Starting /dee2/code/volunteer_pipeline.sh SRR18274409 current disk space = 3057225474048 free memory = 1322322384 SRR18274409 SRAfilesize 418bf2bd4db09a8ba7c325a1a057d077 SRR18274409.sra SRR18274409.sra file validated SRR18274409 is paired end SRR18274409 is conventional basespace SRR18274409 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18274409_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.2425 32.0 32.0 32.0 32.0 32.0 2 30.89 32.0 32.0 32.0 32.0 32.0 3 35.06625 37.0 32.0 37.0 32.0 37.0 4 35.8525 37.0 37.0 37.0 32.0 37.0 5 35.95875 37.0 37.0 37.0 32.0 37.0 6 39.3365 41.0 41.0 41.0 37.0 41.0 7 39.642 41.0 41.0 41.0 37.0 41.0 8 39.42975 41.0 41.0 41.0 37.0 41.0 9 39.388 41.0 41.0 41.0 37.0 41.0 10-14 39.5476 41.0 41.0 41.0 37.0 41.0 15-19 39.5711 41.0 41.0 41.0 37.0 41.0 20-24 39.3535 41.0 41.0 41.0 37.0 41.0 25-29 39.3516 41.0 41.0 41.0 37.0 41.0 30-34 39.3091 41.0 41.0 41.0 37.0 41.0 35-39 39.2418 41.0 41.0 41.0 37.0 41.0 40-44 38.93065 41.0 41.0 41.0 35.0 41.0 45-49 39.03505 41.0 41.0 41.0 36.0 41.0 50-54 39.01465 41.0 41.0 41.0 36.0 41.0 55-59 38.841300000000004 41.0 41.0 41.0 34.0 41.0 60-64 38.8729 41.0 41.0 41.0 33.0 41.0 65-69 38.668899999999994 41.0 41.0 41.0 32.0 41.0 70-74 38.660450000000004 41.0 41.0 41.0 32.0 41.0 75-79 38.428250000000006 41.0 40.2 41.0 33.0 41.0 80-84 38.751149999999996 41.0 41.0 41.0 31.0 41.0 85-89 38.99295 41.0 41.0 41.0 34.0 41.0 90-94 38.857350000000004 41.0 41.0 41.0 32.0 41.0 95-99 38.7833 41.0 41.0 41.0 32.0 41.0 100-104 38.49385 41.0 41.0 41.0 32.0 41.0 105-109 38.7143 41.0 41.0 41.0 32.0 41.0 110-114 38.572849999999995 41.0 41.0 41.0 32.0 41.0 115-119 38.47815 41.0 41.0 41.0 32.0 41.0 120-124 38.57845 41.0 41.0 41.0 32.0 41.0 125-129 38.367000000000004 41.0 40.2 41.0 32.0 41.0 130-134 37.58794999999999 41.0 37.0 41.0 29.0 41.0 135-139 37.986450000000005 41.0 38.6 41.0 31.0 41.0 140-144 37.46375 41.0 37.0 41.0 26.0 41.0 145-149 37.6515 41.0 37.0 41.0 27.0 41.0 150 37.32775 41.0 37.0 41.0 27.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 2.0 18 0.0 19 8.0 20 12.0 21 10.0 22 15.0 23 18.0 24 23.0 25 15.0 26 20.0 27 24.0 28 17.0 29 38.0 30 52.0 31 65.0 32 55.0 33 76.0 34 78.0 35 105.0 36 144.0 37 179.0 38 248.0 39 413.0 40 2383.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.024132730015083 28.079436902966314 15.585721468074409 38.3107088989442 2 22.877478393492627 23.919674631418403 35.104219623792574 18.09862735129639 3 19.55 26.375 28.499999999999996 25.575 4 22.05 24.15 28.599999999999998 25.2 5 25.224999999999998 25.5 26.650000000000002 22.625 6 23.625 26.950000000000003 26.625 22.8 7 23.849999999999998 25.324999999999996 27.400000000000002 23.425 8 21.575 23.225 30.975 24.224999999999998 9 21.775 24.0 30.45 23.775 10-14 24.05 24.72 26.405 24.825 15-19 24.610000000000003 24.825 25.069999999999997 25.495 20-24 25.074999999999996 24.43 25.345000000000002 25.15 25-29 24.44 24.485 25.555 25.52 30-34 24.95 24.58 24.855 25.615 35-39 24.88 25.230000000000004 24.41 25.480000000000004 40-44 25.0 24.93 25.1 24.97 45-49 25.169999999999998 24.455 25.275 25.1 50-54 24.565 25.25 25.455 24.73 55-59 24.63123156157808 24.341217060853044 25.186259312965646 25.841292064603234 60-64 24.88624431221561 23.92119605980299 25.501275063753187 25.691284564228212 65-69 24.756237811890593 24.856242812140607 25.766288314415718 24.62123106155308 70-74 24.285 25.145 25.55 25.019999999999996 75-79 24.560000000000002 24.47 25.3 25.669999999999998 80-84 25.235000000000003 24.385 25.21 25.169999999999998 85-89 25.330000000000002 25.345000000000002 24.855 24.47 90-94 24.75 25.490000000000002 25.4 24.36 95-99 25.14 24.935 24.735 25.19 100-104 25.503825573836075 25.2137820673101 24.68370255538331 24.59868980347052 105-109 25.485000000000003 24.490000000000002 24.955 25.069999999999997 110-114 24.586229311465573 24.8112405620281 25.426271313565678 25.17625881294065 115-119 24.933740061009154 25.353803070460568 24.80872130819623 24.90373556033405 120-124 25.035007001400277 25.190038007601522 25.12002400480096 24.65493098619724 125-129 25.285000000000004 25.174999999999997 25.295 24.245 130-134 24.529999999999998 25.474999999999998 25.314999999999998 24.68 135-139 25.41 25.480000000000004 24.87 24.240000000000002 140-144 25.765 25.47 24.615000000000002 24.15 145-149 25.61 26.450000000000003 24.47 23.47 150 25.874999999999996 27.775 23.35 23.0 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.5 2 2.0 3 3.5 4 3.0 5 0.5 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.5 12 0.5 13 0.0 14 0.5 15 1.0 16 1.5 17 1.0 18 0.5 19 1.0 20 1.0 21 1.0 22 1.0 23 1.0 24 2.5 25 2.0 26 2.5 27 6.0 28 7.5 29 7.0 30 7.5 31 10.0 32 10.5 33 14.0 34 26.0 35 40.5 36 44.5 37 44.0 38 52.0 39 73.5 40 92.0 41 119.0 42 143.5 43 156.0 44 189.0 45 212.0 46 190.5 47 172.0 48 170.5 49 172.5 50 182.0 51 169.0 52 153.5 53 142.5 54 140.5 55 138.0 56 128.5 57 117.5 58 102.5 59 116.5 60 113.0 61 77.0 62 61.0 63 57.0 64 43.5 65 30.5 66 27.5 67 42.5 68 43.0 69 25.5 70 22.5 71 19.0 72 10.5 73 6.0 74 5.5 75 6.0 76 7.0 77 9.0 78 8.5 79 4.0 80 1.5 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 0.5499999999999999 2 1.6500000000000001 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 0.005 60-64 0.005 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 0.015 105-109 0.0 110-114 0.005 115-119 0.015 120-124 0.02 125-129 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 86.1 #Duplication Level Percentage of deduplicated Percentage of total 1 88.15331010452961 75.9 2 8.739837398373984 15.049999999999999 3 2.2938443670150988 5.925 4 0.6097560975609756 2.1 5 0.11614401858304298 0.5 6 0.05807200929152149 0.3 7 0.0 0.0 8 0.0 0.0 9 0.029036004645760744 0.22499999999999998 >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 CGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGGACCCAAGGCCGCTT 9 0.22499999999999998 No Hit CTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTA 6 0.15 No Hit CGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACAA 6 0.15 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACT 5 0.125 No Hit CGCTTCGGCGGCCGATCCGGGCGGAAGACATTGTCAGGTGGGGAGTTTGG 5 0.125 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 5 0.125 No Hit CGAAGCTCCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGAC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGATC 20 0.0061444547 28.795 140-144 >>END_MODULE SRR18274409 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18274409_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 26.84875 32.0 32.0 32.0 2.0 32.0 2 30.4275 32.0 32.0 32.0 27.0 32.0 3 32.82875 37.0 32.0 37.0 27.0 37.0 4 34.43 37.0 37.0 37.0 32.0 37.0 5 34.6525 37.0 37.0 37.0 32.0 37.0 6 37.22625 41.0 37.0 41.0 27.0 41.0 7 37.804 41.0 37.0 41.0 32.0 41.0 8 38.0995 41.0 37.0 41.0 32.0 41.0 9 37.2365 41.0 37.0 41.0 27.0 41.0 10-14 38.111149999999995 41.0 39.4 41.0 31.0 41.0 15-19 37.99335 41.0 38.6 41.0 29.0 41.0 20-24 37.78585 41.0 37.0 41.0 28.0 41.0 25-29 37.718650000000004 41.0 37.8 41.0 28.0 41.0 30-34 37.7935 41.0 37.0 41.0 28.0 41.0 35-39 37.8848 41.0 37.0 41.0 27.0 41.0 40-44 37.7614 41.0 37.0 41.0 27.0 41.0 45-49 37.763549999999995 41.0 37.0 41.0 27.0 41.0 50-54 37.822950000000006 41.0 37.0 41.0 27.0 41.0 55-59 37.55785 41.0 37.0 41.0 27.0 41.0 60-64 37.317049999999995 41.0 37.0 41.0 27.0 41.0 65-69 37.73925 41.0 37.8 41.0 28.0 41.0 70-74 38.366 41.0 41.0 41.0 32.0 41.0 75-79 37.42465 41.0 37.8 41.0 27.0 41.0 80-84 38.0168 41.0 39.4 41.0 30.0 41.0 85-89 37.8515 41.0 38.6 41.0 29.0 41.0 90-94 38.0603 41.0 40.2 41.0 31.0 41.0 95-99 38.06485 41.0 40.2 41.0 31.0 41.0 100-104 37.78855 41.0 37.8 41.0 29.0 41.0 105-109 37.9156 41.0 37.8 41.0 30.0 41.0 110-114 37.73780000000001 41.0 37.0 41.0 28.0 41.0 115-119 37.58715 41.0 37.0 41.0 28.0 41.0 120-124 36.6612 41.0 36.0 41.0 23.0 41.0 125-129 36.6545 41.0 37.0 41.0 24.0 41.0 130-134 36.89155000000001 41.0 37.0 41.0 26.0 41.0 135-139 36.55365 41.0 37.0 41.0 23.0 41.0 140-144 36.1693 41.0 35.0 41.0 22.0 41.0 145-149 35.661699999999996 41.0 32.0 41.0 22.0 41.0 150 35.75475 41.0 32.0 41.0 22.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 3.0 17 10.0 18 13.0 19 15.0 20 9.0 21 22.0 22 20.0 23 25.0 24 39.0 25 39.0 26 40.0 27 48.0 28 50.0 29 71.0 30 63.0 31 75.0 32 97.0 33 113.0 34 124.0 35 147.0 36 185.0 37 227.0 38 252.0 39 511.0 40 1802.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 17.263751763046546 29.393511988716504 16.530324400564176 36.81241184767278 2 22.725 23.25 35.05 18.975 3 19.075 26.400000000000002 29.2 25.324999999999996 4 21.099999999999998 25.575 28.125 25.2 5 25.525 25.0 26.400000000000002 23.075000000000003 6 23.724999999999998 26.85 24.474999999999998 24.95 7 23.150000000000002 27.1 25.7 24.05 8 20.775 23.474999999999998 29.925 25.825 9 21.725 23.775 30.175 24.325 10-14 23.16 25.365 26.369999999999997 25.105 15-19 24.185000000000002 25.535000000000004 25.085 25.195 20-24 23.745 25.445 25.235000000000003 25.575 25-29 23.765 24.275 25.985000000000003 25.974999999999998 30-34 24.385 24.990000000000002 25.465 25.16 35-39 24.165 25.3 24.575 25.96 40-44 24.98 25.115 24.665 25.240000000000002 45-49 24.310000000000002 25.255 25.119999999999997 25.314999999999998 50-54 24.807442232669803 24.68740622186656 25.22256677003101 25.282584775432632 55-59 24.555 24.97 24.834999999999997 25.64 60-64 24.67 24.775 25.14 25.415 65-69 24.68 25.025 24.845 25.45 70-74 25.095 25.074999999999996 24.85 24.98 75-79 25.0 24.87 24.87 25.259999999999998 80-84 25.019999999999996 25.085 24.135 25.759999999999998 85-89 24.495 25.430000000000003 24.825 25.25 90-94 24.575 25.8 24.765 24.86 95-99 24.675 25.34 24.43 25.555 100-104 24.779999999999998 25.564999999999998 24.89 24.765 105-109 24.41 25.525 24.560000000000002 25.505 110-114 24.725 24.95 25.374999999999996 24.95 115-119 24.925 24.92 24.43 25.724999999999998 120-124 24.945 25.6 25.0 24.455 125-129 25.06 24.905 24.81 25.224999999999998 130-134 24.8 25.080000000000002 25.215 24.905 135-139 25.28 24.785 24.95 24.985 140-144 24.925 25.564999999999998 24.8 24.709999999999997 145-149 25.035 26.055 24.474999999999998 24.435000000000002 150 25.1 27.750000000000004 24.0 23.150000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 1.0 3 1.0 4 0.5 5 1.0 6 0.5 7 0.5 8 1.0 9 1.0 10 1.0 11 0.5 12 0.5 13 0.5 14 0.5 15 1.5 16 1.5 17 1.0 18 1.0 19 1.5 20 2.5 21 2.0 22 0.5 23 1.0 24 3.0 25 3.0 26 7.0 27 8.0 28 7.0 29 9.0 30 10.5 31 16.5 32 19.0 33 16.5 34 24.5 35 35.5 36 36.5 37 51.5 38 67.0 39 82.5 40 101.0 41 121.5 42 137.5 43 142.5 44 177.5 45 205.5 46 186.0 47 174.5 48 178.5 49 162.5 50 167.0 51 172.5 52 159.5 53 158.5 54 138.5 55 122.0 56 133.5 57 132.0 58 97.5 59 95.5 60 97.0 61 72.5 62 65.5 63 57.0 64 49.0 65 40.5 66 26.5 67 28.5 68 39.5 69 33.0 70 25.0 71 19.0 72 12.0 73 8.5 74 7.5 75 5.5 76 8.0 77 10.5 78 6.5 79 2.5 80 1.5 81 1.0 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 warn #Base N-Count 1 11.375 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 0.03 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 90.0 #Duplication Level Percentage of deduplicated Percentage of total 1 91.27777777777779 82.15 2 6.944444444444445 12.5 3 1.3055555555555556 3.5249999999999995 4 0.3611111111111111 1.3 5 0.08333333333333334 0.375 6 0.027777777777777776 0.15 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 CTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCGCCGAAGCGGCCTT 6 0.15 No Hit ATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTT 5 0.125 No Hit AAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCGCCGAAGCGGC 5 0.125 No Hit ATTTCACCTTCGCCGAAGCTCCCACTTATCCTACACCTCTCAAGTCATTT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAATCAA 30 0.0018524947 71.95 7 AAAAAAA 30 0.0015092845 23.983332 60-64 AGCGGCC 50 0.001399471 17.268 135-139 >>END_MODULE Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772302 spots for SRR18274409.sra Written 772302 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra Read 772299 spots for SRR18274409.sra Written 772299 spots for SRR18274409.sra SRR ids: ['SRR18274409.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_j2xebxl0 SRR18274409.sra spots: 15445983 blocks: [[1, 772299], [772300, 1544598], [1544599, 2316897], [2316898, 3089196], [3089197, 3861495], [3861496, 4633794], [4633795, 5406093], [5406094, 6178392], [6178393, 6950691], [6950692, 7722990], [7722991, 8495289], [8495290, 9267588], [9267589, 10039887], [10039888, 10812186], [10812187, 11584485], [11584486, 12356784], [12356785, 13129083], [13129084, 13901382], [13901383, 14673681], [14673682, 15445983]] SRR18274409 file size 5668954 SRR18274409 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 SRR18274409 SRR18274409_1.fastq SRR18274409_2.fastq Input file: SRR18274409_1.fastq Paired file: SRR18274409_2.fastq trimmed: SRR18274409-trimmed-pair1.fastq, SRR18274409-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 Tue Feb 11 01:07:27 2025 >> started Tue Feb 11 01:07:45 2025 >> done (18.198s) 15445983 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 15445983 (100.00%) read pairs available; of these: 2185280 (14.15%) trimmed read pairs available after processing 13260703 (85.85%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 27 1 0.00% 28 0 0.00% 29 0 0.00% 30 0 0.00% 31 0 0.00% 32 0 0.00% 33 0 0.00% 34 0 0.00% 35 0 0.00% 36 0 0.00% 37 0 0.00% 38 0 0.00% 39 0 0.00% 40 0 0.00% 41 0 0.00% 42 0 0.00% 43 0 0.00% 44 0 0.00% 45 0 0.00% 46 0 0.00% 47 0 0.00% 48 0 0.00% 49 0 0.00% 50 0 0.00% 51 0 0.00% 52 0 0.00% 53 1 0.00% 54 0 0.00% 55 0 0.00% 56 0 0.00% 57 0 0.00% 58 1 0.00% 59 0 0.00% 60 0 0.00% 61 0 0.00% 62 0 0.00% 63 0 0.00% 64 0 0.00% 65 0 0.00% 66 0 0.00% 67 0 0.00% 68 0 0.00% 69 0 0.00% 70 0 0.00% 71 0 0.00% 72 0 0.00% 73 0 0.00% 74 0 0.00% 75 0 0.00% 76 0 0.00% 77 0 0.00% 78 0 0.00% 79 0 0.00% 80 0 0.00% 81 0 0.00% 82 0 0.00% 83 0 0.00% 84 0 0.00% 85 0 0.00% 86 0 0.00% 87 1 0.00% 88 0 0.00% 89 0 0.00% 90 0 0.00% 91 0 0.00% 92 1 0.00% 93 0 0.00% 94 0 0.00% 95 0 0.00% 96 0 0.00% 97 0 0.00% 98 0 0.00% 99 0 0.00% 100 0 0.00% 101 0 0.00% 102 2 0.00% 103 0 0.00% 104 1 0.00% 105 0 0.00% 106 0 0.00% 107 0 0.00% 108 0 0.00% 109 0 0.00% 110 0 0.00% 111 0 0.00% 112 1 0.00% 113 0 0.00% 114 0 0.00% 115 0 0.00% 116 0 0.00% 117 0 0.00% 118 0 0.00% 119 1 0.00% 120 0 0.00% 121 0 0.00% 122 0 0.00% 123 0 0.00% 124 1 0.00% 125 3 0.00% 126 2 0.00% 127 0 0.00% 128 3 0.00% 129 5 0.00% 130 2 0.00% 131 3 0.00% 132 1 0.00% 133 0 0.00% 134 0 0.00% 135 1 0.00% 136 1 0.00% 137 1 0.00% 138 10 0.00% 139 92 0.00% 140 1971 0.01% 141 202046 1.31% 142 201689 1.31% 143 201046 1.30% 144 200870 1.30% 145 201390 1.30% 146 201533 1.30% 147 205094 1.33% 148 227164 1.47% 149 542342 3.51% 150 13260703 85.85% 15445983 reads passed initial QC criterion=sequence-density sequence-density=1.30 sequence-density-rank=1 fanout-score=2.53 fanout-score-rank=21 prefix-density=1.28 prefix-fanout=2.5 sequence=TTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCGGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGAAGGTGAAATACCACTACTTTTAACGTTATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGGACCCAAGGCCGCTTCGGCGGCCGATCCGGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACCTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=38 fanout-score=171.31 fanout-score-rank=1 prefix-density=2.63 prefix-fanout=1.3 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCTCCGCTT criterion=sequence-density sequence-density=1.29 sequence-density-rank=1 fanout-score=2.50 fanout-score-rank=28 prefix-density=1.27 prefix-fanout=2.5 sequence=TTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCGGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGAAGGTGAAATACCACTACTTTTAACGTTATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGGACCCAAGGCCGCTTCGGCGGCCGATCCGGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACCTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAG criterion=fanout-score sequence-density=0.03 sequence-density-rank=39 fanout-score=123.65 fanout-score-rank=1 prefix-density=2.53 prefix-fanout=1.4 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCTCCGCTT SRR18274409 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 01:09:05 Started mapping on | Feb 11 01:09:05 Finished on | Feb 11 01:15:03 Mapping speed, Million of reads per hour | 155.32 Number of input reads | 15445983 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 4006061 Uniquely mapped reads % | 25.94% Average mapped length | 280.79 Number of splices: Total | 2147485 Number of splices: Annotated (sjdb) | 2079065 Number of splices: GT/AG | 2094040 Number of splices: GC/AG | 28133 Number of splices: AT/AC | 2432 Number of splices: Non-canonical | 22880 Mismatch rate per base, % | 0.70% Deletion rate per base | 0.01% Deletion average length | 2.13 Insertion rate per base | 0.03% Insertion average length | 3.49 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 368160 % of reads mapped to multiple loci | 2.38% Number of reads mapped to too many loci | 7499605 % of reads mapped to too many loci | 48.55% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 12.02% % of reads unmapped: other | 11.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 11071762 11071762 11071762 N_multimapping 368160 368160 368160 N_noFeature 1259783 2600391 2622961 N_ambiguous 68447 13018 13050 UnstrandedReadsAssigned:2677831 PositiveStrandReadsAssigned:1392652 NegativeStrandReadsAssigned:1370050 Dataset is classified unstranded MeadianReadLen=142 20thPercentileLength=142 echo kmer=137 SRR18274409 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: SRR18274409-trimmed-pair1.fastq SRR18274409-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,445,983 reads, 12,268,834 reads pseudoaligned [quant] estimated average fragment length: 182.426 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,026 rounds 52401 SRR18274409.ke.tsv 34699 SRR18274409.se.tsv 87100 total ==> SRR18274409.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1836.57 179 5.01971 Potri.005G024800.1.v4.1 1035 853.574 39 2.35319 Potri.004G059700.1.v4.1 961 779.58 7 0.462457 Potri.007G009000.2.v4.1 1416 1234.57 0 0 Potri.003G141000.2.v4.1 2943 2761.57 48.4278 0.903176 Potri.016G087400.1.v4.1 270 96.7748 135 71.8465 Potri.015G069301.1.v4.1 564 382.632 0 0 Potri.010G195200.1.v4.1 1773 1591.57 4 0.12944 Potri.012G127500.1.v4.1 977 795.58 33 2.13631 ==> SRR18274409.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 138 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 96 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR18274409 completed mapping pipeline successfully