Starting /dee2/code/volunteer_pipeline.sh SRR8096899 current disk space = 1508690997248 free memory = 1418862936 SRR8096899 SRAfilesize 2a858777db738817e0be0719db575011 SRR8096899.sra SRR8096899.sra file validated SRR8096899 is paired end SRR8096899 is conventional basespace SRR8096899 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096899_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.82275 34.0 33.0 34.0 32.0 34.0 2 32.88375 34.0 33.0 34.0 31.0 34.0 3 32.99325 34.0 33.0 34.0 31.0 34.0 4 33.19925 34.0 33.0 34.0 32.0 34.0 5 33.22975 34.0 33.0 34.0 33.0 34.0 6 36.99525 38.0 37.0 38.0 36.0 38.0 7 37.246 38.0 38.0 38.0 36.0 38.0 8 37.286 38.0 38.0 38.0 37.0 38.0 9 37.401 38.0 38.0 38.0 37.0 38.0 10-14 37.255250000000004 38.0 38.0 38.0 36.8 38.0 15-19 37.279250000000005 38.0 38.0 38.0 36.8 38.0 20-24 37.201550000000005 38.0 38.0 38.0 36.6 38.0 25-29 37.1507 38.0 38.0 38.0 36.6 38.0 30-34 37.028650000000006 38.0 38.0 38.0 36.2 38.0 35-39 37.0124 38.0 38.0 38.0 36.4 38.0 40-44 36.81769999999999 38.0 38.0 38.0 35.8 38.0 45-49 36.81805000000001 38.0 38.0 38.0 35.8 38.0 50-54 36.75795 38.0 38.0 38.0 35.8 38.0 55-59 36.65505 38.0 38.0 38.0 35.6 38.0 60-64 36.482800000000005 38.0 38.0 38.0 35.2 38.0 65-69 36.01370000000001 38.0 38.0 38.0 33.8 38.0 70-74 35.75985000000001 38.0 38.0 38.0 32.8 38.0 75-79 34.96985 38.0 38.0 38.0 29.8 38.0 80-84 34.90285 38.0 38.0 38.0 29.4 38.0 85-89 34.79865 38.0 38.0 38.0 29.4 38.0 90-94 34.7375 38.0 38.0 38.0 28.8 38.0 95-99 34.6339 38.0 38.0 38.0 28.4 38.0 100-104 34.35185 38.0 38.0 38.0 24.6 38.0 105-109 34.263 38.0 37.8 38.0 23.6 38.0 110-114 34.12485 38.0 37.0 38.0 23.0 38.0 115-119 33.8774 38.0 36.8 38.0 17.4 38.0 120-124 33.63685 38.0 36.2 38.0 15.0 38.0 125-129 33.472899999999996 38.0 35.8 38.0 14.4 38.0 130-134 33.31315 38.0 35.4 38.0 14.0 38.0 135-139 32.8928 38.0 35.0 38.0 13.0 38.0 140-144 32.4979 38.0 33.0 38.0 4.2 38.0 145-149 31.7829 38.0 33.0 38.0 2.0 38.0 150 24.6455 32.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 2.0 7 3.0 8 7.0 9 5.0 10 1.0 11 7.0 12 3.0 13 13.0 14 9.0 15 12.0 16 31.0 17 23.0 18 47.0 19 88.0 20 12.0 21 10.0 22 8.0 23 13.0 24 10.0 25 22.0 26 20.0 27 18.0 28 30.0 29 36.0 30 53.0 31 53.0 32 59.0 33 102.0 34 116.0 35 178.0 36 462.0 37 2547.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.7522816166884 16.192959582790092 6.936114732724902 27.11864406779661 2 21.75 19.400000000000002 34.775 24.075 3 20.25 21.425 27.85 30.475 4 25.974999999999998 26.325 21.725 25.974999999999998 5 27.675 31.075000000000003 22.7 18.55 6 23.1 31.8 23.400000000000002 21.7 7 17.9 25.55 38.824999999999996 17.724999999999998 8 16.975 24.7 30.85 27.474999999999998 9 22.425 20.325 31.525 25.724999999999998 10-14 22.37 26.82 25.47 25.34 15-19 22.759999999999998 24.595 26.950000000000003 25.695 20-24 22.455 25.919999999999998 27.205000000000002 24.42 25-29 23.294999999999998 24.97 26.33 25.405 30-34 22.56 24.98 27.134999999999998 25.324999999999996 35-39 23.265 26.295 26.44 24.0 40-44 21.634999999999998 25.085 27.82 25.46 45-49 22.985 25.435000000000002 27.58 24.0 50-54 22.945 24.11 26.755000000000003 26.19 55-59 22.465 24.865000000000002 27.79 24.88 60-64 22.205 25.82 27.065 24.91 65-69 21.261063053152657 29.186459322966147 25.44627231361568 24.106205310265512 70-74 22.645 28.395 25.085 23.875 75-79 22.37 27.515 25.695 24.42 80-84 22.275 26.135 25.96 25.629999999999995 85-89 23.055 26.05 25.905 24.990000000000002 90-94 23.27 25.224999999999998 26.025 25.480000000000004 95-99 22.759999999999998 25.430000000000003 26.96 24.85 100-104 22.814999999999998 26.755000000000003 26.14 24.29 105-109 22.555 27.0 25.56 24.884999999999998 110-114 22.445 27.189999999999998 25.61 24.755 115-119 22.79 26.634999999999998 25.645 24.93 120-124 22.895 27.27 24.89 24.945 125-129 22.770000000000003 27.415 24.845 24.97 130-134 22.675 27.22 24.865000000000002 25.240000000000002 135-139 22.759999999999998 26.584999999999997 25.135 25.52 140-144 22.905 27.36 25.155 24.58 145-149 23.189999999999998 26.52 24.985 25.305 150 23.525 26.075 25.525 24.875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 26.0 1 16.0 2 4.0 3 3.5 4 5.5 5 4.0 6 2.0 7 4.5 8 4.0 9 1.0 10 1.0 11 0.5 12 0.5 13 0.5 14 0.5 15 1.0 16 1.0 17 1.0 18 1.0 19 2.5 20 2.5 21 1.0 22 1.0 23 0.5 24 0.5 25 0.5 26 1.0 27 4.0 28 6.0 29 7.0 30 10.5 31 14.0 32 17.0 33 22.0 34 27.5 35 35.0 36 55.5 37 72.5 38 88.5 39 113.5 40 141.0 41 164.5 42 177.5 43 185.5 44 191.0 45 208.0 46 213.5 47 201.0 48 195.5 49 180.0 50 154.0 51 141.0 52 135.0 53 116.5 54 89.0 55 75.0 56 82.5 57 84.0 58 72.5 59 66.5 60 67.5 61 66.0 62 61.5 63 62.0 64 58.5 65 52.5 66 47.0 67 42.5 68 34.5 69 25.0 70 20.0 71 13.5 72 10.0 73 7.0 74 5.0 75 4.0 76 1.0 77 1.0 78 1.0 79 0.0 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 4.125 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 0.005 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 91.875 #Duplication Level Percentage of deduplicated Percentage of total 1 97.98639455782313 90.025 2 1.3605442176870748 2.5 3 0.19047619047619047 0.525 4 0.10884353741496598 0.4 5 0.0 0.0 6 0.0816326530612245 0.44999999999999996 7 0.0 0.0 8 0.05442176870748299 0.4 9 0.0816326530612245 0.675 >10 0.10884353741496598 1.95 >50 0.0 0.0 >100 0.027210884353741496 3.075 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGC 123 3.075 TruSeq Adapter, Index 3 (97% over 37bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 0.775 No Hit ATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCC 23 0.575 TruSeq Adapter, Index 3 (97% over 36bp) AGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTG 14 0.35000000000000003 RNA PCR Primer, Index 17 (97% over 40bp) AAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTT 10 0.25 RNA PCR Primer, Index 17 (100% over 36bp) CACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCT 9 0.22499999999999998 RNA PCR Primer, Index 17 (100% over 41bp) ACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 9 0.22499999999999998 RNA PCR Primer, Index 17 (100% over 41bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATG 9 0.22499999999999998 TruSeq Adapter, Index 3 (97% over 37bp) GCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGC 8 0.2 RNA PCR Primer, Index 17 (100% over 40bp) NATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGC 8 0.2 TruSeq Adapter, Index 18 (97% over 35bp) AGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTC 6 0.15 RNA PCR Primer, Index 17 (97% over 38bp) GAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCT 6 0.15 RNA PCR Primer, Index 17 (100% over 38bp) ACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGA 6 0.15 RNA PCR Primer, Index 17 (97% over 44bp) >>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 0.225 0.0 0.0 0.0 0.0 2 0.225 0.0 0.0 0.0 0.0 3 0.225 0.0 0.0 0.0 0.0 4 0.225 0.0 0.0 0.0 0.0 5 0.225 0.0 0.0 0.0 0.0 6 0.225 0.0 0.0 0.0 0.0 7 0.225 0.0 0.0 0.0 0.0 8 0.225 0.0 0.0 0.0 0.0 9 0.225 0.0 0.0 0.0 0.0 10-11 0.225 0.0 0.0 0.0 0.0 12-13 0.225 0.0 0.0 0.0 0.0 14-15 0.225 0.0 0.0 0.0 0.0 16-17 0.225 0.0 0.0 0.0 0.0 18-19 0.225 0.0 0.0 0.0 0.0 20-21 0.225 0.0 0.0 0.0 0.0 22-23 0.225 0.0 0.0 0.0 0.0 24-25 0.225 0.0 0.0 0.0 0.0 26-27 0.225 0.0 0.0 0.0 0.0 28-29 0.225 0.0 0.0 0.0 0.0 30-31 0.225 0.0 0.0 0.0 0.0 32-33 0.225 0.0 0.0 0.0 0.0 34-35 0.225 0.0 0.0 0.0 0.0 36-37 0.225 0.0 0.0 0.0 0.0 38-39 0.275 0.0 0.0 0.0 0.0 40-41 0.3 0.0 0.0 0.0 0.0 42-43 0.3 0.0 0.0 0.0 0.0 44-45 0.35 0.0 0.0 0.0 0.0 46-47 0.35 0.0 0.0 0.0 0.0 48-49 0.4125 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.55 0.0 0.0 0.0 0.0 54-55 0.5625 0.0 0.0 0.0 0.0 56-57 0.6 0.0 0.0 0.0 0.0 58-59 0.6125 0.0 0.0 0.0 0.0 60-61 0.65 0.0 0.0 0.0 0.0 62-63 0.65 0.0 0.0 0.0 0.0 64-65 0.65 0.0 0.0 0.0 0.0 66-67 0.65 0.0 0.0 0.0 0.0 68-69 0.65 0.0 0.0 0.0 0.0 70-71 0.65 0.0 0.0 0.0 0.0 72-73 0.65 0.0 0.0 0.0 0.0 74-75 0.65 0.0 0.0 0.0 0.0 76-77 0.675 0.0 0.0 0.0 0.0 78-79 0.675 0.0 0.0 0.0 0.0 80-81 0.675 0.0 0.0 0.0 0.0 82-83 0.675 0.0 0.0 0.0 0.0 84-85 0.675 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.675 0.0 0.0 0.0 0.0 90-91 0.7125 0.0 0.0 0.0 0.0 92-93 0.775 0.0 0.0 0.0 0.0 94-95 0.85 0.0 0.0 0.0 0.0 96-97 0.875 0.0 0.0 0.0 0.0 98-99 0.9125000000000001 0.0 0.0 0.0 0.0 100-101 1.0 0.0 0.0 0.0 0.0 102-103 1.1125 0.0 0.0 0.0 0.0 104-105 1.15 0.0 0.0 0.0 0.0 106-107 1.1625 0.0 0.0 0.0 0.0 108-109 1.2 0.0 0.0 0.0 0.0 110-111 1.275 0.0 0.0 0.0 0.0 112-113 1.3624999999999998 0.0 0.0 0.0 0.0 114-115 1.4625 0.0 0.0 0.0 0.0 116-117 1.5499999999999998 0.0 0.0 0.0 0.0 118-119 1.7125 0.0 0.0 0.0 0.0 120-121 1.7999999999999998 0.0 0.0 0.0 0.0 122-123 2.0 0.0 0.0 0.0 0.0 124-125 2.175 0.0 0.0 0.0 0.0 126-127 2.3375 0.0 0.0 0.0 0.0 128-129 2.5875 0.0 0.0 0.0 0.0 130-131 2.8125 0.0 0.0 0.0 0.0 132-133 3.1375 0.0 0.0 0.0 0.0 134-135 3.3625 0.0 0.0 0.0 0.0 136-137 3.5125 0.0 0.0 0.0 0.0 138 3.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACTCCA 10 0.0069808904 143.95 4 >>END_MODULE SRR8096899 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096899_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 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.759 33.0 31.0 33.0 18.0 34.0 2 29.856 33.0 30.0 33.0 18.0 34.0 3 29.72725 33.0 31.0 33.0 18.0 34.0 4 29.80725 33.0 31.0 34.0 15.0 34.0 5 28.45625 33.0 28.0 33.0 15.0 34.0 6 32.785 38.0 33.0 38.0 16.0 38.0 7 33.03 38.0 34.0 38.0 16.0 38.0 8 33.309 38.0 34.0 38.0 16.0 38.0 9 33.2655 38.0 34.0 38.0 16.0 38.0 10-14 33.24485 38.0 34.4 38.0 16.0 38.0 15-19 33.1043 38.0 34.6 38.0 16.0 38.0 20-24 32.9222 38.0 34.0 38.0 16.0 38.0 25-29 32.6406 38.0 34.0 38.0 16.0 38.0 30-34 32.58315 38.0 33.8 38.0 16.0 38.0 35-39 32.46495 38.0 33.8 38.0 16.0 38.0 40-44 32.24035 38.0 33.0 38.0 15.0 38.0 45-49 31.935750000000002 38.0 33.0 38.0 14.2 38.0 50-54 31.90435 38.0 32.6 38.0 14.0 38.0 55-59 31.54475 38.0 30.6 38.0 14.0 38.0 60-64 31.184949999999997 37.8 29.6 38.0 14.0 38.0 65-69 30.793100000000003 37.4 28.8 38.0 9.2 38.0 70-74 30.217450000000003 37.0 28.0 38.0 2.0 38.0 75-79 29.929250000000003 37.0 27.2 38.0 2.0 38.0 80-84 29.626600000000003 37.0 26.4 38.0 2.0 38.0 85-89 29.081 36.4 23.8 38.0 2.0 38.0 90-94 28.64685 36.0 22.6 38.0 2.0 38.0 95-99 28.034100000000002 35.4 16.6 38.0 2.0 38.0 100-104 27.5488 35.0 15.0 38.0 2.0 38.0 105-109 26.7349 34.4 15.0 38.0 2.0 38.0 110-114 25.7708 34.0 14.6 38.0 2.0 38.0 115-119 25.1406 33.0 14.0 38.0 2.0 38.0 120-124 24.419 32.0 13.0 37.6 2.0 38.0 125-129 23.4695 30.2 8.6 37.0 2.0 38.0 130-134 22.04545 26.8 2.0 36.0 2.0 38.0 135-139 20.4681 23.2 2.0 35.2 2.0 38.0 140-144 18.746950000000002 18.4 2.0 33.8 2.0 38.0 145-149 15.966150000000003 8.6 2.0 33.2 2.0 38.0 150 10.69625 2.0 2.0 23.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 197.0 3 36.0 4 20.0 5 14.0 6 19.0 7 23.0 8 12.0 9 15.0 10 29.0 11 18.0 12 27.0 13 24.0 14 35.0 15 43.0 16 46.0 17 45.0 18 45.0 19 39.0 20 38.0 21 59.0 22 63.0 23 69.0 24 65.0 25 88.0 26 90.0 27 99.0 28 138.0 29 163.0 30 170.0 31 210.0 32 250.0 33 327.0 34 409.0 35 467.0 36 439.0 37 169.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.443241882708286 23.131135162345835 8.608104706770703 24.817518248175183 2 25.597785049081303 27.686886483765417 27.938585451799646 18.776743015353638 3 22.652907123080794 26.101182985149762 28.03926503901334 23.206644852756103 4 27.133148754090108 30.30455575132142 18.07198590485779 24.490309589730682 5 29.171910395167377 33.19909388371507 18.248175182481752 19.380820538635792 6 24.238610621696452 35.08683614397181 17.996476214447522 22.678077019884217 7 23.18147495595268 22.300528567832874 32.11678832116788 22.401208155046564 8 20.689655172413794 26.050843191542917 24.691668764158067 28.567832871885223 9 26.277372262773724 23.408004027183487 24.163100931286184 26.151522778756608 10-14 26.53913918952932 25.819280140951424 22.516989680342313 25.124590989176944 15-19 25.622954945884725 25.532343317392396 24.208406745532344 24.636294991190535 20-24 26.584445003775485 27.17342058897558 23.231814749559526 23.010319657689404 25-29 24.90562238888609 27.321689233402125 23.667388131071625 24.10530024664016 30-34 25.64670357322597 25.858077503774535 24.932058379466532 23.563160543532966 35-39 24.449028881956323 26.295662674851567 24.75596256415417 24.49934587903794 40-44 27.146090017601203 25.36082474226804 23.902439024390244 23.590646215740506 45-49 25.35097871483923 25.713279323705528 23.94203190258139 24.993710058873848 50-54 25.33098414296501 25.844450037754847 24.59602315630506 24.22854266297508 55-59 24.691668764158067 27.27913415554996 24.46513969292726 23.564057387364713 60-64 24.71683866096149 28.613138686131386 23.251950667002266 23.41807198590486 65-69 24.545683362698213 28.633274603574126 23.241882708280894 23.579159325446767 70-74 25.104455071734204 28.15504656430909 22.949911905361187 23.79058645859552 75-79 24.757110495846966 27.63654669015857 23.287188522527057 24.319154291467406 80-84 25.31588220488296 27.404983639567078 23.53888749056129 23.740246664988675 85-89 25.089353133652153 27.359677825320915 23.51875157311855 24.03221746790838 90-94 24.505411527812736 28.270828089604834 22.919708029197082 24.304052353385348 95-99 24.86785804178203 27.520765164862826 23.720110747545935 23.89126604580921 100-104 24.384596023156305 27.86307576138938 23.327460357412537 24.424867858041782 105-109 24.268814497860557 28.62824062421344 22.77875660709791 24.32418827082809 110-114 24.218474704253712 28.03926503901334 23.46337780015102 24.278882456581925 115-119 24.249899315344344 28.85118807893677 22.71445831655256 24.184454289166332 120-124 24.06987866888184 28.862709560489353 23.490912752353623 23.576499018275186 125-129 23.93153788069469 30.06795872136924 22.300528567832874 23.699974830103194 130-134 23.861062169645102 30.138434432418826 22.109237352126858 23.89126604580921 135-139 24.520513465894787 29.297759879184493 22.260256732947393 23.92146992197332 140-144 24.223508683614398 29.856531588220488 21.3742763654669 24.545683362698213 145-149 23.66281125309359 30.27425627556947 21.970806606394262 24.092125864942673 150 23.609363201610872 33.048074502894536 20.312106720362447 23.03045557513214 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 24.0 1 12.5 2 0.5 3 0.5 4 0.5 5 0.0 6 0.5 7 1.5 8 1.5 9 1.0 10 1.0 11 1.0 12 0.5 13 0.5 14 0.5 15 0.5 16 1.0 17 0.5 18 0.0 19 0.0 20 1.0 21 2.0 22 1.5 23 2.0 24 3.0 25 3.0 26 3.0 27 5.0 28 7.0 29 6.5 30 10.5 31 13.5 32 15.0 33 28.0 34 30.5 35 33.0 36 48.5 37 64.0 38 78.0 39 94.5 40 121.0 41 143.5 42 164.0 43 170.0 44 178.0 45 200.0 46 197.0 47 176.5 48 168.5 49 164.0 50 143.5 51 128.5 52 130.0 53 119.0 54 106.0 55 103.0 56 97.0 57 95.0 58 87.0 59 80.0 60 90.0 61 91.5 62 78.5 63 70.0 64 69.5 65 66.0 66 50.0 67 40.0 68 41.5 69 41.0 70 35.0 71 26.5 72 18.0 73 11.0 74 7.0 75 3.0 76 1.5 77 1.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.675 2 0.675 3 0.675 4 0.675 5 0.675 6 0.675 7 0.675 8 0.675 9 0.675 10-14 0.675 15-19 0.675 20-24 0.675 25-29 0.6649999999999999 30-34 0.65 35-39 0.63 40-44 0.575 45-49 0.635 50-54 0.675 55-59 0.675 60-64 0.675 65-69 0.675 70-74 0.675 75-79 0.675 80-84 0.675 85-89 0.675 90-94 0.675 95-99 0.675 100-104 0.675 105-109 0.675 110-114 0.675 115-119 0.6799999999999999 120-124 0.685 125-129 0.675 130-134 0.675 135-139 0.675 140-144 0.675 145-149 1.005 150 0.675 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.55 #Duplication Level Percentage of deduplicated Percentage of total 1 98.67944070429829 95.275 2 1.035732780942517 2.0 3 0.20714655618850336 0.6 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.02589331952356292 0.2 9 0.0 0.0 >10 0.02589331952356292 0.575 >50 0.02589331952356292 1.35 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 54 1.35 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 23 0.575 No Hit AAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCAGACGTGT 8 0.2 RNA PCR Primer, Index 17 (97% over 42bp) >>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 0.175 0.0 0.0 0.0 0.0 2 0.175 0.0 0.0 0.0 0.0 3 0.175 0.0 0.0 0.0 0.0 4 0.175 0.0 0.0 0.0 0.0 5 0.175 0.0 0.0 0.0 0.0 6 0.175 0.0 0.0 0.0 0.0 7 0.175 0.0 0.0 0.0 0.0 8 0.175 0.0 0.0 0.0 0.0 9 0.175 0.0 0.0 0.0 0.0 10-11 0.175 0.0 0.0 0.0 0.0 12-13 0.175 0.0 0.0 0.0 0.0 14-15 0.175 0.0 0.0 0.0 0.0 16-17 0.175 0.0 0.0 0.0 0.0 18-19 0.175 0.0 0.0 0.0 0.0 20-21 0.175 0.0 0.0 0.0 0.0 22-23 0.175 0.0 0.0 0.0 0.0 24-25 0.175 0.0 0.0 0.0 0.0 26-27 0.175 0.0 0.0 0.0 0.0 28-29 0.175 0.0 0.0 0.0 0.0 30-31 0.175 0.0 0.0 0.0 0.0 32-33 0.175 0.0 0.0 0.0 0.0 34-35 0.175 0.0 0.0 0.0 0.0 36-37 0.175 0.0 0.0 0.0 0.0 38-39 0.2 0.0 0.0 0.0 0.0 40-41 0.275 0.0 0.0 0.0 0.0 42-43 0.30000000000000004 0.0 0.0 0.0 0.0 44-45 0.35 0.0 0.0 0.0 0.0 46-47 0.35 0.0 0.0 0.0 0.0 48-49 0.375 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.5625 0.0 0.0 0.0 0.0 54-55 0.6 0.0 0.0 0.0 0.0 56-57 0.65 0.0 0.0 0.0 0.0 58-59 0.6625000000000001 0.0 0.0 0.0 0.0 60-61 0.675 0.0 0.0 0.0 0.0 62-63 0.7 0.0 0.0 0.0 0.0 64-65 0.75 0.0 0.0 0.0 0.0 66-67 0.775 0.0 0.0 0.0 0.0 68-69 0.775 0.0 0.0 0.0 0.0 70-71 0.775 0.0 0.0 0.0 0.0 72-73 0.775 0.0 0.0 0.0 0.0 74-75 0.775 0.0 0.0 0.0 0.0 76-77 0.775 0.0 0.0 0.0 0.0 78-79 0.775 0.0 0.0 0.0 0.0 80-81 0.775 0.0 0.0 0.0 0.0 82-83 0.775 0.0 0.0 0.0 0.0 84-85 0.775 0.0 0.0 0.0 0.0 86-87 0.775 0.0 0.0 0.0 0.0 88-89 0.775 0.0 0.0 0.0 0.0 90-91 0.8 0.0 0.0 0.0 0.0 92-93 0.8374999999999999 0.0 0.0 0.0 0.0 94-95 0.875 0.0 0.0 0.0 0.0 96-97 0.875 0.0 0.0 0.0 0.0 98-99 0.875 0.0 0.0 0.0 0.0 100-101 0.925 0.0 0.0 0.0 0.0 102-103 1.0 0.0 0.0 0.0 0.0 104-105 1.025 0.0 0.0 0.0 0.0 106-107 1.0499999999999998 0.0 0.0 0.0 0.0 108-109 1.075 0.0 0.0 0.0 0.0 110-111 1.125 0.0 0.0 0.0 0.0 112-113 1.1749999999999998 0.0 0.0 0.0 0.0 114-115 1.2625 0.0 0.0 0.0 0.0 116-117 1.3125 0.0 0.0 0.0 0.0 118-119 1.3875 0.0 0.0 0.0 0.0 120-121 1.4249999999999998 0.0 0.0 0.0 0.0 122-123 1.55 0.0 0.0 0.0 0.0 124-125 1.6875 0.0 0.0 0.0 0.0 126-127 1.7875 0.0 0.0 0.0 0.0 128-129 1.95 0.0 0.0 0.0 0.0 130-131 2.075 0.0 0.0 0.0 0.0 132-133 2.2125 0.0 0.0 0.0 0.0 134-135 2.35 0.0 0.0 0.0 0.0 136-137 2.4875 0.0 0.0 0.0 0.0 138 2.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGACTGC 10 0.0069845165 143.925 5 >>END_MODULE Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820829 spots for SRR8096899.sra Written 1820829 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra Read 1820816 spots for SRR8096899.sra Written 1820816 spots for SRR8096899.sra SRR ids: ['SRR8096899.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_n97vqt02 SRR8096899.sra spots: 36416333 blocks: [[1, 1820816], [1820817, 3641632], [3641633, 5462448], [5462449, 7283264], [7283265, 9104080], [9104081, 10924896], [10924897, 12745712], [12745713, 14566528], [14566529, 16387344], [16387345, 18208160], [18208161, 20028976], [20028977, 21849792], [21849793, 23670608], [23670609, 25491424], [25491425, 27312240], [27312241, 29133056], [29133057, 30953872], [30953873, 32774688], [32774689, 34595504], [34595505, 36416333]] SRR8096899 file size 12247474 SRR8096899 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 SRR8096899 SRR8096899_1.fastq SRR8096899_2.fastq Input file: SRR8096899_1.fastq Paired file: SRR8096899_2.fastq trimmed: SRR8096899-trimmed-pair1.fastq, SRR8096899-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 Sun Dec 8 12:16:03 2024 >> started Sun Dec 8 12:21:03 2024 >> done (300.563s) 36416333 read pairs processed; of these: 367099 ( 1.01%) short read pairs filtered out after trimming by size control 3108600 ( 8.54%) empty read pairs filtered out after trimming by size control 32940634 (90.46%) read pairs available; of these: 18419259 (55.92%) trimmed read pairs available after processing 14521375 (44.08%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 106 0.00% 19 226 0.00% 20 160 0.00% 21 295 0.00% 22 269 0.00% 23 257 0.00% 24 365 0.00% 25 424 0.00% 26 476 0.00% 27 365 0.00% 28 374 0.00% 29 448 0.00% 30 635 0.00% 31 671 0.00% 32 1024 0.00% 33 1286 0.00% 34 2144 0.01% 35 3832 0.01% 36 3880 0.01% 37 6268 0.02% 38 5364 0.02% 39 14445 0.04% 40 16764 0.05% 41 20327 0.06% 42 14083 0.04% 43 17693 0.05% 44 14696 0.04% 45 18253 0.06% 46 18610 0.06% 47 27047 0.08% 48 16514 0.05% 49 25956 0.08% 50 20774 0.06% 51 21791 0.07% 52 20235 0.06% 53 22894 0.07% 54 21029 0.06% 55 22163 0.07% 56 25461 0.08% 57 18386 0.06% 58 17607 0.05% 59 13690 0.04% 60 11430 0.03% 61 27180 0.08% 62 19233 0.06% 63 7205 0.02% 64 7050 0.02% 65 8051 0.02% 66 7711 0.02% 67 8440 0.03% 68 9143 0.03% 69 11899 0.04% 70 13449 0.04% 71 11661 0.04% 72 10062 0.03% 73 9621 0.03% 74 8937 0.03% 75 8863 0.03% 76 9051 0.03% 77 9546 0.03% 78 9664 0.03% 79 10354 0.03% 80 11505 0.03% 81 12249 0.04% 82 13925 0.04% 83 20048 0.06% 84 50200 0.15% 85 35620 0.11% 86 39449 0.12% 87 40143 0.12% 88 37454 0.11% 89 37673 0.11% 90 35765 0.11% 91 35404 0.11% 92 34660 0.11% 93 33498 0.10% 94 34580 0.10% 95 35250 0.11% 96 37686 0.11% 97 39145 0.12% 98 41710 0.13% 99 43220 0.13% 100 44983 0.14% 101 46914 0.14% 102 48982 0.15% 103 51014 0.15% 104 53583 0.16% 105 55015 0.17% 106 57580 0.17% 107 59033 0.18% 108 60240 0.18% 109 60044 0.18% 110 61430 0.19% 111 63569 0.19% 112 63507 0.19% 113 63057 0.19% 114 64738 0.20% 115 67034 0.20% 116 68990 0.21% 117 71532 0.22% 118 73400 0.22% 119 76433 0.23% 120 79204 0.24% 121 82007 0.25% 122 85050 0.26% 123 88054 0.27% 124 91122 0.28% 125 95009 0.29% 126 100622 0.31% 127 105238 0.32% 128 109470 0.33% 129 115674 0.35% 130 122609 0.37% 131 130126 0.40% 132 135806 0.41% 133 141878 0.43% 134 151543 0.46% 135 161889 0.49% 136 172486 0.52% 137 184057 0.56% 138 203023 0.62% 139 218351 0.66% 140 239916 0.73% 141 266859 0.81% 142 297839 0.90% 143 341404 1.04% 144 412268 1.25% 145 508015 1.54% 146 663964 2.02% 147 981440 2.98% 148 1851837 5.62% 149 7746400 23.52% 150 14521375 44.08% 32940634 reads passed initial QC criterion=sequence-density sequence-density=1.25 sequence-density-rank=1 fanout-score=2.99 fanout-score-rank=12 prefix-density=1.31 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.10 sequence-density-rank=26 fanout-score=13.46 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=2.8 sequence=GCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAGCCTGGCGGGTGGTGCCCCATTCGGACTTCTTGGGAAGGAAAGACGATTTGAGGATAGTAGCCGAGGCCATTGTTTCTGGCTCCAAAGGCAAGAGGATCAGGTGCTACCCTCTTCTTTGACACAAGCTTGCAATTGCAGCC criterion=sequence-density sequence-density=0.88 sequence-density-rank=1 fanout-score=2.28 fanout-score-rank=14 prefix-density=0.93 prefix-fanout=2.1 sequence=ATCCGCTCCAAGTGGGTTCCTTGCCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=24 fanout-score=54.60 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=5.0 sequence=AGGAAAGGCTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTGCCTTTGGAGCCAGAAACAATGGCCTCGGCTACTATCCTCAAATCGTCTTTCCTTCCCAAGAAGTCCGAATGGGGCACCACCCGCCAGGCTGCCACTCCCAAGCAGATGACCGTCTCCATGGTTGTCCGTGCCAGCGCATACGCTGATGAACTTGTCAAGACCGCGAAAACCATCGCATCACCAGGAAGGGGCATCCTAGCCATGGATGAGTCCAATGCTACCTGTGGAAAGAGACTTGACTCGATTGGCCTTGAGAACACTGAGGCTAACCGCCAGGCTTACCGTACCCTCCTTGTCACTCCACCAGGCCTGGGAAATTACATCTCTGGTGCTATCCTCTTCGAGGAGACCCTCTACCAATCGACTGTTGATGGCAAGAAGATTGTTGACATCCTTGTCGAGCAGGGAATCGTTCCCGGCATCAAGGTTGACAAGGGTCTTGTGCCACTCGTT SRR8096899 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 08 12:25:53 Started mapping on | Dec 08 12:25:53 Finished on | Dec 08 13:08:51 Mapping speed, Million of reads per hour | 46.00 Number of input reads | 32940634 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 30553867 Uniquely mapped reads % | 92.75% Average mapped length | 290.08 Number of splices: Total | 32183051 Number of splices: Annotated (sjdb) | 30421621 Number of splices: GT/AG | 31757995 Number of splices: GC/AG | 373671 Number of splices: AT/AC | 9564 Number of splices: Non-canonical | 41821 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.89 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 371805 % of reads mapped to multiple loci | 1.13% Number of reads mapped to too many loci | 9972 % of reads mapped to too many loci | 0.03% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.91% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2337415 2337415 2337415 N_multimapping 371805 371805 371805 N_noFeature 1095235 29628926 1329210 N_ambiguous 825629 3804 138029 UnstrandedReadsAssigned:28633003 PositiveStrandReadsAssigned:921137 NegativeStrandReadsAssigned:29086628 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR8096899 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: SRR8096899-trimmed-pair1.fastq SRR8096899-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,940,634 reads, 29,212,824 reads pseudoaligned [quant] estimated average fragment length: 278.543 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,176 rounds 52973 SRR8096899.ke.tsv 35125 SRR8096899.se.tsv 88098 total ==> SRR8096899.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 659.045 0 0 PNS24247 1044 766.457 83.0266 5.1031 PNS24249 1928 1650.46 50.0532 1.42867 PNS24246 1044 766.457 83.0266 5.1031 PNS24248 1044 766.457 83.0266 5.1031 PNS24244 1471 1193.46 172.867 6.82354 PNS24243 293 82.2973 0 0 KQK14069 1603 1325.46 4782.05 169.962 KQK14071 474 218.202 80.242 17.3239 ==> SRR8096899.se.tsv <== BRADI_1g14170v3 5529 BRADI_1g53295v3 13 BRADI_1g59795v3 1682 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 259 BRADI_1g74790v3 72 BRADI_1g09890v3 0 BRADI_1g77505v3 387 BRADI_1g48960v3 0 SRR8096899 completed mapping pipeline successfully