Starting /dee2/code/volunteer_pipeline.sh ERR3317443 current disk space = 1525107523584 free memory = 1602281964 ERR3317443 SRAfilesize c5c4c8dc110b63982b56aa33b849f7c9 ERR3317443.sra ERR3317443.sra file validated ERR3317443 is paired end ERR3317443 is conventional basespace ERR3317443 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317443_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.4075 34.0 31.0 34.0 30.0 34.0 2 32.23775 34.0 31.0 34.0 30.0 34.0 3 32.871 34.0 31.0 34.0 31.0 34.0 4 36.4205 37.0 37.0 37.0 35.0 37.0 5 36.44875 37.0 37.0 37.0 35.0 37.0 6 36.45125 37.0 37.0 37.0 35.0 37.0 7 36.4715 37.0 37.0 37.0 35.0 37.0 8 36.473 37.0 37.0 37.0 35.0 37.0 9 38.298 39.0 39.0 39.0 37.0 39.0 10-11 38.277875 39.0 39.0 39.0 37.0 39.0 12-13 38.2095 39.0 39.0 39.0 37.0 39.0 14-15 39.743 41.0 40.0 41.0 37.0 41.0 16-17 39.75975 41.0 40.0 41.0 37.5 41.0 18-19 39.759125 41.0 40.0 41.0 37.5 41.0 20-21 39.621750000000006 41.0 40.0 41.0 37.0 41.0 22-23 39.55925 41.0 40.0 41.0 37.0 41.0 24-25 39.448125000000005 41.0 40.0 41.0 36.5 41.0 26-27 39.29 41.0 39.0 41.0 36.0 41.0 28-29 39.07725 41.0 39.0 41.0 35.5 41.0 30-31 38.95025 40.5 39.0 41.0 35.0 41.0 32-33 38.61725 40.0 38.0 41.0 34.5 41.0 34-35 38.53275 40.0 38.0 41.0 35.0 41.0 36-37 38.388875 40.0 38.0 41.0 34.0 41.0 38-39 38.050875 40.0 38.0 41.0 33.5 41.0 40-41 37.827625 40.0 37.5 41.0 33.0 41.0 42-43 37.88775 40.0 38.0 41.0 33.0 41.0 44-45 37.77175 40.0 37.5 41.0 33.0 41.0 46-47 37.491625 40.0 37.0 41.0 32.5 41.0 48-49 37.095749999999995 40.0 36.0 41.0 31.5 41.0 50-51 37.440875000000005 40.0 36.0 41.0 32.5 41.0 52-53 37.345625 40.0 36.0 41.0 33.0 41.0 54-55 37.1295 39.5 35.0 41.0 33.0 41.0 56-57 36.77225 39.0 35.0 41.0 32.0 41.0 58-59 36.446250000000006 39.0 35.0 41.0 31.5 41.0 60-61 36.098625 37.5 35.0 41.0 31.0 41.0 62-63 35.692125000000004 37.0 35.0 40.0 31.0 41.0 64-65 35.2015 36.5 35.0 40.0 30.0 41.0 66-67 34.880375 36.0 35.0 39.0 29.5 41.0 68-69 34.47925 35.5 34.0 39.0 29.5 41.0 70-71 34.066 35.0 34.0 37.5 29.0 40.0 72-73 33.765125 35.0 34.0 37.0 29.0 39.0 74-75 33.39625 35.0 34.0 37.0 29.0 39.0 76-77 32.133875 34.5 32.5 35.5 25.5 37.0 78-79 32.577 35.0 33.0 36.0 27.0 37.0 80-81 32.362375 35.0 33.0 35.0 26.5 37.0 82-83 32.097125000000005 35.0 33.0 35.0 26.0 36.0 84-85 31.791375000000002 35.0 33.0 35.0 25.0 36.0 86-87 31.52825 35.0 33.0 35.0 24.0 36.0 88-89 31.326 35.0 33.0 35.0 24.0 36.0 90-91 31.122999999999998 35.0 33.0 35.0 22.0 35.0 92-93 30.890625 35.0 33.0 35.0 20.0 35.0 94-95 30.620874999999998 35.0 32.0 35.0 17.5 35.0 96-97 30.25175 35.0 32.0 35.0 4.5 35.0 98-99 29.851750000000003 35.0 32.0 35.0 2.0 35.0 100-101 27.625124999999997 33.0 27.5 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 3 0.0 4 0.0 5 1.0 6 0.0 7 2.0 8 0.0 9 5.0 10 3.0 11 11.0 12 8.0 13 8.0 14 6.0 15 12.0 16 14.0 17 11.0 18 15.0 19 9.0 20 18.0 21 8.0 22 23.0 23 12.0 24 16.0 25 21.0 26 33.0 27 45.0 28 45.0 29 51.0 30 49.0 31 77.0 32 80.0 33 128.0 34 182.0 35 300.0 36 539.0 37 1054.0 38 1075.0 39 137.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 28.811777076761302 26.34069400630915 18.08622502628812 26.76130389064143 2 27.575 25.575 17.175 29.675 3 26.275 26.75 17.75 29.225 4 27.425 25.05 17.5 30.025000000000002 5 29.025000000000002 25.674999999999997 15.375 29.925 6 29.025000000000002 27.575 18.475 24.925 7 30.175 23.5 22.15 24.175 8 32.125 24.275 24.099999999999998 19.5 9 32.425 26.875 24.6 16.1 10-11 34.137499999999996 25.900000000000002 21.825 18.1375 12-13 31.087500000000002 25.662499999999998 23.7875 19.4625 14-15 27.8875 25.7875 24.6875 21.637500000000003 16-17 27.762500000000003 25.387500000000003 24.375 22.475 18-19 25.4 26.6125 25.9875 22.0 20-21 25.7125 26.625 26.025 21.637500000000003 22-23 25.374999999999996 26.8 25.525 22.3 24-25 25.45 26.137500000000003 25.7125 22.7 26-27 25.55 26.237500000000004 25.687500000000004 22.525000000000002 28-29 27.037499999999998 25.55 24.6125 22.8 30-31 25.587500000000002 26.4125 25.687500000000004 22.3125 32-33 25.874999999999996 25.887500000000003 25.7625 22.475 34-35 25.424999999999997 26.2875 24.3 23.9875 36-37 25.8 26.25 25.4875 22.4625 38-39 26.125 26.35 25.387500000000003 22.1375 40-41 25.837500000000002 26.3 24.6625 23.200000000000003 42-43 25.8125 25.8625 25.2875 23.0375 44-45 27.037499999999998 25.387500000000003 25.650000000000002 21.925 46-47 26.650000000000002 25.05 24.5625 23.7375 48-49 26.400000000000002 26.125 24.637500000000003 22.8375 50-51 25.55 26.875 24.4 23.175 52-53 25.687500000000004 26.437500000000004 24.8 23.075000000000003 54-55 26.900000000000002 26.150000000000002 24.725 22.225 56-57 25.7875 26.887499999999996 24.425 22.900000000000002 58-59 25.8125 27.037499999999998 24.325 22.825 60-61 25.85 26.2875 24.7375 23.125 62-63 25.7875 27.175 24.7 22.3375 64-65 26.487500000000004 26.5125 24.349999999999998 22.650000000000002 66-67 25.275 26.1 24.875 23.75 68-69 26.6 25.85 24.95 22.6 70-71 25.074999999999996 26.724999999999998 24.45 23.75 72-73 25.8 26.5875 24.9875 22.625 74-75 25.25 27.5125 24.587500000000002 22.650000000000002 76-77 25.5 27.3625 24.587500000000002 22.55 78-79 26.437500000000004 26.437500000000004 25.087500000000002 22.037499999999998 80-81 25.337500000000002 26.625 24.349999999999998 23.6875 82-83 26.087500000000002 26.875 23.6125 23.425 84-85 26.237500000000004 26.487500000000004 24.825 22.45 86-87 24.575 26.6625 24.6125 24.15 88-89 26.275 26.9125 23.1 23.7125 90-91 25.387500000000003 26.7625 24.3875 23.4625 92-93 25.0125 27.0 24.15 23.8375 94-95 25.95 27.200000000000003 23.8875 22.9625 96-97 25.15 26.950000000000003 24.3625 23.5375 98-99 25.1 25.7125 24.4 24.7875 100-101 25.45 26.0375 23.849999999999998 24.6625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.5 5 1.5 6 1.0 7 1.5 8 2.0 9 0.5 10 0.0 11 0.0 12 0.5 13 1.0 14 1.0 15 0.5 16 0.0 17 1.0 18 1.5 19 1.5 20 2.0 21 1.0 22 0.5 23 1.5 24 1.5 25 1.5 26 4.0 27 6.5 28 6.0 29 5.5 30 8.5 31 9.5 32 9.5 33 17.0 34 23.0 35 27.5 36 43.0 37 62.0 38 78.0 39 96.0 40 120.5 41 142.0 42 148.0 43 172.0 44 210.5 45 218.0 46 199.5 47 205.0 48 217.0 49 191.0 50 162.5 51 152.5 52 142.0 53 125.0 54 120.5 55 106.0 56 93.5 57 86.0 58 72.5 59 66.0 60 63.0 61 59.5 62 51.0 63 47.0 64 42.0 65 35.0 66 31.5 67 37.0 68 35.0 69 29.0 70 28.0 71 23.5 72 20.5 73 22.0 74 18.0 75 12.5 76 13.0 77 10.5 78 9.0 79 7.0 80 4.5 81 6.0 82 4.0 83 2.0 84 4.0 85 4.0 86 2.0 87 1.5 88 2.5 89 2.0 90 1.0 91 1.5 92 1.0 93 0.0 94 0.5 95 0.5 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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.4952818158633 96.55 2 1.1731701096659015 2.3 3 0.22953328232593728 0.675 4 0.0510073960724305 0.2 5 0.02550369803621525 0.125 6 0.02550369803621525 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 TGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTG 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 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 0.125 0.0 0.0 0.0 0.0 26-27 0.1375 0.0 0.0 0.0 0.0 28-29 0.1875 0.0 0.0 0.0 0.0 30-31 0.21250000000000002 0.0 0.0 0.0 0.0 32-33 0.2375 0.0 0.0 0.0 0.0 34-35 0.275 0.0 0.0 0.0 0.0 36-37 0.375 0.0 0.0 0.0 0.0 38-39 0.4375 0.0 0.0 0.0 0.0 40-41 0.575 0.0 0.0 0.0 0.0 42-43 0.625 0.0 0.0 0.0 0.0 44-45 0.725 0.0 0.0 0.0 0.0 46-47 0.7875 0.0 0.0 0.0 0.0 48-49 0.9125 0.0 0.0 0.0 0.0 50-51 1.1 0.0 0.0 0.0 0.0 52-53 1.1749999999999998 0.0 0.0 0.0 0.0 54-55 1.3250000000000002 0.0 0.0 0.0 0.0 56-57 1.55 0.0 0.0 0.0 0.0 58-59 1.775 0.0 0.0 0.0 0.0 60-61 1.9874999999999998 0.0 0.0 0.0 0.0 62-63 2.2 0.0 0.0 0.0 0.0 64-65 2.425 0.0 0.0 0.0 0.0 66-67 2.6875 0.0 0.0 0.0 0.0 68-69 2.9875 0.0 0.0 0.0 0.0 70-71 3.3499999999999996 0.0 0.0 0.0 0.0 72-73 3.7 0.0 0.0 0.0 0.0 74-75 4.175 0.0 0.0 0.0 0.0 76-77 4.5625 0.0 0.0 0.0 0.0 78-79 4.975 0.0 0.0 0.0 0.0 80-81 5.5 0.0 0.0 0.0 0.0 82-83 6.05 0.0 0.0 0.0 0.0 84-85 6.5375 0.0 0.0 0.0 0.0 86-87 7.1 0.0 0.0 0.0 0.0 88-89 7.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAAGAGT 15 0.00998312 47.46875 32-33 >>END_MODULE ERR3317443 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317443_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.16675 34.0 31.0 34.0 31.0 34.0 2 31.85675 34.0 31.0 34.0 30.0 34.0 3 32.32475 34.0 31.0 34.0 31.0 34.0 4 35.41025 37.0 35.0 37.0 35.0 37.0 5 35.671 37.0 37.0 37.0 35.0 37.0 6 35.7135 37.0 37.0 37.0 35.0 37.0 7 35.73875 37.0 37.0 37.0 35.0 37.0 8 35.771 37.0 37.0 37.0 35.0 37.0 9 37.60375 39.0 39.0 39.0 37.0 39.0 10-11 37.5115 39.0 39.0 39.0 35.5 39.0 12-13 37.529125 39.0 39.0 39.0 36.0 39.0 14-15 39.129 41.0 40.0 41.0 37.0 41.0 16-17 39.068 41.0 40.0 41.0 37.0 41.0 18-19 38.96425 41.0 40.0 41.0 36.0 41.0 20-21 38.898250000000004 41.0 40.0 41.0 36.0 41.0 22-23 38.834875 41.0 40.0 41.0 35.5 41.0 24-25 38.760625000000005 41.0 39.5 41.0 35.0 41.0 26-27 38.750625 41.0 39.0 41.0 35.0 41.0 28-29 38.690375 41.0 39.0 41.0 35.0 41.0 30-31 38.496875 41.0 39.0 41.0 35.0 41.0 32-33 38.434375 41.0 39.0 41.0 35.0 41.0 34-35 38.3185 40.5 38.5 41.0 35.0 41.0 36-37 38.10625 40.0 38.0 41.0 34.5 41.0 38-39 38.096875 40.0 38.0 41.0 34.0 41.0 40-41 38.2075 41.0 38.5 41.0 35.0 41.0 42-43 38.1075 41.0 38.0 41.0 34.0 41.0 44-45 37.93775 40.5 38.0 41.0 34.0 41.0 46-47 37.765625 40.0 38.0 41.0 33.0 41.0 48-49 37.712125 40.0 38.0 41.0 33.0 41.0 50-51 36.92 39.5 36.5 40.5 32.0 41.0 52-53 36.784875 39.5 36.0 40.5 32.0 41.0 54-55 36.992625000000004 40.0 36.0 41.0 32.0 41.0 56-57 36.8655 40.0 35.5 41.0 32.0 41.0 58-59 36.581375 39.0 35.0 41.0 32.0 41.0 60-61 36.321 39.0 35.0 41.0 32.0 41.0 62-63 35.9815 38.0 35.0 41.0 31.0 41.0 64-65 35.606375 37.5 35.0 40.0 30.5 41.0 66-67 35.646125 37.0 35.0 40.0 31.0 41.0 68-69 35.354124999999996 37.0 35.0 39.5 31.0 41.0 70-71 35.012875 36.0 35.0 39.0 31.0 41.0 72-73 34.574749999999995 36.0 35.0 39.0 31.0 41.0 74-75 34.181375 35.0 35.0 37.5 30.0 39.5 76-77 33.8005 35.0 35.0 37.0 29.5 39.0 78-79 33.518375 35.0 34.5 36.5 29.5 39.0 80-81 33.159499999999994 35.0 34.0 36.0 29.0 37.0 82-83 32.9475 35.0 34.0 36.0 29.0 37.0 84-85 32.58225 35.0 34.0 35.0 27.0 36.5 86-87 32.43375 35.0 34.0 35.0 28.0 36.0 88-89 32.25375 35.0 34.0 35.0 27.5 36.0 90-91 32.025875 35.0 34.0 35.0 27.0 36.0 92-93 31.894 35.0 34.0 35.0 26.5 35.5 94-95 31.740000000000002 35.0 33.5 35.0 25.0 35.0 96-97 31.613999999999997 35.0 33.0 35.0 25.0 35.0 98-99 31.436625 35.0 33.0 35.0 25.0 35.0 100-101 29.546375 33.5 30.0 34.5 12.5 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 62.0 3 3.0 4 1.0 5 5.0 6 2.0 7 5.0 8 2.0 9 5.0 10 2.0 11 3.0 12 8.0 13 5.0 14 8.0 15 10.0 16 6.0 17 5.0 18 7.0 19 7.0 20 8.0 21 17.0 22 7.0 23 8.0 24 18.0 25 16.0 26 16.0 27 16.0 28 26.0 29 35.0 30 30.0 31 49.0 32 66.0 33 89.0 34 142.0 35 239.0 36 449.0 37 931.0 38 1393.0 39 299.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 28.925 11.65 29.325000000000003 30.099999999999998 2 26.174999999999997 11.200000000000001 26.0 36.625 3 22.650000000000002 12.45 30.075000000000003 34.825 4 23.7 11.425 27.075 37.8 5 25.650000000000002 15.2 23.65 35.5 6 26.174999999999997 18.7 28.749999999999996 26.375 7 19.8 23.65 39.625 16.925 8 19.0 23.775 36.05 21.175 9 17.224999999999998 28.95 34.8 19.025 10-11 18.4875 26.900000000000002 32.2 22.412499999999998 12-13 19.400000000000002 27.1 32.887499999999996 20.6125 14-15 20.2875 26.200000000000003 31.35 22.162499999999998 16-17 20.1125 25.324999999999996 30.012499999999996 24.55 18-19 19.892473118279568 26.469117279319832 30.49512378094524 23.143285821455365 20-21 20.75 26.5 28.462500000000002 24.2875 22-23 21.4875 24.6125 28.625 25.275 24-25 20.0375 25.912499999999998 29.475 24.575 26-27 22.075 25.374999999999996 27.55 25.0 28-29 20.674999999999997 25.687500000000004 27.075 26.5625 30-31 20.175 25.912499999999998 28.9875 24.925 32-33 22.4625 24.9375 28.025 24.575 34-35 21.1375 24.837500000000002 27.950000000000003 26.075 36-37 21.712500000000002 25.8125 27.8625 24.6125 38-39 21.525 25.025 27.875 25.575 40-41 21.9625 24.4125 27.625 26.0 42-43 22.2625 25.85 27.3125 24.575 44-45 22.537499999999998 26.8625 25.124999999999996 25.474999999999998 46-47 21.85 25.7875 27.1 25.2625 48-49 21.2875 26.400000000000002 27.287499999999998 25.025 50-51 22.2125 26.474999999999998 26.174999999999997 25.137500000000003 52-53 22.287499999999998 25.4875 26.325 25.900000000000002 54-55 21.075 25.912499999999998 27.762500000000003 25.25 56-57 21.775 25.4375 27.575 25.2125 58-59 21.375 25.374999999999996 26.674999999999997 26.575 60-61 20.375 26.5625 28.199999999999996 24.8625 62-63 22.6125 26.2875 26.424999999999997 24.675 64-65 22.0875 24.6875 27.787499999999998 25.4375 66-67 21.95 26.5625 27.537499999999998 23.95 68-69 22.5 26.775 25.874999999999996 24.85 70-71 22.3875 26.3 26.2875 25.025 72-73 22.4875 25.474999999999998 26.950000000000003 25.087500000000002 74-75 23.0 25.775 26.275 24.95 76-77 22.75 27.200000000000003 24.6875 25.362499999999997 78-79 22.125 26.8375 25.8125 25.224999999999998 80-81 23.2125 26.575 26.0 24.212500000000002 82-83 23.9375 25.7875 24.425 25.85 84-85 23.7 25.974999999999998 25.9625 24.3625 86-87 23.9375 25.650000000000002 25.8625 24.55 88-89 24.0125 24.6625 25.575 25.75 90-91 23.7375 25.874999999999996 26.7125 23.674999999999997 92-93 23.8125 25.6 26.0625 24.525 94-95 24.0 25.775 26.0625 24.1625 96-97 24.55 25.324999999999996 26.187500000000004 23.9375 98-99 23.8375 26.2125 25.662499999999998 24.2875 100-101 24.95 25.2375 24.9125 24.9 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 12.0 1 14.0 2 9.5 3 2.5 4 1.5 5 1.0 6 2.0 7 2.0 8 1.5 9 2.5 10 2.0 11 0.5 12 0.5 13 1.5 14 2.5 15 2.5 16 1.0 17 1.5 18 1.5 19 0.5 20 1.5 21 2.0 22 2.0 23 2.0 24 3.5 25 4.0 26 3.5 27 6.0 28 9.0 29 10.0 30 13.5 31 21.5 32 24.0 33 29.0 34 39.0 35 44.0 36 55.5 37 65.0 38 87.5 39 128.5 40 148.5 41 181.0 42 208.0 43 209.0 44 207.5 45 203.5 46 190.5 47 182.5 48 184.0 49 168.0 50 154.5 51 151.5 52 137.0 53 105.0 54 95.5 55 99.5 56 81.0 57 60.5 58 58.5 59 62.0 60 63.5 61 57.5 62 49.0 63 47.0 64 38.0 65 28.5 66 30.5 67 26.5 68 18.0 69 18.0 70 17.5 71 14.0 72 12.5 73 13.0 74 12.0 75 12.5 76 13.0 77 9.5 78 5.5 79 3.5 80 3.5 81 4.5 82 2.5 83 0.0 84 1.0 85 1.5 86 0.5 87 0.0 88 0.0 89 0.5 90 1.0 91 0.5 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.025 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.975 #Duplication Level Percentage of deduplicated Percentage of total 1 99.10691502934422 97.1 2 0.6379178361826996 1.25 3 0.07655014034192395 0.22499999999999998 4 0.05103342689461597 0.2 5 0.05103342689461597 0.25 6 0.025516713447307986 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.05103342689461597 0.8250000000000001 >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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 22 0.5499999999999999 No Hit TCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 11 0.27499999999999997 No Hit TGGGGATGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 6 0.15 No Hit CTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit TCTTCGTATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 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 0.125 0.0 0.0 0.0 0.0 26-27 0.1375 0.0 0.0 0.0 0.0 28-29 0.16249999999999998 0.0 0.0 0.0 0.0 30-31 0.1875 0.0 0.0 0.0 0.0 32-33 0.21250000000000002 0.0 0.0 0.0 0.0 34-35 0.2625 0.0 0.0 0.0 0.0 36-37 0.375 0.0 0.0 0.0 0.0 38-39 0.4375 0.0 0.0 0.0 0.0 40-41 0.575 0.0 0.0 0.0 0.0 42-43 0.625 0.0 0.0 0.0 0.0 44-45 0.725 0.0 0.0 0.0 0.0 46-47 0.8125 0.0 0.0 0.0 0.0 48-49 0.9875 0.0 0.0 0.0 0.0 50-51 1.1625 0.0 0.0 0.0 0.0 52-53 1.25 0.0 0.0 0.0 0.0 54-55 1.4 0.0 0.0 0.0 0.0 56-57 1.625 0.0 0.0 0.0 0.0 58-59 1.8375 0.0 0.0 0.0 0.0 60-61 2.0625 0.0 0.0 0.0 0.0 62-63 2.2750000000000004 0.0 0.0 0.0 0.0 64-65 2.5 0.0 0.0 0.0 0.0 66-67 2.7625 0.0 0.0 0.0 0.0 68-69 3.0625 0.0 0.0 0.0 0.0 70-71 3.4000000000000004 0.0 0.0 0.0 0.0 72-73 3.7625 0.0 0.0 0.0 0.0 74-75 4.225 0.0 0.0 0.0 0.0 76-77 4.612500000000001 0.0 0.0 0.0 0.0 78-79 5.0125 0.0 0.0 0.0 0.0 80-81 5.5625 0.0 0.0 0.0 0.0 82-83 6.125 0.0 0.0 0.0 0.0 84-85 6.6375 0.0 0.0 0.0 0.0 86-87 7.175 0.0 0.0 0.0 0.0 88-89 7.75 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734814 spots for ERR3317443.sra Written 1734814 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra Read 1734795 spots for ERR3317443.sra Written 1734795 spots for ERR3317443.sra SRR ids: ['ERR3317443.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lhsu2e05 ERR3317443.sra spots: 34695919 blocks: [[1, 1734795], [1734796, 3469590], [3469591, 5204385], [5204386, 6939180], [6939181, 8673975], [8673976, 10408770], [10408771, 12143565], [12143566, 13878360], [13878361, 15613155], [15613156, 17347950], [17347951, 19082745], [19082746, 20817540], [20817541, 22552335], [22552336, 24287130], [24287131, 26021925], [26021926, 27756720], [27756721, 29491515], [29491516, 31226310], [31226311, 32961105], [32961106, 34695919]] ERR3317443 file size 8347334 ERR3317443 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 ERR3317443 ERR3317443_1.fastq ERR3317443_2.fastq Input file: ERR3317443_1.fastq Paired file: ERR3317443_2.fastq trimmed: ERR3317443-trimmed-pair1.fastq, ERR3317443-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 Dec 10 09:29:59 2024 >> started Tue Dec 10 09:30:31 2024 >> done (32.418s) 34695919 read pairs processed; of these: 200785 ( 0.58%) short read pairs filtered out after trimming by size control 545207 ( 1.57%) empty read pairs filtered out after trimming by size control 33949927 (97.85%) read pairs available; of these: 10154918 (29.91%) trimmed read pairs available after processing 23795009 (70.09%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 703 0.00% 19 826 0.00% 20 1153 0.00% 21 1297 0.00% 22 1617 0.00% 23 2254 0.01% 24 2844 0.01% 25 3288 0.01% 26 3881 0.01% 27 4547 0.01% 28 4981 0.01% 29 6020 0.02% 30 6937 0.02% 31 8941 0.03% 32 8350 0.02% 33 8929 0.03% 34 11090 0.03% 35 11051 0.03% 36 12642 0.04% 37 13262 0.04% 38 15939 0.05% 39 16321 0.05% 40 16969 0.05% 41 18382 0.05% 42 19362 0.06% 43 20195 0.06% 44 21603 0.06% 45 22601 0.07% 46 24002 0.07% 47 27934 0.08% 48 28608 0.08% 49 29942 0.09% 50 34387 0.10% 51 33630 0.10% 52 34842 0.10% 53 39069 0.12% 54 43255 0.13% 55 48930 0.14% 56 47651 0.14% 57 48577 0.14% 58 52688 0.16% 59 66572 0.20% 60 75672 0.22% 61 80420 0.24% 62 86214 0.25% 63 89997 0.27% 64 96082 0.28% 65 100709 0.30% 66 111635 0.33% 67 112741 0.33% 68 113610 0.33% 69 116280 0.34% 70 125429 0.37% 71 134048 0.39% 72 133938 0.39% 73 139687 0.41% 74 139449 0.41% 75 140323 0.41% 76 140413 0.41% 77 146949 0.43% 78 157859 0.46% 79 158464 0.47% 80 162727 0.48% 81 167531 0.49% 82 168034 0.49% 83 174434 0.51% 84 181706 0.54% 85 195060 0.57% 86 203435 0.60% 87 207904 0.61% 88 209070 0.62% 89 231684 0.68% 90 221096 0.65% 91 229549 0.68% 92 242965 0.72% 93 253501 0.75% 94 274146 0.81% 95 295257 0.87% 96 327611 0.96% 97 380633 1.12% 98 486091 1.43% 99 638431 1.88% 100 1678062 4.94% 101 23795009 70.09% 33949927 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=3.07 fanout-score-rank=16 prefix-density=0.67 prefix-fanout=2.7 sequence=AAGGAGCTGGAGGAGGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=21.52 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=4.9 sequence=CCTCCGCCTCAGGGCCTCCTACCTGCGCTACGACCTCAAGACCGTCATCTCCTCCAAGGCCACCAAGGAGGAGAAGAAGGACCTCAAGGACCTCACCGGGAAGCTCTTCGACACCCTCGACGGGCTTGACCATGCAGCCAAGATCAAGAGCCCCGCCGAAGCCGAGAAGTACTACGGCGAGACCAAGACCGTTCTTAGCGATGTCCTCGCCAAGCTAGGATAGATGCATGGATCCGCATAATGGCCGTGTGCTTTCAGTTTCAGGCCTTTTGTGTTTGTTCATATGGAACCGGCGATGTAACTTCTTTGTTGATAATATGTCAGCAAGCACTTAAGTA criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=2.68 fanout-score-rank=27 prefix-density=0.57 prefix-fanout=1.0 sequence=ATGCACTGCACCTGCCGGGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=264.67 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=7.9 sequence=TCCTCCTTGTTGTACATCCCAGGGAGCTGCACGTTGGTGGGGGCATCCGCGATGTTCATCAGGGTGGCGTTAACCATCTGGTTGTTGACAGTGTACTGGGTGGTCCCGCCCATCCGACCCGCACCAGCGTCGAGATCGTTGATGAAGAGGCAGCACATCTTACCCTTCTTGATCAAGTCTGCGGCCTCACGGTACCGCTGCCTGATCAGCTTGGCTGGCTCTCCGGCGTTTCCGCTCTCCAGCTCTCCGGCACTCATCATGATTGGGTTGATGCCCATCTTGGCGAAGACAAGCTCACATTGGAAGGATTTTCCTTGACCCTTGCCTCCCCAGATACCCAAGATGAGTGGCACCTTGATGTTGGGC ERR3317443 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 09:31:47 Started mapping on | Dec 10 09:31:47 Finished on | Dec 10 09:33:24 Mapping speed, Million of reads per hour | 1260.00 Number of input reads | 33949927 Average input read length | 192 UNIQUE READS: Uniquely mapped reads number | 30858277 Uniquely mapped reads % | 90.89% Average mapped length | 190.96 Number of splices: Total | 19698225 Number of splices: Annotated (sjdb) | 18720249 Number of splices: GT/AG | 19413377 Number of splices: GC/AG | 254661 Number of splices: AT/AC | 14560 Number of splices: Non-canonical | 15627 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.00% Deletion average length | 1.23 Insertion rate per base | 0.00% Insertion average length | 1.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2091262 % of reads mapped to multiple loci | 6.16% Number of reads mapped to too many loci | 57460 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.89% % of reads unmapped: other | 0.89% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1151101 1151101 1151101 N_multimapping 2091262 2091262 2091262 N_noFeature 1103133 2311341 29005265 N_ambiguous 891416 272319 14610 UnstrandedReadsAssigned:28863728 PositiveStrandReadsAssigned:28274617 NegativeStrandReadsAssigned:1838402 Dataset is classified positive stranded MeadianReadLen=101 20thPercentileLength=99 echo kmer=95 ERR3317443 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: ERR3317443-trimmed-pair1.fastq ERR3317443-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,949,927 reads, 29,937,977 reads pseudoaligned [quant] estimated average fragment length: 182.487 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,399 rounds 52973 ERR3317443.ke.tsv 35125 ERR3317443.se.tsv 88098 total ==> ERR3317443.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 754.655 0 0 PNS24247 1044 862.513 44.4087 2.59066 PNS24249 1928 1746.51 142.897 4.11679 PNS24246 1044 862.513 44.4087 2.59066 PNS24248 1044 862.513 44.4087 2.59066 PNS24244 1471 1289.51 233.877 9.12576 PNS24243 293 137.033 3 1.10155 KQK14069 1603 1421.51 10481.2 370.994 KQK14071 474 298.994 34.6272 5.82724 ==> ERR3317443.se.tsv <== BRADI_1g14170v3 11843 BRADI_1g53295v3 103 BRADI_1g59795v3 699 BRADI_1g07683v3 0 BRADI_1g00485v3 76 BRADI_1g20270v3 1841 BRADI_1g74790v3 593 BRADI_1g09890v3 14 BRADI_1g77505v3 361 BRADI_1g48960v3 0 ERR3317443 completed mapping pipeline successfully