 27.785 27.33 24.22 90-94 20.849999999999998 26.605 27.92 24.625 95-99 20.585 27.255000000000003 27.88 24.279999999999998 100-104 20.474999999999998 27.29 27.689999999999998 24.545 105-109 20.48 27.089999999999996 28.025 24.404999999999998 110-114 21.165 26.950000000000003 27.445000000000004 24.44 115-119 21.426427928378512 27.393217965389617 27.043112933880163 24.137241172351708 120-124 20.585 27.200000000000003 27.36 24.855 125-129 21.615000000000002 26.87 26.889999999999997 24.625 130-134 21.035 27.474999999999998 26.83 24.66 135-139 20.974999999999998 27.41 27.169999999999998 24.445 140-144 21.279999999999998 26.745 26.86 25.115 145-149 21.665 27.02 26.965 24.349999999999998 150-151 21.125 27.450000000000003 27.200000000000003 24.224999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.0 21 0.5 22 1.0 23 1.0 24 2.5 25 3.0 26 3.5 27 4.0 28 5.0 29 8.0 30 8.0 31 13.5 32 27.0 33 32.5 34 38.5 35 52.0 36 61.5 37 79.0 38 116.0 39 152.0 40 178.0 41 208.0 42 226.0 43 255.0 44 275.0 45 275.5 46 267.5 47 245.0 48 240.0 49 216.0 50 168.5 51 143.0 52 128.5 53 103.0 54 80.5 55 63.5 56 42.5 57 37.5 58 41.0 59 31.5 60 23.5 61 21.5 62 20.0 63 15.0 64 11.5 65 10.0 66 11.5 67 11.5 68 9.0 69 8.0 70 5.5 71 2.0 72 2.0 73 5.0 74 4.0 75 2.0 76 1.0 77 0.0 78 0.0 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 1.825 2 0.05 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 0.01 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 0.03 120-124 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 98.7 #Duplication Level Percentage of deduplicated Percentage of total 1 98.98682877406281 97.7 2 0.8105369807497468 1.6 3 0.12664640324214793 0.375 4 0.050658561296859174 0.2 5 0.025329280648429587 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GTGCGAATCAACGGTTCCTCTCGTACTAGGTTGGATTACTATTGCGACAC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 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 0.0625 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.0875 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.2125 0.0 0.0 0.0 0.0 92-93 0.275 0.0 0.0 0.0 0.0 94-95 0.3625 0.0 0.0 0.0 0.0 96-97 0.4625 0.0 0.0 0.0 0.0 98-99 0.625 0.0 0.0 0.0 0.0 100-101 0.6875 0.0 0.0 0.0 0.0 102-103 0.7875 0.0 0.0 0.0 0.0 104-105 0.95 0.0 0.0 0.0 0.0 106-107 1.0875 0.0 0.0 0.0 0.0 108-109 1.2374999999999998 0.0 0.0 0.0 0.0 110-111 1.6375000000000002 0.0 0.0 0.0 0.0 112-113 1.8375 0.0 0.0 0.0 0.0 114-115 2.175 0.0 0.0 0.0 0.0 116-117 2.5125 0.0 0.0 0.0 0.0 118-119 2.95 0.0 0.0 0.0 0.0 120-121 3.3625 0.0 0.0 0.0 0.0 122-123 3.6875 0.0 0.0 0.0 0.0 124-125 4.0 0.0 0.0 0.0 0.0 126-127 4.3625 0.0 0.0 0.0 0.0 128-129 4.9625 0.0 0.0 0.0 0.0 130-131 5.525 0.0 0.0 0.0 0.0 132-133 5.9875 0.0 0.0 0.0 0.0 134-135 6.525 0.0 0.0 0.0 0.0 136-137 7.0 0.0 0.0 0.0 0.0 138-139 7.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGCTGAA 10 0.006830828 145.0 3 TCGCTGA 10 0.006830828 145.0 2 CCTGGGT 10 0.006830828 145.0 1 >>END_MODULE SRR7171465 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171465_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.59525 33.0 33.0 34.0 32.0 34.0 2 32.60075 34.0 33.0 34.0 31.0 34.0 3 32.6355 34.0 33.0 34.0 31.0 34.0 4 32.56975 34.0 33.0 34.0 32.0 34.0 5 32.65875 34.0 33.0 34.0 32.0 34.0 6 36.69325 38.0 38.0 38.0 35.0 38.0 7 36.6465 38.0 38.0 38.0 35.0 38.0 8 36.66125 38.0 38.0 38.0 35.0 38.0 9 36.72375 38.0 38.0 38.0 35.0 38.0 10-14 36.552350000000004 38.0 38.0 38.0 34.2 38.0 15-19 36.53835 38.0 38.0 38.0 34.2 38.0 20-24 36.5486 38.0 38.0 38.0 34.2 38.0 25-29 36.54125 38.0 38.0 38.0 34.2 38.0 30-34 36.52795 38.0 38.0 38.0 34.4 38.0 35-39 36.50855 38.0 38.0 38.0 34.4 38.0 40-44 36.594049999999996 38.0 38.0 38.0 34.4 38.0 45-49 36.6068 38.0 38.0 38.0 34.6 38.0 50-54 36.515750000000004 38.0 38.0 38.0 34.4 38.0 55-59 36.408550000000005 38.0 38.0 38.0 34.0 38.0 60-64 36.192499999999995 38.0 38.0 38.0 33.0 38.0 65-69 36.25115000000001 38.0 38.0 38.0 33.2 38.0 70-74 36.15175000000001 38.0 38.0 38.0 33.0 38.0 75-79 36.24210000000001 38.0 38.0 38.0 33.2 38.0 80-84 36.162549999999996 38.0 38.0 38.0 33.2 38.0 85-89 36.0125 38.0 37.8 38.0 32.0 38.0 90-94 35.8566 38.0 37.2 38.0 31.0 38.0 95-99 35.8061 38.0 37.0 38.0 31.0 38.0 100-104 35.57135000000001 38.0 37.0 38.0 29.8 38.0 105-109 35.44355 38.0 37.0 38.0 28.4 38.0 110-114 35.2375 38.0 36.4 38.0 27.4 38.0 115-119 35.262950000000004 38.0 36.0 38.0 28.0 38.0 120-124 34.814499999999995 38.0 35.2 38.0 24.6 38.0 125-129 34.87405 38.0 35.0 38.0 25.4 38.0 130-134 34.652550000000005 38.0 35.0 38.0 23.8 38.0 135-139 33.97915 38.0 34.0 38.0 21.0 38.0 140-144 33.5493 38.0 33.2 38.0 19.8 38.0 145-149 33.4585 38.0 33.6 38.0 19.8 38.0 150-151 31.012875 35.5 27.0 38.0 17.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 0.0 15 1.0 16 10.0 17 21.0 18 13.0 19 14.0 20 9.0 21 11.0 22 19.0 23 19.0 24 28.0 25 23.0 26 28.0 27 39.0 28 42.0 29 47.0 30 71.0 31 74.0 32 96.0 33 130.0 34 163.0 35 278.0 36 614.0 37 2249.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.54077791718946 19.29736511919699 15.533249686323714 27.628607277289834 2 25.974999999999998 25.525 29.625 18.875 3 21.85 28.925 28.425 20.8 4 24.712356178089045 32.24112056028014 23.486743371685844 19.559779889944974 5 25.062531265632813 34.417208604302154 21.735867933966986 18.78439219609805 6 21.7 38.3 22.875 17.125 7 21.125 22.075 36.7 20.1 8 22.85 25.1 27.1 24.95 9 23.51175587793897 24.212106053026513 30.015007503751878 22.26113056528264 10-14 24.137068534267133 28.724362181090545 25.522761380690344 21.615807903951975 15-19 24.272136068034015 28.274137068534266 26.498249124562278 20.955477738869437 20-24 24.258490471665084 28.41494523083079 26.614315010253588 20.712249287250536 25-29 24.335 27.565 26.889999999999997 21.21 30-34 24.005000000000003 28.325 26.755000000000003 20.915 35-39 24.12 28.610000000000003 26.255 21.015 40-44 24.415 28.544999999999998 26.46 20.580000000000002 45-49 24.392317695308595 27.8333500050015 26.39291787536261 21.381414424327296 50-54 24.66486594637855 28.376350540216087 26.310524209683873 20.64825930372149 55-59 23.806903451725862 28.3591795897949 26.788394197098548 21.045522761380692 60-64 24.647323661830917 28.29414707353677 26.728364182091045 20.33016508254127 65-69 24.596149037259316 27.316829207301822 26.911727931983 21.175293823455867 70-74 24.345 27.700000000000003 26.71 21.245 75-79 24.349999999999998 27.83 26.985 20.835 80-84 24.115000000000002 28.215 26.96 20.71 85-89 24.25 27.505000000000003 26.815 21.43 90-94 24.56991398279656 27.510502100420087 27.090418083616726 20.829165833166634 95-99 24.551047971587213 27.547396328347755 27.042168976039214 20.85938672402581 100-104 24.251526985080606 27.986382296986083 26.965054570942225 20.79703614699109 105-109 24.88359285034797 27.692384719371148 26.635958544034445 20.788063886246434 110-114 24.496644295302016 28.142842832815784 26.535109686466996 20.825403185415205 115-119 25.10636167976375 27.94434155863657 25.73702387506882 21.212272886530858 120-124 25.170102061236744 27.47148288973384 26.82609565739444 20.53231939163498 125-129 25.430000000000003 27.55 26.295 20.724999999999998 130-134 25.45 27.38 26.905 20.265 135-139 25.73415378458152 27.60518285056781 26.52458852368803 20.13607484116264 140-144 26.155309668051867 27.46708055875432 26.520803084163617 19.85680668903019 145-149 26.4726507713885 27.604688439190543 26.08695652173913 19.835704267681827 150-151 27.029058116232463 27.70541082164329 25.776553106212425 19.488977955911825 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.0 18 1.0 19 0.5 20 0.5 21 1.0 22 1.5 23 1.0 24 1.0 25 2.0 26 2.0 27 1.0 28 2.5 29 5.0 30 9.5 31 11.5 32 16.0 33 26.5 34 37.5 35 50.5 36 63.5 37 87.0 38 122.5 39 147.0 40 191.0 41 233.5 42 238.0 43 255.0 44 265.0 45 281.0 46 295.0 47 270.0 48 232.0 49 193.0 50 159.5 51 140.0 52 120.5 53 89.0 54 65.0 55 51.0 56 50.5 57 45.5 58 31.0 59 26.0 60 27.0 61 27.0 62 26.0 63 20.5 64 13.0 65 9.0 66 9.0 67 7.5 68 4.0 69 5.0 70 5.5 71 4.0 72 3.5 73 3.0 74 2.5 75 4.0 76 2.5 77 1.5 78 2.0 79 0.5 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 0.375 2 0.0 3 0.0 4 0.05 5 0.05 6 0.0 7 0.0 8 0.0 9 0.05 10-14 0.05 15-19 0.05 20-24 0.034999999999999996 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.03 50-54 0.04 55-59 0.05 60-64 0.05 65-69 0.025 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.02 95-99 0.045 100-104 0.13 105-109 0.135 110-114 0.16999999999999998 115-119 0.105 120-124 0.06 125-129 0.0 130-134 0.0 135-139 0.055 140-144 0.135 145-149 0.18 150-151 0.2 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.7 #Duplication Level Percentage of deduplicated Percentage of total 1 98.93617021276596 97.65 2 0.8611955420466059 1.7000000000000002 3 0.1519756838905775 0.44999999999999996 4 0.050658561296859174 0.2 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 warn #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 0.0125 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 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 0.0625 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.0875 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.125 0.0 0.0 0.0 0.0 90-91 0.1875 0.0 0.0 0.0 0.0 92-93 0.25 0.0 0.0 0.0 0.0 94-95 0.325 0.0 0.0 0.0 0.0 96-97 0.4125 0.0 0.0 0.0 0.0 98-99 0.5875 0.0 0.0 0.0 0.0 100-101 0.6625000000000001 0.0 0.0 0.0 0.0 102-103 0.7625 0.0 0.0 0.0 0.0 104-105 0.925 0.0 0.0 0.0 0.0 106-107 1.0625 0.0 0.0 0.0 0.0 108-109 1.2125 0.0 0.0 0.0 0.0 110-111 1.6124999999999998 0.0 0.0 0.0 0.0 112-113 1.8125 0.0 0.0 0.0 0.0 114-115 2.15 0.0 0.0 0.0 0.0 116-117 2.475 0.0 0.0 0.0 0.0 118-119 2.9 0.0 0.0 0.0 0.0 120-121 3.375 0.0 0.0 0.0 0.0 122-123 3.7249999999999996 0.0 0.0 0.0 0.0 124-125 4.025 0.0 0.0 0.0 0.0 126-127 4.3875 0.0 0.0 0.0 0.0 128-129 4.975 0.0 0.0 0.0 0.0 130-131 5.5375 0.0 0.0 0.0 0.0 132-133 6.0125 0.0 0.0 0.0 0.0 134-135 6.5625 0.0 0.0 0.0 0.0 136-137 7.05 0.0 0.0 0.0 0.0 138-139 7.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725842 spots for SRR7171465.sra Written 725842 spots for SRR7171465.sra Read 725847 spots for SRR7171465.sra Written 725847 spots for SRR7171465.sra SRR ids: ['SRR7171465.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xq7i9xtg SRR7171465.sra spots: 14516845 blocks: [[1, 725842], [725843, 1451684], [1451685, 2177526], [2177527, 2903368], [2903369, 3629210], [3629211, 4355052], [4355053, 5080894], [5080895, 5806736], [5806737, 6532578], [6532579, 7258420], [7258421, 7984262], [7984263, 8710104], [8710105, 9435946], [9435947, 10161788], [10161789, 10887630], [10887631, 11613472], [11613473, 12339314], [12339315, 13065156], [13065157, 13790998], [13790999, 14516845]] SRR7171465 file size 4897582 SRR7171465 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 SRR7171465 SRR7171465_1.fastq SRR7171465_2.fastq Input file: SRR7171465_1.fastq Paired file: SRR7171465_2.fastq trimmed: SRR7171465-trimmed-pair1.fastq, SRR7171465-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 Thu Feb 13 18:50:38 2025 >> started Thu Feb 13 18:50:54 2025 >> done (16.744s) 14516845 read pairs processed; of these: 135 ( 0.00%) short read pairs filtered out after trimming by size control 1159 ( 0.01%) empty read pairs filtered out after trimming by size control 14515551 (99.99%) read pairs available; of these: 1971325 (13.58%) trimmed read pairs available after processing 12544226 (86.42%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 3 0.00% 20 1 0.00% 21 0 0.00% 22 0 0.00% 23 0 0.00% 24 1 0.00% 25 1 0.00% 26 0 0.00% 27 0 0.00% 28 2 0.00% 29 1 0.00% 30 1 0.00% 31 1 0.00% 32 1 0.00% 33 1 0.00% 34 0 0.00% 35 2 0.00% 36 2 0.00% 37 1 0.00% 38 5 0.00% 39 2 0.00% 40 1 0.00% 41 3 0.00% 42 3 0.00% 43 4 0.00% 44 1 0.00% 45 8 0.00% 46 9 0.00% 47 7 0.00% 48 10 0.00% 49 1 0.00% 50 11 0.00% 51 13 0.00% 52 18 0.00% 53 17 0.00% 54 25 0.00% 55 19 0.00% 56 28 0.00% 57 34 0.00% 58 31 0.00% 59 37 0.00% 60 54 0.00% 61 66 0.00% 62 75 0.00% 63 87 0.00% 64 95 0.00% 65 125 0.00% 66 142 0.00% 67 159 0.00% 68 205 0.00% 69 197 0.00% 70 245 0.00% 71 314 0.00% 72 357 0.00% 73 464 0.00% 74 515 0.00% 75 554 0.00% 76 650 0.00% 77 770 0.01% 78 897 0.01% 79 1000 0.01% 80 1152 0.01% 81 1354 0.01% 82 1533 0.01% 83 1763 0.01% 84 2067 0.01% 85 2367 0.02% 86 2626 0.02% 87 2980 0.02% 88 3260 0.02% 89 3478 0.02% 90 4027 0.03% 91 4323 0.03% 92 5019 0.03% 93 5729 0.04% 94 6369 0.04% 95 6745 0.05% 96 7654 0.05% 97 8111 0.06% 98 8671 0.06% 99 9369 0.06% 100 10144 0.07% 101 10867 0.07% 102 11788 0.08% 103 12722 0.09% 104 13621 0.09% 105 14828 0.10% 106 15548 0.11% 107 16178 0.11% 108 17007 0.12% 109 17772 0.12% 110 18577 0.13% 111 19692 0.14% 112 20935 0.14% 113 22373 0.15% 114 23569 0.16% 115 25133 0.17% 116 25862 0.18% 117 28232 0.19% 118 31099 0.21% 119 29370 0.20% 120 29555 0.20% 121 30619 0.21% 122 31830 0.22% 123 33665 0.23% 124 34918 0.24% 125 36250 0.25% 126 37673 0.26% 127 38980 0.27% 128 39540 0.27% 129 40056 0.28% 130 41301 0.28% 131 42090 0.29% 132 43749 0.30% 133 44942 0.31% 134 46670 0.32% 135 47611 0.33% 136 49400 0.34% 137 50282 0.35% 138 51280 0.35% 139 52265 0.36% 140 52888 0.36% 141 54549 0.38% 142 59841 0.41% 143 58478 0.40% 144 60274 0.42% 145 62074 0.43% 146 60510 0.42% 147 64373 0.44% 148 63096 0.43% 149 63621 0.44% 150 67754 0.47% 151 12544226 86.42% 14515551 reads passed initial QC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=2.20 fanout-score-rank=31 prefix-density=0.20 prefix-fanout=2.2 sequence=GCAATGATTGTCTCAGTTGTGGTGTTCTCTGAGAAACCTAAGTCAGGGTACATGCCACATTTGCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=55.29 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=6.9 sequence=AACCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCAC criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=2.48 fanout-score-rank=28 prefix-density=0.26 prefix-fanout=2.3 sequence=GGCAGTGGCTGCAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=110.11 fanout-score-rank=1 prefix-density=0.44 prefix-fanout=1.6 sequence=AAAAGATAAGCTAGGCAAGATGGTTTTACTAGACAAGATGTGGGATGATGTTGTTGCTGGACCTCAGCCAGAACGTGGCCTTGGCAAGCTTAGAAAGATCAGCACCAGACCACTTAACATCAAAGATATTGACGTCGGAGAGGGGAGCAGTCCTGTTAATAAGTTTCAGAGGTCCATGACTATGCCAGGAACTCCAGGGACACCGACGACACCAGTGACCCCTACAACCCCAGTGTCGGCGCGTAGCAATGTTTGGAGGAGCGTGTTCCACCCTGGTAGCAACCTTGCTACTAAGAATATTGGTGCTCATGTTTTTGACAAGCCACAGCCTAACACACCCACTGTCTATGACTGGATGTACAGTGGAGAGACGAAGAGCGAGCATCGTTGATGAGGTTGCCTTCAACCAAGGTTG SRR7171465 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 18:51:41 Started mapping on | Feb 13 18:51:41 Finished on | Feb 13 18:54:33 Mapping speed, Million of reads per hour | 303.81 Number of input reads | 14515551 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 12044094 Uniquely mapped reads % | 82.97% Average mapped length | 295.13 Number of splices: Total | 11263278 Number of splices: Annotated (sjdb) | 11042092 Number of splices: GT/AG | 11071378 Number of splices: GC/AG | 151039 Number of splices: AT/AC | 9224 Number of splices: Non-canonical | 31637 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.03% Deletion average length | 2.52 Insertion rate per base | 0.02% Insertion average length | 2.54 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 333046 % of reads mapped to multiple loci | 2.29% Number of reads mapped to too many loci | 883641 % of reads mapped to too many loci | 6.09% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.26% % of reads unmapped: other | 1.38% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2138411 2138411 2138411 N_multimapping 333046 333046 333046 N_noFeature 334832 11931801 388863 N_ambiguous 119142 1060 60084 UnstrandedReadsAssigned:11590120 PositiveStrandReadsAssigned:111233 NegativeStrandReadsAssigned:11595147 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171465 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: SRR7171465-trimmed-pair1.fastq SRR7171465-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,515,551 reads, 12,538,838 reads pseudoaligned [quant] estimated average fragment length: 221.808 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,033 rounds 52401 SRR7171465.ke.tsv 34699 SRR7171465.se.tsv 87100 total ==> SRR7171465.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1797.19 1393 64.7137 Potri.005G024800.1.v4.1 1035 814.192 131 13.4333 Potri.004G059700.1.v4.1 961 740.203 9 1.01515 Potri.007G009000.2.v4.1 1416 1195.19 0 0 Potri.003G141000.2.v4.1 2943 2722.19 532 16.3167 Potri.016G087400.1.v4.1 270 84.663 412.459 406.749 Potri.015G069301.1.v4.1 564 345.167 0 0 Potri.010G195200.1.v4.1 1773 1552.19 808.931 43.5116 Potri.012G127500.1.v4.1 977 756.203 9494 1048.22 ==> SRR7171465.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 13 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 303 Potri.001G212900.v4.1 6 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 439 SRR7171465 completed mapping pipeline successfully