Starting /dee2/code/volunteer_pipeline.sh SRR8096902 current disk space = 1540309131264 free memory = 1604886972 SRR8096902 SRAfilesize 9628e6981c7a642f1491dd85c4c9b839 SRR8096902.sra SRR8096902.sra file validated SRR8096902 is paired end SRR8096902 is conventional basespace SRR8096902 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096902_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.63525 34.0 33.0 34.0 32.0 34.0 2 32.90425 34.0 33.0 34.0 30.0 34.0 3 32.97825 34.0 33.0 34.0 30.0 34.0 4 33.17675 34.0 33.0 34.0 32.0 34.0 5 33.27475 34.0 33.0 34.0 33.0 34.0 6 36.9235 38.0 37.0 38.0 35.0 38.0 7 37.28275 38.0 38.0 38.0 36.0 38.0 8 37.273 38.0 38.0 38.0 37.0 38.0 9 37.36725 38.0 38.0 38.0 37.0 38.0 10-14 37.273799999999994 38.0 38.0 38.0 36.6 38.0 15-19 37.2889 38.0 38.0 38.0 37.0 38.0 20-24 37.2408 38.0 38.0 38.0 36.8 38.0 25-29 37.25575 38.0 38.0 38.0 36.8 38.0 30-34 37.1391 38.0 38.0 38.0 36.6 38.0 35-39 37.176500000000004 38.0 38.0 38.0 37.0 38.0 40-44 37.11625 38.0 38.0 38.0 36.6 38.0 45-49 37.0743 38.0 38.0 38.0 36.4 38.0 50-54 37.091049999999996 38.0 38.0 38.0 36.2 38.0 55-59 37.007549999999995 38.0 38.0 38.0 36.2 38.0 60-64 36.92765000000001 38.0 38.0 38.0 36.0 38.0 65-69 36.7581 38.0 38.0 38.0 35.6 38.0 70-74 36.71025 38.0 38.0 38.0 35.4 38.0 75-79 36.494350000000004 38.0 38.0 38.0 35.6 38.0 80-84 36.44285 38.0 38.0 38.0 35.2 38.0 85-89 36.4031 38.0 38.0 38.0 35.2 38.0 90-94 36.337300000000006 38.0 38.0 38.0 35.0 38.0 95-99 36.18770000000001 38.0 38.0 38.0 34.4 38.0 100-104 36.09935 38.0 38.0 38.0 34.2 38.0 105-109 36.033950000000004 38.0 38.0 38.0 34.0 38.0 110-114 35.8359 38.0 38.0 38.0 33.6 38.0 115-119 35.687349999999995 38.0 38.0 38.0 33.6 38.0 120-124 35.478 38.0 37.8 38.0 32.4 38.0 125-129 35.27145 38.0 37.2 38.0 31.0 38.0 130-134 35.12865 38.0 36.6 38.0 30.2 38.0 135-139 34.897200000000005 38.0 36.0 38.0 29.6 38.0 140-144 34.575900000000004 38.0 36.0 38.0 28.0 38.0 145-149 33.944050000000004 38.0 35.4 38.0 23.8 38.0 150 26.55925 33.0 21.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 1.0 7 2.0 8 2.0 9 2.0 10 2.0 11 4.0 12 4.0 13 2.0 14 7.0 15 3.0 16 7.0 17 5.0 18 13.0 19 25.0 20 4.0 21 11.0 22 9.0 23 9.0 24 6.0 25 9.0 26 16.0 27 22.0 28 28.0 29 21.0 30 42.0 31 43.0 32 59.0 33 79.0 34 128.0 35 204.0 36 471.0 37 2759.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.24500525762355 12.276550998948474 8.149316508937961 37.32912723449001 2 21.3 16.950000000000003 38.275 23.474999999999998 3 21.675 20.275000000000002 27.900000000000002 30.15 4 26.0 26.674999999999997 22.650000000000002 24.675 5 25.7 31.874999999999996 23.65 18.775 6 20.4 32.925 25.124999999999996 21.55 7 16.575 22.95 40.75 19.725 8 17.625 23.775 31.75 26.85 9 20.25 21.025 32.875 25.85 10-14 21.855 27.505000000000003 25.775 24.865000000000002 15-19 22.384999999999998 26.455000000000002 25.835 25.324999999999996 20-24 22.485 26.75 26.290000000000003 24.474999999999998 25-29 22.485 25.825 26.41 25.28 30-34 22.38 26.634999999999998 26.150000000000002 24.834999999999997 35-39 21.759999999999998 25.44 26.715 26.085 40-44 21.990000000000002 25.705 26.815 25.490000000000002 45-49 23.32 26.090000000000003 25.97 24.62 50-54 22.675 25.16 26.56 25.605 55-59 22.605 25.480000000000004 26.965 24.95 60-64 22.495 25.535000000000004 26.545 25.424999999999997 65-69 22.18 27.04 26.284999999999997 24.495 70-74 22.259999999999998 27.015 25.900000000000002 24.825 75-79 22.63 26.08 25.540000000000003 25.75 80-84 22.715 25.669999999999998 26.13 25.485000000000003 85-89 22.93 25.735000000000003 26.169999999999998 25.165 90-94 22.97 26.005 26.055 24.97 95-99 22.84 25.15 26.11 25.900000000000002 100-104 22.505 26.595000000000002 25.874999999999996 25.025 105-109 23.07 25.945 25.66 25.324999999999996 110-114 22.595000000000002 26.445 26.185000000000002 24.775 115-119 23.585 25.72 25.775 24.92 120-124 23.169999999999998 25.835 25.525 25.47 125-129 22.865 25.56 25.995 25.580000000000002 130-134 23.855 26.200000000000003 25.095 24.85 135-139 23.599999999999998 26.279999999999998 25.055 25.064999999999998 140-144 23.400000000000002 25.650000000000002 25.335 25.615 145-149 23.1 26.005 25.540000000000003 25.355 150 24.4 24.775 25.0 25.825 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 14.0 1 8.0 2 2.5 3 2.5 4 1.5 5 1.0 6 2.0 7 2.0 8 0.5 9 0.0 10 1.5 11 2.0 12 0.5 13 0.0 14 1.0 15 1.5 16 0.5 17 0.5 18 1.0 19 0.5 20 0.5 21 0.5 22 0.5 23 1.5 24 1.5 25 1.0 26 2.0 27 4.0 28 7.5 29 8.0 30 9.0 31 14.5 32 19.5 33 21.5 34 30.0 35 40.5 36 63.5 37 82.0 38 91.0 39 115.0 40 139.0 41 167.5 42 187.5 43 194.0 44 218.0 45 219.0 46 202.5 47 186.0 48 165.0 49 172.0 50 159.5 51 148.5 52 139.0 53 113.5 54 100.5 55 91.0 56 80.5 57 75.0 58 74.5 59 69.5 60 63.5 61 71.5 62 67.0 63 51.0 64 51.0 65 44.0 66 37.0 67 40.0 68 35.5 69 24.5 70 19.5 71 16.0 72 10.5 73 5.0 74 3.5 75 3.0 76 2.5 77 2.0 78 1.0 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 4.9 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.5 #Duplication Level Percentage of deduplicated Percentage of total 1 98.47150259067358 95.025 2 1.1398963730569949 2.1999999999999997 3 0.233160621761658 0.675 4 0.07772020725388601 0.3 5 0.0 0.0 6 0.025906735751295335 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.05181347150259067 1.6500000000000001 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGC 47 1.175 TruSeq Adapter, Index 18 (100% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 19 0.475 No Hit GTCAGAAAATGGTAGAAACTTCTATTGCTTATTACAAATTCACATCGAGC 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 0.075 0.0 0.0 0.0 0.0 2 0.075 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.075 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.1 0.0 0.0 0.0 0.0 9 0.1 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.1 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 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 0.125 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.175 0.0 0.0 0.0 0.0 90-91 0.175 0.0 0.0 0.0 0.0 92-93 0.2625 0.0 0.0 0.0 0.0 94-95 0.3 0.0 0.0 0.0 0.0 96-97 0.35 0.0 0.0 0.0 0.0 98-99 0.35 0.0 0.0 0.0 0.0 100-101 0.375 0.0 0.0 0.0 0.0 102-103 0.5125 0.0 0.0 0.0 0.0 104-105 0.625 0.0 0.0 0.0 0.0 106-107 0.7124999999999999 0.0 0.0 0.0 0.0 108-109 0.8375 0.0 0.0 0.0 0.0 110-111 0.9375 0.0 0.0 0.0 0.0 112-113 1.1124999999999998 0.0 0.0 0.0 0.0 114-115 1.2374999999999998 0.0 0.0 0.0 0.0 116-117 1.3875 0.0 0.0 0.0 0.0 118-119 1.5625 0.0 0.0 0.0 0.0 120-121 1.7375 0.0 0.0 0.0 0.0 122-123 2.0250000000000004 0.0 0.0 0.0 0.0 124-125 2.425 0.0 0.0 0.0 0.0 126-127 2.8 0.0 0.0 0.0 0.0 128-129 2.9875 0.0 0.0 0.0 0.0 130-131 3.2249999999999996 0.0 0.0 0.0 0.0 132-133 3.5250000000000004 0.0 0.0 0.0 0.0 134-135 3.9625 0.0 0.0 0.0 0.0 136-137 4.3 0.0 0.0 0.0 0.0 138 4.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR8096902 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096902_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.83675 33.0 32.0 33.0 25.0 34.0 2 30.855 33.0 31.0 33.0 25.0 34.0 3 30.98675 33.0 31.0 34.0 27.0 34.0 4 30.98475 33.0 31.0 34.0 27.0 34.0 5 29.29625 33.0 29.0 33.0 15.0 34.0 6 34.22775 38.0 34.0 38.0 26.0 38.0 7 34.51825 38.0 36.0 38.0 26.0 38.0 8 34.69675 38.0 36.0 38.0 27.0 38.0 9 34.71275 38.0 36.0 38.0 26.0 38.0 10-14 34.90005 38.0 36.2 38.0 28.0 38.0 15-19 34.8264 38.0 36.0 38.0 27.2 38.0 20-24 34.59525000000001 38.0 36.0 38.0 24.0 38.0 25-29 34.33245 38.0 35.6 38.0 23.0 38.0 30-34 34.36665 38.0 35.6 38.0 25.0 38.0 35-39 34.34085 38.0 35.8 38.0 25.0 38.0 40-44 34.231700000000004 38.0 35.0 38.0 24.8 38.0 45-49 33.93605 38.0 34.6 38.0 19.2 38.0 50-54 33.868399999999994 38.0 34.6 38.0 17.6 38.0 55-59 33.61625 38.0 34.0 38.0 16.0 38.0 60-64 33.185950000000005 38.0 33.8 38.0 16.0 38.0 65-69 33.026799999999994 38.0 33.2 38.0 16.0 38.0 70-74 32.8048 38.0 33.4 38.0 15.8 38.0 75-79 32.5258 37.8 32.6 38.0 15.2 38.0 80-84 32.1853 37.6 31.6 38.0 15.0 38.0 85-89 31.657550000000004 37.0 30.0 38.0 15.0 38.0 90-94 31.30485 37.0 29.0 38.0 14.8 38.0 95-99 30.54865 36.2 27.4 38.0 13.6 38.0 100-104 29.998649999999998 36.0 25.4 38.0 13.0 38.0 105-109 29.1582 35.2 23.0 38.0 10.8 38.0 110-114 28.22355 34.0 21.4 38.0 2.0 38.0 115-119 27.556100000000004 34.0 15.0 38.0 2.0 38.0 120-124 26.539700000000003 33.8 15.0 38.0 2.0 38.0 125-129 25.7346 33.6 14.2 38.0 2.0 38.0 130-134 24.1758 31.0 13.2 36.8 2.0 38.0 135-139 22.464250000000003 26.6 6.4 35.4 2.0 38.0 140-144 20.4437 23.4 2.0 34.2 2.0 38.0 145-149 17.52305 14.4 2.0 33.2 2.0 38.0 150 12.01175 2.0 2.0 28.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 63.0 3 14.0 4 8.0 5 11.0 6 7.0 7 3.0 8 12.0 9 11.0 10 13.0 11 5.0 12 12.0 13 14.0 14 16.0 15 32.0 16 29.0 17 36.0 18 41.0 19 43.0 20 45.0 21 66.0 22 59.0 23 68.0 24 92.0 25 68.0 26 104.0 27 116.0 28 130.0 29 166.0 30 209.0 31 244.0 32 277.0 33 325.0 34 429.0 35 517.0 36 536.0 37 179.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.41320231796423 19.62711010330058 8.591584782060972 31.368102796674226 2 26.6683455049106 23.847897255099472 31.251573910853693 18.232183329136237 3 23.822714681440445 23.89826240241753 28.834046839587007 23.444976076555022 4 25.799949609473423 32.779037540942305 17.913832199546487 23.507180650037792 5 28.470647518266567 33.03099017384732 19.778281683043588 18.72008062484253 6 21.869488536155202 35.57571176618796 20.105820105820104 22.448979591836736 7 22.096245905769717 19.098009574200052 36.860670194003525 21.945074326026706 8 22.877299067775258 23.381204333585288 25.27084908037289 28.470647518266567 9 25.875535399344923 20.98765432098765 26.127488032249936 27.009322247417483 10-14 25.923313347105353 25.55046102685544 23.514888900085655 25.01133672595354 15-19 26.127260819184844 25.341327018993397 24.40425210338052 24.127160058441234 20-24 26.179803575925458 26.567615210274493 23.76731301939058 23.48526819440947 25-29 25.79832779288808 26.851012390450286 23.64259091366979 23.70806890299184 30-34 25.973306471921433 25.807101485771845 24.56811886174767 23.651473180559055 35-39 25.740330378726835 25.448227236099918 24.52659145850121 24.28485092667204 40-44 26.517250062956432 25.293376983127676 24.457315537647947 23.732057416267942 45-49 26.048854192898514 24.925711407705865 25.036514731805593 23.98891966759003 50-54 25.467183800936887 25.5628872210749 24.91311136855891 24.056817609429302 55-59 25.295925049110966 26.041404321764972 24.948370523346597 23.714300105777465 60-64 24.930733968062064 27.232884993199335 24.51765654123218 23.318724497506423 65-69 25.14988160612625 27.265857222026295 24.086855760995515 23.497405410851933 70-74 25.409299279633267 26.24049166288852 24.50254395244572 23.847665105032494 75-79 25.968660250919534 26.09966241749383 24.58306041215297 23.348616919433667 80-84 25.30102272154768 26.278401934606276 24.45967051236838 23.960904831477656 85-89 25.39418669084681 26.235454133293036 24.668782429096773 23.701576746763386 90-94 25.202801430946742 26.019045699601957 25.107069078450145 23.67108379100116 95-99 25.404343225676424 26.583362724845067 24.588098957021213 23.424195092457296 100-104 25.254408060453397 26.53904282115869 24.6448362720403 23.561712846347607 105-109 25.550350108306887 26.169966248551713 24.72923278424261 23.5504508588988 110-114 25.259445843828715 26.025188916876573 24.7808564231738 23.934508816120907 115-119 25.92349947084614 26.749987401098625 24.073980748878697 23.252532379176536 120-124 25.059220805402955 26.722443425230587 24.1116879189557 24.106647850410763 125-129 25.38418904620346 27.051947397591576 24.129591374011188 23.434272182193784 130-134 25.16626360338573 27.564490124949614 24.450826279725916 22.818419991938736 135-139 25.23675196453758 27.352407817852104 24.229296796292566 23.181543421317752 140-144 25.736738703339885 27.736637952747973 23.620976273235605 22.90564707067654 145-149 24.85225034096075 28.05980704147093 23.301510329847957 23.78643228772036 150 25.069286974048875 30.209120685311163 22.448979591836736 22.272612748803226 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 28.0 1 14.5 2 0.5 3 0.0 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 0.5 14 0.5 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 1.0 21 0.5 22 2.0 23 3.0 24 2.0 25 3.0 26 4.0 27 3.0 28 3.5 29 4.0 30 5.5 31 13.0 32 18.0 33 21.0 34 31.5 35 35.5 36 42.5 37 57.5 38 74.5 39 105.0 40 137.0 41 139.5 42 150.5 43 170.5 44 174.5 45 201.5 46 199.0 47 176.0 48 177.0 49 168.0 50 150.0 51 138.0 52 128.5 53 103.5 54 92.0 55 102.5 56 101.5 57 103.5 58 101.0 59 96.0 60 92.0 61 92.5 62 84.0 63 64.5 64 61.5 65 55.5 66 54.5 67 51.5 68 40.5 69 32.5 70 26.5 71 21.5 72 17.5 73 14.5 74 7.5 75 4.0 76 3.0 77 1.5 78 1.0 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 0.775 2 0.7250000000000001 3 0.7250000000000001 4 0.775 5 0.775 6 0.775 7 0.775 8 0.775 9 0.775 10-14 0.765 15-19 0.755 20-24 0.7250000000000001 25-29 0.73 30-34 0.7250000000000001 35-39 0.72 40-44 0.7250000000000001 45-49 0.7250000000000001 50-54 0.735 55-59 0.735 60-64 0.745 65-69 0.755 70-74 0.745 75-79 0.765 80-84 0.755 85-89 0.745 90-94 0.765 95-99 0.765 100-104 0.75 105-109 0.745 110-114 0.75 115-119 0.7849999999999999 120-124 0.795 125-129 0.765 130-134 0.76 135-139 0.74 140-144 0.745 145-149 1.015 150 0.775 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.8 #Duplication Level Percentage of deduplicated Percentage of total 1 99.15644171779141 96.975 2 0.6134969325153374 1.2 3 0.1278118609406953 0.375 4 0.051124744376278126 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 0.051124744376278126 1.25 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 28 0.7000000000000001 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 22 0.5499999999999999 Illumina Single End PCR Primer 1 (100% over 50bp) >>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 0.075 0.0 0.0 0.0 0.0 2 0.075 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.075 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.1 0.0 0.0 0.0 0.0 9 0.1 0.0 0.0 0.0 0.0 10-11 0.1 0.0 0.0 0.0 0.0 12-13 0.1 0.0 0.0 0.0 0.0 14-15 0.1 0.0 0.0 0.0 0.0 16-17 0.1 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.1 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 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 0.125 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.15 0.0 0.0 0.0 0.0 92-93 0.21250000000000002 0.0 0.0 0.0 0.0 94-95 0.25 0.0 0.0 0.0 0.0 96-97 0.3 0.0 0.0 0.0 0.0 98-99 0.3 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 0.5125 0.0 0.0 0.0 0.0 106-107 0.575 0.0 0.0 0.0 0.0 108-109 0.6875 0.0 0.0 0.0 0.0 110-111 0.75 0.0 0.0 0.0 0.0 112-113 0.8625 0.0 0.0 0.0 0.0 114-115 0.9125000000000001 0.0 0.0 0.0 0.0 116-117 0.975 0.0 0.0 0.0 0.0 118-119 1.025 0.0 0.0 0.0 0.0 120-121 1.125 0.0 0.0 0.0 0.0 122-123 1.3 0.0 0.0 0.0 0.0 124-125 1.475 0.0 0.0 0.0 0.0 126-127 1.65 0.0 0.0 0.0 0.0 128-129 1.75 0.0 0.0 0.0 0.0 130-131 1.95 0.0 0.0 0.0 0.0 132-133 2.1375 0.0 0.0 0.0 0.0 134-135 2.3625 0.0 0.0 0.0 0.0 136-137 2.5625 0.0 0.0 0.0 0.0 138 2.725 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCAAGAA 10 0.0069790767 143.96251 8 TGTTCAA 10 0.0069790767 143.96251 5 CAATTAT 10 0.0069790767 143.96251 4 >>END_MODULE Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254997 spots for SRR8096902.sra Written 2254997 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra Read 2254986 spots for SRR8096902.sra Written 2254986 spots for SRR8096902.sra SRR ids: ['SRR8096902.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__9j8vvms SRR8096902.sra spots: 45099731 blocks: [[1, 2254986], [2254987, 4509972], [4509973, 6764958], [6764959, 9019944], [9019945, 11274930], [11274931, 13529916], [13529917, 15784902], [15784903, 18039888], [18039889, 20294874], [20294875, 22549860], [22549861, 24804846], [24804847, 27059832], [27059833, 29314818], [29314819, 31569804], [31569805, 33824790], [33824791, 36079776], [36079777, 38334762], [38334763, 40589748], [40589749, 42844734], [42844735, 45099731]] SRR8096902 file size 15173033 SRR8096902 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 SRR8096902 SRR8096902_1.fastq SRR8096902_2.fastq Input file: SRR8096902_1.fastq Paired file: SRR8096902_2.fastq trimmed: SRR8096902-trimmed-pair1.fastq, SRR8096902-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 19:17:35 2024 >> started Sat Dec 7 19:19:52 2024 >> done (136.850s) 45099731 read pairs processed; of these: 136462 ( 0.30%) short read pairs filtered out after trimming by size control 1383518 ( 3.07%) empty read pairs filtered out after trimming by size control 43579751 (96.63%) read pairs available; of these: 23463903 (53.84%) trimmed read pairs available after processing 20115848 (46.16%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 112 0.00% 19 489 0.00% 20 130 0.00% 21 132 0.00% 22 240 0.00% 23 139 0.00% 24 132 0.00% 25 128 0.00% 26 144 0.00% 27 142 0.00% 28 134 0.00% 29 168 0.00% 30 246 0.00% 31 174 0.00% 32 259 0.00% 33 197 0.00% 34 291 0.00% 35 307 0.00% 36 330 0.00% 37 383 0.00% 38 418 0.00% 39 484 0.00% 40 525 0.00% 41 599 0.00% 42 605 0.00% 43 708 0.00% 44 866 0.00% 45 1693 0.00% 46 1340 0.00% 47 1278 0.00% 48 1203 0.00% 49 1212 0.00% 50 1259 0.00% 51 1395 0.00% 52 1390 0.00% 53 1856 0.00% 54 1801 0.00% 55 1917 0.00% 56 3127 0.01% 57 2303 0.01% 58 4958 0.01% 59 3371 0.01% 60 2810 0.01% 61 9992 0.02% 62 4771 0.01% 63 2089 0.00% 64 2200 0.01% 65 2316 0.01% 66 2384 0.01% 67 2597 0.01% 68 3066 0.01% 69 3877 0.01% 70 4147 0.01% 71 3770 0.01% 72 3817 0.01% 73 4092 0.01% 74 4191 0.01% 75 4482 0.01% 76 4965 0.01% 77 5375 0.01% 78 5862 0.01% 79 6851 0.02% 80 7627 0.02% 81 8274 0.02% 82 9636 0.02% 83 12443 0.03% 84 22620 0.05% 85 23408 0.05% 86 26492 0.06% 87 28771 0.07% 88 27725 0.06% 89 28582 0.07% 90 26816 0.06% 91 27162 0.06% 92 27523 0.06% 93 27446 0.06% 94 29123 0.07% 95 30963 0.07% 96 33763 0.08% 97 36598 0.08% 98 39810 0.09% 99 42181 0.10% 100 44232 0.10% 101 46424 0.11% 102 49213 0.11% 103 52412 0.12% 104 55585 0.13% 105 57046 0.13% 106 60582 0.14% 107 63105 0.14% 108 65183 0.15% 109 66206 0.15% 110 68347 0.16% 111 70825 0.16% 112 71825 0.16% 113 73207 0.17% 114 75686 0.17% 115 80010 0.18% 116 82809 0.19% 117 86913 0.20% 118 89363 0.21% 119 93971 0.22% 120 99110 0.23% 121 104170 0.24% 122 108649 0.25% 123 113113 0.26% 124 119358 0.27% 125 124941 0.29% 126 131818 0.30% 127 138888 0.32% 128 145369 0.33% 129 155251 0.36% 130 164591 0.38% 131 172628 0.40% 132 180594 0.41% 133 189639 0.44% 134 203448 0.47% 135 216276 0.50% 136 230595 0.53% 137 246044 0.56% 138 270771 0.62% 139 293151 0.67% 140 319559 0.73% 141 358110 0.82% 142 398151 0.91% 143 455159 1.04% 144 548852 1.26% 145 677159 1.55% 146 883821 2.03% 147 1305011 2.99% 148 2486937 5.71% 149 10630594 24.39% 150 20115848 46.16% 43579751 reads passed initial QC criterion=sequence-density sequence-density=1.17 sequence-density-rank=1 fanout-score=3.01 fanout-score-rank=17 prefix-density=1.24 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.10 sequence-density-rank=28 fanout-score=11.72 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=2.6 sequence=GCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAGCCTGGCGGGTGGTGCCCCATTCGGACTTCTTGGGAAGGAAAGACGATTTGAGGATAGTAGCCGAGGCCATTGTTTCTGGCTCCAAAGGCAAGAGGATCAGGTGCTACCCTCTTCTTTGACACAAGCTTGCAAT criterion=sequence-density sequence-density=0.83 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=27 prefix-density=0.86 prefix-fanout=2.0 sequence=ATCCGCTCCAAGTGGGTTCCTTGCCT criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=31.56 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=7.8 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR8096902 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 19:22:57 Started mapping on | Dec 07 19:22:58 Finished on | Dec 07 19:29:21 Mapping speed, Million of reads per hour | 409.63 Number of input reads | 43579751 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 42140730 Uniquely mapped reads % | 96.70% Average mapped length | 290.91 Number of splices: Total | 44790451 Number of splices: Annotated (sjdb) | 42336874 Number of splices: GT/AG | 44196763 Number of splices: GC/AG | 519167 Number of splices: AT/AC | 14381 Number of splices: Non-canonical | 60140 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 2.03 Insertion rate per base | 0.01% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 505606 % of reads mapped to multiple loci | 1.16% Number of reads mapped to too many loci | 11685 % of reads mapped to too many loci | 0.03% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.95% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1136466 1136466 1136466 N_multimapping 505606 505606 505606 N_noFeature 1653713 40840837 1976546 N_ambiguous 1152334 4938 178787 UnstrandedReadsAssigned:39334683 PositiveStrandReadsAssigned:1294955 NegativeStrandReadsAssigned:39985397 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR8096902 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: SRR8096902-trimmed-pair1.fastq SRR8096902-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 43,579,751 reads, 40,095,900 reads pseudoaligned [quant] estimated average fragment length: 270.191 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,283 rounds 52973 SRR8096902.ke.tsv 35125 SRR8096902.se.tsv 88098 total ==> SRR8096902.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 667.374 0 0 PNS24247 1044 774.809 103.667 4.65665 PNS24249 1928 1658.81 56.0746 1.17651 PNS24246 1044 774.809 103.667 4.65665 PNS24248 1044 774.809 103.667 4.65665 PNS24244 1471 1201.81 249.924 7.23767 PNS24243 293 84.9453 0 0 KQK14069 1603 1333.81 7931.16 206.952 KQK14071 474 223.811 147.537 22.9428 ==> SRR8096902.se.tsv <== BRADI_1g14170v3 9840 BRADI_1g53295v3 55 BRADI_1g59795v3 2554 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 505 BRADI_1g74790v3 127 BRADI_1g09890v3 0 BRADI_1g77505v3 656 BRADI_1g48960v3 1 SRR8096902 completed mapping pipeline successfully