Starting /dee2/code/volunteer_pipeline.sh SRR7230818 current disk space = 3054661328896 free memory = 1507590120 SRR7230818 SRAfilesize a91a96ba0134007d29135cde0ffa3a75 SRR7230818.sra SRR7230818.sra file validated SRR7230818 is paired end SRR7230818 is conventional basespace SRR7230818 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230818_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.50125 34.0 34.0 34.0 33.0 34.0 2 33.573 34.0 34.0 34.0 33.0 34.0 3 33.6125 34.0 34.0 34.0 33.0 34.0 4 33.57225 34.0 34.0 34.0 33.0 34.0 5 33.5585 34.0 34.0 34.0 33.0 34.0 6 37.235 38.0 38.0 38.0 36.0 38.0 7 37.4265 38.0 38.0 38.0 37.0 38.0 8 37.4695 38.0 38.0 38.0 38.0 38.0 9 37.506 38.0 38.0 38.0 38.0 38.0 10-14 37.43955 38.0 38.0 38.0 37.4 38.0 15-19 37.46725000000001 38.0 38.0 38.0 38.0 38.0 20-24 37.30995 38.0 38.0 38.0 37.4 38.0 25-29 37.0416 38.0 38.0 38.0 36.0 38.0 30-34 36.984700000000004 38.0 38.0 38.0 36.0 38.0 35-39 36.893950000000004 38.0 38.0 38.0 35.8 38.0 40-44 36.6408 38.0 38.0 38.0 34.6 38.0 45-49 36.63535 38.0 37.8 38.0 34.2 38.0 50-54 36.8822 38.0 37.8 38.0 35.4 38.0 55-59 37.0598 38.0 38.0 38.0 36.2 38.0 60-64 37.025150000000004 38.0 38.0 38.0 36.0 38.0 65-69 36.98685 38.0 38.0 38.0 36.0 38.0 70-74 33.18065 38.0 34.8 38.0 15.6 38.0 75-79 33.83245 38.0 37.0 38.0 22.4 38.0 80-84 35.794200000000004 38.0 38.0 38.0 31.2 38.0 85-89 36.5769 38.0 38.0 38.0 35.4 38.0 90-94 36.5844 38.0 38.0 38.0 35.0 38.0 95-99 36.60725 38.0 38.0 38.0 35.0 38.0 100-104 36.38595 38.0 38.0 38.0 34.2 38.0 105-109 36.37135 38.0 38.0 38.0 34.4 38.0 110-114 36.1815 38.0 37.8 38.0 33.4 38.0 115-119 35.263549999999995 38.0 36.2 38.0 28.6 38.0 120-124 35.47420000000001 38.0 36.6 38.0 30.8 38.0 125-129 35.2043 38.0 36.0 38.0 29.2 38.0 130-134 34.84125 38.0 35.4 38.0 27.6 38.0 135-139 35.1325 38.0 36.0 38.0 30.4 38.0 140-144 34.34915 38.0 35.2 38.0 24.8 38.0 145-149 33.9159 38.0 33.6 38.0 25.6 38.0 150-151 29.97825 35.5 27.0 38.0 11.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 1.0 10 1.0 11 3.0 12 4.0 13 3.0 14 1.0 15 2.0 16 1.0 17 6.0 18 8.0 19 7.0 20 9.0 21 6.0 22 3.0 23 6.0 24 10.0 25 18.0 26 17.0 27 24.0 28 29.0 29 30.0 30 33.0 31 53.0 32 90.0 33 127.0 34 270.0 35 371.0 36 801.0 37 2065.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.13503375843961 15.328832208052013 13.053263315828959 31.48287071767942 2 21.175 18.875 32.550000000000004 27.400000000000002 3 19.3 25.874999999999996 26.625 28.199999999999996 4 20.974999999999998 31.75 24.325 22.95 5 20.8 34.325 24.675 20.200000000000003 6 18.099999999999998 35.199999999999996 26.450000000000003 20.25 7 14.35 23.825 42.15 19.675 8 17.150000000000002 25.2 30.075000000000003 27.575 9 16.625 25.8 31.525 26.05 10-14 19.515 30.45 26.38 23.655 15-19 19.325966298314913 29.466473323666182 27.366368318415923 23.84119205960298 20-24 19.675 29.69 26.974999999999998 23.66 25-29 19.235 28.9 27.735 24.13 30-34 19.735 29.459999999999997 26.915 23.89 35-39 19.671556601411904 28.904020427577233 27.33690482150904 24.087518149501825 40-44 20.42854275391409 29.034524287434767 27.13769570453633 23.399237254114812 45-49 20.088035214085632 29.371748699479795 26.54561824729892 23.994597839135654 50-54 19.67 29.435 27.18 23.715 55-59 19.615 28.910000000000004 27.46 24.015 60-64 20.064999999999998 28.57 27.49 23.875 65-69 19.965 28.765 27.215 24.055 70-74 19.751097283182396 29.42941274515251 27.17928773820768 23.640202233457412 75-79 19.67151115673456 29.207412610081583 26.732940731536008 24.38813550164785 80-84 20.08892068683565 28.12755519215045 27.826042518397383 23.957481602616518 85-89 20.03812964077865 28.36644591611479 27.11719847481437 24.478225968292193 90-94 19.93 27.98 27.544999999999998 24.545 95-99 20.45 28.155 26.945000000000004 24.45 100-104 20.315 28.384999999999998 26.955000000000002 24.345 105-109 19.895 28.689999999999998 26.52 24.895 110-114 20.86 28.78 26.465 23.895 115-119 20.674999999999997 28.810000000000002 26.240000000000002 24.275 120-124 21.255 28.32 26.090000000000003 24.335 125-129 21.38 27.83 26.484999999999996 24.305 130-134 21.245 28.54 25.840000000000003 24.375 135-139 20.8 28.49 25.724999999999998 24.985 140-144 21.445 28.305000000000003 25.145 25.105 145-149 21.16 29.01 25.424999999999997 24.404999999999998 150-151 20.962500000000002 28.775000000000002 24.587500000000002 25.674999999999997 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 4.0 1 3.0 2 1.0 3 1.0 4 1.5 5 1.0 6 0.5 7 1.0 8 1.0 9 1.0 10 1.0 11 0.5 12 0.5 13 0.0 14 0.5 15 1.0 16 1.0 17 0.5 18 0.0 19 0.5 20 2.0 21 3.0 22 3.0 23 4.0 24 5.0 25 7.5 26 7.5 27 10.5 28 15.5 29 20.5 30 37.5 31 47.0 32 52.0 33 67.5 34 82.0 35 97.5 36 111.5 37 126.5 38 151.0 39 166.5 40 189.0 41 205.0 42 204.5 43 202.0 44 221.5 45 232.5 46 210.5 47 202.5 48 207.0 49 182.0 50 135.5 51 118.5 52 119.0 53 116.5 54 102.0 55 80.5 56 54.5 57 38.5 58 40.5 59 33.0 60 18.5 61 18.5 62 15.0 63 6.0 64 4.0 65 2.0 66 0.0 67 1.0 68 1.0 69 0.0 70 0.5 71 1.0 72 0.5 73 0.0 74 0.5 75 0.5 76 0.0 77 0.0 78 0.0 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 warn #Base N-Count 1 0.025 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 0.005 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.135 40-44 0.36 45-49 0.04 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 10.005 75-79 7.455 80-84 2.16 85-89 0.33999999999999997 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.975 #Duplication Level Percentage of deduplicated Percentage of total 1 96.9523313362855 93.05 2 2.5527481114873662 4.9 3 0.23443605105496224 0.675 4 0.10419380046887211 0.4 5 0.052096900234436055 0.25 6 0.052096900234436055 0.3 7 0.0 0.0 8 0.026048450117218028 0.2 9 0.026048450117218028 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGC 9 0.22499999999999998 TruSeq Adapter, Index 13 (98% over 50bp) GCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGGA 8 0.2 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit CCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCT 6 0.15 No Hit CTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGACTA 5 0.125 No Hit GGCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.21250000000000002 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.2625 0.0 0.0 0.0 0.0 84-85 0.3125 0.0 0.0 0.0 0.0 86-87 0.3625 0.0 0.0 0.0 0.0 88-89 0.4625 0.0 0.0 0.0 0.0 90-91 0.675 0.0 0.0 0.0 0.0 92-93 0.8 0.0 0.0 0.0 0.0 94-95 0.9875 0.0 0.0 0.0 0.0 96-97 1.1875 0.0 0.0 0.0 0.0 98-99 1.375 0.0 0.0 0.0 0.0 100-101 1.575 0.0 0.0 0.0 0.0 102-103 1.8875 0.0 0.0 0.0 0.0 104-105 2.3625 0.0 0.0 0.0 0.0 106-107 2.6625 0.0 0.0 0.0 0.0 108-109 3.0374999999999996 0.0 0.0 0.0 0.0 110-111 3.5625 0.0 0.0 0.0 0.0 112-113 3.825 0.0 0.0 0.0 0.0 114-115 4.3 0.0 0.0 0.0 0.0 116-117 4.7875 0.0 0.0 0.0 0.0 118-119 5.2625 0.0 0.0 0.0 0.0 120-121 5.6375 0.0 0.0 0.0 0.0 122-123 6.5125 0.0 0.0 0.0 0.0 124-125 7.5375 0.0 0.0 0.0 0.0 126-127 8.162500000000001 0.0 0.0 0.0 0.0 128-129 8.6625 0.0 0.0 0.0 0.0 130-131 9.4375 0.0 0.0 0.0 0.0 132-133 10.0625 0.0 0.0 0.0 0.0 134-135 10.725 0.0 0.0 0.0 0.0 136-137 11.2625 0.0 0.0 0.0 0.0 138-139 12.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7230818 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230818_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 32.7215 34.0 33.0 34.0 32.0 34.0 2 32.944 34.0 33.0 34.0 32.0 34.0 3 32.99825 34.0 33.0 34.0 33.0 34.0 4 32.847 34.0 33.0 34.0 33.0 34.0 5 32.90025 34.0 33.0 34.0 33.0 34.0 6 36.89025 38.0 38.0 38.0 37.0 38.0 7 36.86425 38.0 38.0 38.0 37.0 38.0 8 36.93 38.0 38.0 38.0 37.0 38.0 9 36.86975 38.0 38.0 38.0 37.0 38.0 10-14 36.54705 38.0 38.0 38.0 35.4 38.0 15-19 36.829699999999995 38.0 38.0 38.0 37.0 38.0 20-24 36.80865 38.0 38.0 38.0 37.0 38.0 25-29 36.78574999999999 38.0 38.0 38.0 37.0 38.0 30-34 36.7607 38.0 38.0 38.0 37.0 38.0 35-39 36.566250000000004 38.0 38.0 38.0 36.4 38.0 40-44 36.60205 38.0 38.0 38.0 36.8 38.0 45-49 36.52405 38.0 38.0 38.0 36.4 38.0 50-54 36.6234 38.0 38.0 38.0 36.8 38.0 55-59 36.4246 38.0 38.0 38.0 36.0 38.0 60-64 36.5971 38.0 38.0 38.0 36.8 38.0 65-69 36.41 38.0 38.0 38.0 36.4 38.0 70-74 36.280649999999994 38.0 38.0 38.0 36.0 38.0 75-79 36.363 38.0 38.0 38.0 35.6 38.0 80-84 36.359750000000005 38.0 38.0 38.0 36.0 38.0 85-89 36.26585 38.0 38.0 38.0 35.8 38.0 90-94 36.1779 38.0 38.0 38.0 35.2 38.0 95-99 36.00095 38.0 38.0 38.0 34.4 38.0 100-104 35.90755 38.0 38.0 38.0 34.0 38.0 105-109 35.80375 38.0 38.0 38.0 34.0 38.0 110-114 35.693799999999996 38.0 38.0 38.0 34.0 38.0 115-119 35.65925 38.0 38.0 38.0 33.4 38.0 120-124 35.34565 38.0 38.0 38.0 31.8 38.0 125-129 35.181850000000004 38.0 38.0 38.0 31.2 38.0 130-134 34.929700000000004 38.0 37.0 38.0 29.6 38.0 135-139 34.580799999999996 38.0 36.0 38.0 27.6 38.0 140-144 33.8918 38.0 35.6 38.0 22.6 38.0 145-149 32.42495 38.0 33.0 38.0 10.6 38.0 150-151 27.239874999999998 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 21.0 3 11.0 4 10.0 5 6.0 6 10.0 7 3.0 8 4.0 9 3.0 10 0.0 11 4.0 12 4.0 13 4.0 14 8.0 15 7.0 16 10.0 17 10.0 18 5.0 19 6.0 20 3.0 21 10.0 22 10.0 23 10.0 24 18.0 25 12.0 26 13.0 27 21.0 28 23.0 29 23.0 30 35.0 31 42.0 32 53.0 33 70.0 34 137.0 35 159.0 36 478.0 37 2757.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.0045294413689 17.765475591343733 17.31253145445395 21.917463512833418 2 27.500000000000004 23.275000000000002 29.275000000000002 19.950000000000003 3 21.975 29.2 29.65 19.175 4 26.05 32.725 21.975 19.25 5 26.0 35.099999999999994 21.3 17.599999999999998 6 22.175 34.75 24.099999999999998 18.975 7 20.724999999999998 19.8 39.225 20.25 8 23.400000000000002 23.5 27.125 25.974999999999998 9 23.45 25.5 27.85 23.200000000000003 10-14 25.169999999999998 26.919999999999998 25.81 22.1 15-19 24.725 27.515 26.775 20.985 20-24 24.845 27.689999999999998 27.224999999999998 20.24 25-29 24.67 27.74 26.779999999999998 20.810000000000002 30-34 24.595 27.575 27.310000000000002 20.52 35-39 24.560000000000002 26.740000000000002 27.46 21.240000000000002 40-44 25.124999999999996 27.42 27.26 20.195 45-49 24.467818682694716 27.08740295517155 27.563235662409213 20.881542699724516 50-54 24.712010417710108 27.296403886607234 27.481718922167687 20.509866773514975 55-59 24.603413654618475 27.379518072289155 27.23895582329317 20.778112449799195 60-64 24.365000000000002 27.66 27.49 20.485 65-69 24.753367719965947 27.247233211477788 27.407481596474536 20.59191747208173 70-74 24.483849902044508 26.829758376450496 27.75405636208369 20.93233535942131 75-79 24.075 27.560000000000002 27.665 20.7 80-84 24.6 26.755000000000003 28.375 20.27 85-89 24.62 26.845000000000002 28.1 20.435 90-94 24.325 27.805000000000003 27.779999999999998 20.09 95-99 24.95 26.974999999999998 27.875 20.200000000000003 100-104 24.959999999999997 27.224999999999998 27.744999999999997 20.07 105-109 24.29 27.779999999999998 27.73 20.200000000000003 110-114 24.52 27.57 27.805000000000003 20.105 115-119 24.985 27.705000000000002 27.6 19.71 120-124 24.755 27.88 28.01 19.355 125-129 25.16 27.625 27.655 19.56 130-134 26.08 27.68 27.045 19.195 135-139 26.57 27.165 27.084999999999997 19.18 140-144 26.095000000000002 27.68 26.875 19.35 145-149 26.87 27.195000000000004 26.895000000000003 19.040000000000003 150-151 27.762500000000003 28.749999999999996 25.387500000000003 18.099999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 1.0 10 1.0 11 0.5 12 1.0 13 0.5 14 0.5 15 1.0 16 0.5 17 0.0 18 0.0 19 0.5 20 1.0 21 1.5 22 1.5 23 1.5 24 2.5 25 3.0 26 2.5 27 1.5 28 3.5 29 7.0 30 10.0 31 16.0 32 20.0 33 27.0 34 48.0 35 68.0 36 81.0 37 85.5 38 105.5 39 140.5 40 168.5 41 202.5 42 222.5 43 229.0 44 234.0 45 218.5 46 224.0 47 249.5 48 244.5 49 216.0 50 173.0 51 155.5 52 152.5 53 141.0 54 132.0 55 100.5 56 76.0 57 60.0 58 42.5 59 37.0 60 24.5 61 21.0 62 19.0 63 9.5 64 5.5 65 2.5 66 1.0 67 1.0 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 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 0.65 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 0.17500000000000002 50-54 0.16999999999999998 55-59 0.4 60-64 0.0 65-69 0.155 70-74 0.46499999999999997 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.525 #Duplication Level Percentage of deduplicated Percentage of total 1 97.12509712509713 93.75 2 2.4087024087024087 4.65 3 0.3885003885003885 1.125 4 0.0259000259000259 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0259000259000259 0.17500000000000002 8 0.0259000259000259 0.2 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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 8 0.2 Illumina Single End PCR Primer 1 (100% over 50bp) CTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA 7 0.17500000000000002 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.2625 0.0 0.0 0.0 0.0 84-85 0.2875 0.0 0.0 0.0 0.0 86-87 0.325 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.625 0.0 0.0 0.0 0.0 92-93 0.75 0.0 0.0 0.0 0.0 94-95 0.95 0.0 0.0 0.0 0.0 96-97 1.1375 0.0 0.0 0.0 0.0 98-99 1.325 0.0 0.0 0.0 0.0 100-101 1.525 0.0 0.0 0.0 0.0 102-103 1.825 0.0 0.0 0.0 0.0 104-105 2.2625 0.0 0.0 0.0 0.0 106-107 2.575 0.0 0.0 0.0 0.0 108-109 2.9625000000000004 0.0 0.0 0.0 0.0 110-111 3.5250000000000004 0.0 0.0 0.0 0.0 112-113 3.7875 0.0 0.0 0.0 0.0 114-115 4.2875 0.0 0.0 0.0 0.0 116-117 4.7625 0.0 0.0 0.0 0.0 118-119 5.1875 0.0 0.0 0.0 0.0 120-121 5.5625 0.0 0.0 0.0 0.0 122-123 6.35 0.0 0.0 0.0 0.0 124-125 7.3375 0.0 0.0 0.0 0.0 126-127 7.949999999999999 0.0 0.0 0.0 0.0 128-129 8.4625 0.0 0.0 0.0 0.0 130-131 9.2875 0.0 0.0 0.0 0.0 132-133 9.925 0.0 0.0 0.0 0.0 134-135 10.6125 0.0 0.0 0.0 0.0 136-137 11.0875 0.0 0.0 0.0 0.0 138-139 11.725 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGGTCAG 10 0.0068910434 144.575 5 GACCCAC 10 0.0068910434 144.575 6 ACGGTGG 10 0.0068910434 144.575 9 >>END_MODULE Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra Read 648562 spots for SRR7230818.sra Written 648562 spots for SRR7230818.sra SRR ids: ['SRR7230818.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yu2j6ddh SRR7230818.sra spots: 12971240 blocks: [[1, 648562], [648563, 1297124], [1297125, 1945686], [1945687, 2594248], [2594249, 3242810], [3242811, 3891372], [3891373, 4539934], [4539935, 5188496], [5188497, 5837058], [5837059, 6485620], [6485621, 7134182], [7134183, 7782744], [7782745, 8431306], [8431307, 9079868], [9079869, 9728430], [9728431, 10376992], [10376993, 11025554], [11025555, 11674116], [11674117, 12322678], [12322679, 12971240]] SRR7230818 file size 4373827 SRR7230818 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 SRR7230818 SRR7230818_1.fastq SRR7230818_2.fastq Input file: SRR7230818_1.fastq Paired file: SRR7230818_2.fastq trimmed: SRR7230818-trimmed-pair1.fastq, SRR7230818-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 09:38:44 2025 >> started Tue Feb 11 09:38:58 2025 >> done (14.689s) 12971240 read pairs processed; of these: 47453 ( 0.37%) short read pairs filtered out after trimming by size control 63636 ( 0.49%) empty read pairs filtered out after trimming by size control 12860151 (99.14%) read pairs available; of these: 6416074 (49.89%) trimmed read pairs available after processing 6444077 (50.11%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 5 0.00% 20 7 0.00% 21 11 0.00% 22 27 0.00% 23 14 0.00% 24 19 0.00% 25 23 0.00% 26 18 0.00% 27 26 0.00% 28 18 0.00% 29 39 0.00% 30 26 0.00% 31 31 0.00% 32 25 0.00% 33 28 0.00% 34 23 0.00% 35 44 0.00% 36 39 0.00% 37 35 0.00% 38 50 0.00% 39 35 0.00% 40 64 0.00% 41 63 0.00% 42 70 0.00% 43 59 0.00% 44 84 0.00% 45 96 0.00% 46 125 0.00% 47 126 0.00% 48 133 0.00% 49 155 0.00% 50 163 0.00% 51 193 0.00% 52 203 0.00% 53 219 0.00% 54 243 0.00% 55 252 0.00% 56 253 0.00% 57 326 0.00% 58 367 0.00% 59 393 0.00% 60 418 0.00% 61 487 0.00% 62 530 0.00% 63 657 0.01% 64 700 0.01% 65 870 0.01% 66 1096 0.01% 67 1383 0.01% 68 2487 0.02% 69 6948 0.05% 70 9837 0.08% 71 7600 0.06% 72 4392 0.03% 73 3025 0.02% 74 2622 0.02% 75 2689 0.02% 76 2774 0.02% 77 3093 0.02% 78 3172 0.02% 79 3794 0.03% 80 4015 0.03% 81 4477 0.03% 82 5004 0.04% 83 5966 0.05% 84 8816 0.07% 85 10385 0.08% 86 11517 0.09% 87 12506 0.10% 88 12767 0.10% 89 13427 0.10% 90 13673 0.11% 91 14304 0.11% 92 14887 0.12% 93 16274 0.13% 94 16554 0.13% 95 17650 0.14% 96 18751 0.15% 97 18942 0.15% 98 20402 0.16% 99 21557 0.17% 100 22669 0.18% 101 23018 0.18% 102 25267 0.20% 103 26635 0.21% 104 28399 0.22% 105 30686 0.24% 106 30235 0.24% 107 30563 0.24% 108 32062 0.25% 109 35225 0.27% 110 35036 0.27% 111 35482 0.28% 112 37112 0.29% 113 39550 0.31% 114 39877 0.31% 115 42075 0.33% 116 42678 0.33% 117 42118 0.33% 118 43768 0.34% 119 44605 0.35% 120 46723 0.36% 121 47000 0.37% 122 49365 0.38% 123 50838 0.40% 124 53126 0.41% 125 54026 0.42% 126 55339 0.43% 127 56094 0.44% 128 57486 0.45% 129 58957 0.46% 130 59863 0.47% 131 61226 0.48% 132 64072 0.50% 133 66434 0.52% 134 68775 0.53% 135 71312 0.55% 136 73073 0.57% 137 76316 0.59% 138 77718 0.60% 139 79682 0.62% 140 81552 0.63% 141 87344 0.68% 142 89762 0.70% 143 97235 0.76% 144 106990 0.83% 145 120224 0.93% 146 139268 1.08% 147 173129 1.35% 148 235452 1.83% 149 433565 3.37% 150 2612487 20.31% 151 6444077 50.11% 12860151 reads passed initial QC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=37 prefix-density=0.47 prefix-fanout=1.9 sequence=GTTAGGGTAAGCTTTCTTCGCCTCCTCGAGCTCAATCAGCACCTGAGATGCCTCAGTGCATCCAAACATGGGTAGTTTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGGGACTGGTGGTGCTCGCGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=73.39 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=1.9 sequence=AGGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTATGCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGGCCGGACCGCTGGCAACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCAGCACCTGTCTCACGGTTCCCGAAGG criterion=sequence-density sequence-density=0.94 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=33 prefix-density=0.97 prefix-fanout=2.0 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=59.58 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=7.8 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCC SRR7230818 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 09:39:49 Started mapping on | Feb 11 09:39:50 Finished on | Feb 11 09:42:25 Mapping speed, Million of reads per hour | 298.69 Number of input reads | 12860151 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 10640033 Uniquely mapped reads % | 82.74% Average mapped length | 289.56 Number of splices: Total | 8236865 Number of splices: Annotated (sjdb) | 8047450 Number of splices: GT/AG | 8058926 Number of splices: GC/AG | 139809 Number of splices: AT/AC | 6228 Number of splices: Non-canonical | 31902 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.63 Insertion rate per base | 0.03% Insertion average length | 2.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 323981 % of reads mapped to multiple loci | 2.52% Number of reads mapped to too many loci | 87130 % of reads mapped to too many loci | 0.68% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 13.80% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1941460 1941460 1941460 N_multimapping 323981 323981 323981 N_noFeature 281130 10427531 347725 N_ambiguous 222019 716 75910 UnstrandedReadsAssigned:10136884 PositiveStrandReadsAssigned:211786 NegativeStrandReadsAssigned:10216398 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=145 echo kmer=141 SRR7230818 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: SRR7230818-trimmed-pair1.fastq SRR7230818-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,860,151 reads, 10,407,501 reads pseudoaligned [quant] estimated average fragment length: 212.293 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,150 rounds 52401 SRR7230818.ke.tsv 34699 SRR7230818.se.tsv 87100 total ==> SRR7230818.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1806.71 468 22.0255 Potri.005G024800.1.v4.1 1035 823.707 130 13.4195 Potri.004G059700.1.v4.1 961 749.732 9 1.02071 Potri.007G009000.2.v4.1 1416 1204.71 0 0 Potri.003G141000.2.v4.1 2943 2731.71 429 13.3534 Potri.016G087400.1.v4.1 270 92.8114 460.617 421.994 Potri.015G069301.1.v4.1 564 355.231 0 0 Potri.010G195200.1.v4.1 1773 1561.71 77 4.19236 Potri.012G127500.1.v4.1 977 765.722 347 38.5324 ==> SRR7230818.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 310 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 274 Potri.001G212900.v4.1 72 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR7230818 completed mapping pipeline successfully