Starting /dee2/code/volunteer_pipeline.sh ERR10610862 current disk space = 1548946939904 free memory = 1381367460 ERR10610862 SRAfilesize 38401fda84f91f0450bf7018e6539459 ERR10610862.sra ERR10610862.sra file validated ERR10610862 is paired end ERR10610862 is conventional basespace ERR10610862 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR10610862_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 47 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 23.9395 18.0 18.0 31.0 18.0 33.0 2 30.0975 32.0 27.0 33.0 25.0 33.0 3 30.6345 33.0 31.0 33.0 25.0 33.0 4 30.104 33.0 30.0 33.0 25.0 33.0 5 31.126 33.0 32.0 33.0 27.0 34.0 6 33.68825 37.0 33.0 38.0 16.0 38.0 7 34.2445 38.0 34.0 38.0 26.0 38.0 8 34.50875 38.0 34.0 38.0 26.0 38.0 9 34.76 38.0 35.0 38.0 26.0 38.0 10-11 34.735749999999996 38.0 35.0 38.0 26.0 38.0 12-13 34.543875 38.0 35.0 38.0 26.0 38.0 14-15 34.541624999999996 38.0 35.0 38.0 26.0 38.0 16-17 34.72425 38.0 35.5 38.0 26.0 38.0 18-19 34.738875 38.0 35.5 38.0 26.0 38.0 20-21 23.950875 22.0 21.5 28.5 15.0 33.0 22-23 32.427625 35.5 30.5 37.0 20.0 37.5 24-25 34.472750000000005 38.0 34.5 38.0 25.0 38.0 26-27 34.722625 38.0 36.0 38.0 25.0 38.0 28-29 34.786500000000004 38.0 35.5 38.0 25.0 38.0 30-31 34.954125000000005 38.0 36.0 38.0 27.0 38.0 32-33 34.8335 38.0 36.0 38.0 26.0 38.0 34-35 34.874875 38.0 35.5 38.0 27.0 38.0 36-37 34.868625 38.0 36.0 38.0 26.0 38.0 38-39 34.953 38.0 36.0 38.0 26.0 38.0 40-41 35.03425 38.0 36.0 38.0 27.0 38.0 42-43 34.811375 38.0 35.5 38.0 25.0 38.0 44-45 34.842375000000004 38.0 35.5 38.0 26.0 38.0 46-47 34.927375 38.0 36.0 38.0 27.0 38.0 48-49 27.494749999999996 27.0 26.0 31.5 20.5 35.5 50-51 29.845 31.5 27.5 33.5 16.0 37.5 52-53 33.788250000000005 37.5 33.5 38.0 24.5 38.0 54-55 27.35 27.0 25.5 31.5 19.5 37.0 56-57 29.677500000000002 31.0 27.5 33.0 20.0 37.5 58-59 33.779624999999996 37.5 33.5 38.0 24.5 38.0 60-61 34.65325 38.0 35.0 38.0 25.0 38.0 62-63 35.0095 38.0 36.0 38.0 27.0 38.0 64-65 34.859 38.0 35.5 38.0 26.0 38.0 66-67 34.909875 38.0 36.0 38.0 26.0 38.0 68-69 35.015625 38.0 36.0 38.0 27.0 38.0 70-71 34.80825 38.0 35.5 38.0 25.5 38.0 72-73 24.205125000000002 22.0 21.0 28.0 15.0 37.0 74-75 32.088750000000005 35.5 30.0 37.0 20.0 38.0 76-77 34.39775 38.0 34.0 38.0 25.0 38.0 78-79 34.746875 38.0 35.0 38.0 26.0 38.0 80-81 34.843125 38.0 35.5 38.0 26.0 38.0 82-83 34.921 38.0 36.0 38.0 27.0 38.0 84-85 34.926500000000004 38.0 36.0 38.0 26.5 38.0 86-87 34.765249999999995 38.0 35.0 38.0 25.0 38.0 88-89 34.863875 38.0 35.0 38.0 26.0 38.0 90-91 34.684375 38.0 35.0 38.0 25.0 38.0 92-93 34.686 38.0 35.0 38.0 25.5 38.0 94-95 33.646625 37.5 32.5 38.0 23.5 38.0 96-97 34.364625000000004 38.0 34.5 38.0 23.5 38.0 98-99 25.80225 26.5 24.5 26.5 18.5 32.5 100-101 27.177875 27.5 25.0 32.0 15.0 33.5 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 4.0 18 7.0 19 16.0 20 39.0 21 34.0 22 31.0 23 56.0 24 69.0 25 60.0 26 103.0 27 89.0 28 109.0 29 120.0 30 154.0 31 156.0 32 217.0 33 314.0 34 532.0 35 1390.0 36 447.0 37 53.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 27.976791120080723 12.336024217961656 15.413723511604442 44.27346115035318 2 22.15 17.150000000000002 36.725 23.974999999999998 3 23.150000000000002 21.525 23.150000000000002 32.175 4 25.8 28.249999999999996 22.075 23.875 5 24.575 31.05 24.224999999999998 20.150000000000002 6 20.025000000000002 33.425 27.500000000000004 19.05 7 15.328832208052013 23.50587646911728 42.56064016004001 18.6046511627907 8 20.625 23.474999999999998 29.9 26.0 9 19.25 22.25 32.7 25.8 10-11 21.552694086760845 31.91648956119515 24.05300662582823 22.477809726215778 12-13 20.955238809702426 24.306076519129782 28.457114278569644 26.281570392598148 14-15 21.1408556417313 27.570678008506377 26.870152614460846 24.418313735301474 16-17 22.26113056528264 26.625812906453227 26.000500250125064 25.11255627813907 18-19 22.079059294470856 27.045283962972228 26.45734300725544 24.418313735301474 20-21 20.565424068051037 31.74881160870653 21.278458844133098 26.407305479109333 22-23 20.4352176088044 27.138569284642323 27.51375687843922 24.912456228114056 24-25 21.395523321245467 26.00975365762161 27.5728398149306 25.02188320620233 26-27 22.025 26.474999999999998 26.875 24.625 28-29 21.702712839104887 26.803350418802353 26.60332541567696 24.8906113264158 30-31 22.3875 27.175 26.137500000000003 24.3 32-33 21.587500000000002 26.825 27.275 24.3125 34-35 22.35 26.25 26.400000000000002 25.0 36-37 23.193298324581146 26.131532883220803 25.78144536134033 24.893723430857715 38-39 22.162499999999998 26.8 25.2875 25.75 40-41 23.1625 26.674999999999997 26.1125 24.05 42-43 21.6125 27.2625 26.137500000000003 24.9875 44-45 21.8125 26.0625 26.375 25.75 46-47 22.0625 26.900000000000002 25.162499999999998 25.874999999999996 48-49 24.3125 26.9125 24.825 23.95 50-51 22.325 26.950000000000003 26.05 24.675 52-53 22.375 25.7875 25.924999999999997 25.912499999999998 54-55 21.65 29.2875 24.05 25.0125 56-57 22.5125 26.450000000000003 26.375 24.6625 58-59 21.75 27.212500000000002 26.2875 24.75 60-61 22.6875 25.2875 26.2125 25.8125 62-63 21.6625 26.5125 25.6125 26.2125 64-65 23.3375 26.3125 25.25 25.1 66-67 22.412499999999998 26.575 25.7375 25.275 68-69 22.75 26.25 26.6625 24.337500000000002 70-71 22.162499999999998 26.1 26.187500000000004 25.55 72-73 23.974999999999998 30.587500000000002 23.025000000000002 22.412499999999998 74-75 22.6 26.8625 25.637500000000003 24.9 76-77 22.325 26.724999999999998 25.55 25.4 78-79 22.1 26.8 25.3125 25.7875 80-81 22.1875 26.6625 25.724999999999998 25.424999999999997 82-83 23.4375 25.6 25.2125 25.75 84-85 22.725 26.237500000000004 25.7125 25.324999999999996 86-87 23.25 26.424999999999997 25.2625 25.0625 88-89 22.85571392848212 26.344086021505376 25.568892223055762 25.23130782695674 90-91 23.35 26.087500000000002 24.762500000000003 25.8 92-93 23.24040505063133 27.315914489311165 25.390673834229275 24.05300662582823 94-95 23.1125 26.575 25.474999999999998 24.837500000000002 96-97 23.400000000000002 26.474999999999998 24.8125 25.3125 98-99 23.75 28.000000000000004 24.3125 23.9375 100-101 23.1875 26.8125 24.6875 25.3125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 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 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.5 23 0.5 24 0.0 25 0.0 26 0.0 27 0.5 28 1.0 29 3.0 30 5.0 31 7.5 32 11.0 33 16.5 34 27.5 35 42.0 36 52.5 37 73.0 38 99.5 39 118.0 40 138.5 41 173.0 42 210.0 43 224.5 44 219.5 45 238.5 46 232.5 47 207.5 48 202.5 49 200.5 50 185.5 51 155.5 52 137.5 53 120.5 54 115.5 55 112.0 56 96.5 57 86.0 58 79.0 59 74.5 60 69.0 61 55.0 62 44.5 63 35.0 64 31.5 65 29.5 66 24.5 67 17.0 68 9.5 69 7.5 70 5.5 71 1.0 72 1.0 73 1.0 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 0.8999999999999999 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.025 8 0.0 9 0.0 10-11 0.0125 12-13 0.025 14-15 0.075 16-17 0.05 18-19 0.075 20-21 0.075 22-23 0.05 24-25 0.0375 26-27 0.0 28-29 0.0125 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.025 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 0.025 90-91 0.0 92-93 0.0125 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 99.925 #Duplication Level Percentage of deduplicated Percentage of total 1 99.92494370778083 99.85000000000001 2 0.07505629221916438 0.15 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 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 pass >>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 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 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 0.0875 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.48750000000000004 0.0 0.0 0.0 0.0 86-87 0.65 0.0 0.0 0.0 0.0 88-89 0.7375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR10610862 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR10610862_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 48 >>END_MODULE >>Per base sequence quality warn #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.6145 33.0 31.0 33.0 18.0 34.0 2 31.02825 33.0 32.0 33.0 25.0 34.0 3 30.67775 33.0 31.0 33.0 18.0 34.0 4 30.30625 33.0 31.0 33.0 15.0 34.0 5 30.68725 33.0 32.0 33.0 25.0 34.0 6 33.885 38.0 34.0 38.0 16.0 38.0 7 34.45125 38.0 34.0 38.0 26.0 38.0 8 34.59725 38.0 35.0 38.0 26.0 38.0 9 34.3815 38.0 34.0 38.0 26.0 38.0 10-11 34.29125 38.0 34.0 38.0 21.0 38.0 12-13 34.39825 38.0 34.5 38.0 21.0 38.0 14-15 34.352999999999994 38.0 34.5 38.0 21.0 38.0 16-17 34.426 38.0 34.5 38.0 25.5 38.0 18-19 34.457499999999996 38.0 34.5 38.0 25.0 38.0 20-21 34.271249999999995 38.0 34.5 38.0 20.0 38.0 22-23 34.503375 38.0 34.5 38.0 25.0 38.0 24-25 34.536874999999995 38.0 35.0 38.0 25.0 38.0 26-27 34.385625000000005 38.0 34.5 38.0 24.5 38.0 28-29 34.37875 38.0 35.0 38.0 24.5 38.0 30-31 34.56 38.0 35.0 38.0 25.0 38.0 32-33 34.450625 38.0 35.0 38.0 20.5 38.0 34-35 34.2975 38.0 34.5 38.0 20.5 38.0 36-37 34.297375 38.0 34.0 38.0 20.0 38.0 38-39 34.364000000000004 38.0 35.0 38.0 24.0 38.0 40-41 34.53875 38.0 35.0 38.0 25.0 38.0 42-43 34.727999999999994 38.0 35.5 38.0 25.0 38.0 44-45 34.543625000000006 38.0 35.0 38.0 24.5 38.0 46-47 34.765249999999995 38.0 35.0 38.0 26.0 38.0 48-49 34.551 38.0 35.0 38.0 25.0 38.0 50-51 34.604124999999996 38.0 35.0 38.0 24.5 38.0 52-53 34.46225 38.0 34.5 38.0 25.0 38.0 54-55 34.4275 38.0 34.5 38.0 20.5 38.0 56-57 34.49025 38.0 34.5 38.0 20.5 38.0 58-59 34.54 38.0 35.0 38.0 25.0 38.0 60-61 34.44325 38.0 34.0 38.0 24.5 38.0 62-63 34.471625 38.0 35.0 38.0 25.0 38.0 64-65 34.370375 38.0 34.5 38.0 24.0 38.0 66-67 34.606125000000006 38.0 35.0 38.0 25.0 38.0 68-69 34.6435 38.0 35.5 38.0 25.0 38.0 70-71 34.53375 38.0 35.0 38.0 25.0 38.0 72-73 34.579499999999996 38.0 35.0 38.0 25.0 38.0 74-75 34.3865 38.0 34.5 38.0 24.5 38.0 76-77 34.471000000000004 38.0 35.0 38.0 25.0 38.0 78-79 34.467 38.0 34.5 38.0 25.0 38.0 80-81 34.32275 38.0 34.5 38.0 23.5 38.0 82-83 34.380250000000004 38.0 35.0 38.0 23.5 38.0 84-85 34.46875 38.0 34.5 38.0 24.5 38.0 86-87 34.403000000000006 38.0 34.5 38.0 23.0 38.0 88-89 34.319 38.0 34.5 38.0 23.0 38.0 90-91 34.29 38.0 34.5 38.0 23.0 38.0 92-93 34.284875 38.0 34.5 38.0 22.0 38.0 94-95 33.960375 38.0 34.0 38.0 18.5 38.0 96-97 25.98925 21.5 19.5 36.0 14.5 38.0 98-99 21.66075 20.5 19.0 22.5 14.0 30.5 100-101 28.741500000000002 30.5 23.5 36.0 15.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 7.0 18 15.0 19 27.0 20 35.0 21 44.0 22 48.0 23 59.0 24 60.0 25 88.0 26 74.0 27 70.0 28 93.0 29 109.0 30 117.0 31 140.0 32 144.0 33 211.0 34 306.0 35 451.0 36 1276.0 37 625.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.575000000000003 14.45 15.1 40.875 2 28.275 20.849999999999998 33.225 17.65 3 23.125 24.575 26.075 26.224999999999998 4 26.625 29.849999999999998 19.575 23.95 5 27.825 31.7 20.4 20.075000000000003 6 23.125 34.975 20.925 20.974999999999998 7 21.45 16.8 36.5 25.25 8 23.674999999999997 22.475 24.85 28.999999999999996 9 24.525 21.825 27.85 25.8 10-11 26.5125 28.462500000000002 21.337500000000002 23.6875 12-13 25.474999999999998 22.975 25.424999999999997 26.125 14-15 25.3125 25.5125 25.112499999999997 24.0625 16-17 26.3625 24.8 24.5375 24.3 18-19 25.775 24.9375 24.9375 24.349999999999998 20-21 25.8625 25.2625 26.0125 22.8625 22-23 24.925 25.7375 25.3125 24.025 24-25 25.4375 24.8125 25.424999999999997 24.325 26-27 25.837500000000002 26.200000000000003 24.6875 23.275000000000002 28-29 25.324999999999996 24.7875 25.5375 24.349999999999998 30-31 24.575 25.837500000000002 25.8 23.7875 32-33 25.3125 25.124999999999996 25.575 23.9875 34-35 25.387500000000003 25.7125 25.2375 23.6625 36-37 24.962500000000002 26.650000000000002 24.6 23.7875 38-39 24.95 26.2875 25.5625 23.200000000000003 40-41 25.387500000000003 25.8625 25.587500000000002 23.1625 42-43 25.937500000000004 25.2125 25.224999999999998 23.625 44-45 24.8625 26.8125 25.124999999999996 23.200000000000003 46-47 26.0125 24.6625 25.825 23.5 48-49 25.412499999999998 26.275 24.8625 23.45 50-51 25.0125 26.0125 25.7 23.275000000000002 52-53 25.424999999999997 25.224999999999998 26.0375 23.3125 54-55 25.4375 26.0 25.324999999999996 23.2375 56-57 26.075 25.95 25.775 22.2 58-59 25.162499999999998 25.2875 25.7625 23.7875 60-61 25.4625 25.587500000000002 26.0375 22.912499999999998 62-63 25.4 26.150000000000002 25.15 23.3 64-65 24.3 26.387500000000003 26.0125 23.3 66-67 25.6125 25.4625 25.724999999999998 23.200000000000003 68-69 25.0 25.412499999999998 26.0125 23.575 70-71 25.624999999999996 24.7875 26.137500000000003 23.45 72-73 25.337500000000002 24.8625 26.437500000000004 23.3625 74-75 25.1875 24.9875 26.637499999999996 23.1875 76-77 25.25 25.3 25.900000000000002 23.549999999999997 78-79 24.95 24.525 27.2625 23.2625 80-81 25.05 25.7375 26.025 23.1875 82-83 25.6125 25.9875 25.8 22.6 84-85 24.7 25.7 26.900000000000002 22.7 86-87 25.362499999999997 26.900000000000002 25.35 22.3875 88-89 26.2625 25.8125 25.6125 22.3125 90-91 25.025 26.087500000000002 26.0125 22.875 92-93 25.6 27.025 25.4375 21.9375 94-95 25.724999999999998 26.200000000000003 26.400000000000002 21.675 96-97 25.937500000000004 25.2375 26.575 22.25 98-99 24.224999999999998 28.000000000000004 24.525 23.25 100-101 25.6 25.85 25.45 23.1 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 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 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 0.0 25 0.0 26 0.0 27 0.5 28 3.0 29 4.0 30 3.5 31 4.0 32 6.0 33 11.0 34 14.5 35 22.5 36 32.0 37 38.5 38 62.5 39 88.5 40 111.5 41 149.5 42 187.5 43 207.0 44 203.5 45 211.5 46 231.0 47 226.0 48 212.5 49 195.5 50 173.5 51 161.5 52 148.5 53 142.5 54 130.0 55 110.0 56 111.0 57 108.5 58 95.5 59 95.5 60 93.5 61 83.5 62 73.5 63 56.0 64 50.5 65 45.5 66 33.5 67 24.5 68 12.5 69 8.5 70 5.5 71 1.5 72 3.0 73 2.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 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 0.0 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 0.0 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 99.075 #Duplication Level Percentage of deduplicated Percentage of total 1 99.09159727479182 98.175 2 0.8831693161746152 1.7500000000000002 3 0.025233409033560434 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 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 pass >>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 0.025 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.16249999999999998 0.0 0.0 0.0 0.0 72-73 0.225 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.2875 0.0 0.0 0.0 0.0 78-79 0.3875 0.0 0.0 0.0 0.0 80-81 0.4 0.0 0.0 0.0 0.0 82-83 0.45 0.0 0.0 0.0 0.0 84-85 0.5 0.0 0.0 0.0 0.0 86-87 0.5874999999999999 0.0 0.0 0.0 0.0 88-89 0.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra Read 988494 spots for ERR10610862.sra Written 988494 spots for ERR10610862.sra SRR ids: ['ERR10610862.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yjywdhxw ERR10610862.sra spots: 19769880 blocks: [[1, 988494], [988495, 1976988], [1976989, 2965482], [2965483, 3953976], [3953977, 4942470], [4942471, 5930964], [5930965, 6919458], [6919459, 7907952], [7907953, 8896446], [8896447, 9884940], [9884941, 10873434], [10873435, 11861928], [11861929, 12850422], [12850423, 13838916], [13838917, 14827410], [14827411, 15815904], [15815905, 16804398], [16804399, 17792892], [17792893, 18781386], [18781387, 19769880]] ERR10610862 file size 4766317 ERR10610862 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 ERR10610862 ERR10610862_1.fastq ERR10610862_2.fastq Input file: ERR10610862_1.fastq Paired file: ERR10610862_2.fastq trimmed: ERR10610862-trimmed-pair1.fastq, ERR10610862-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 Fri Dec 6 21:37:28 2024 >> started Fri Dec 6 21:38:51 2024 >> done (83.046s) 19769880 read pairs processed; of these: 48 ( 0.00%) short read pairs filtered out after trimming by size control 2078 ( 0.01%) empty read pairs filtered out after trimming by size control 19767754 (99.99%) read pairs available; of these: 642632 ( 3.25%) trimmed read pairs available after processing 19125122 (96.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 0 0.00% 20 1 0.00% 21 3 0.00% 22 0 0.00% 23 1 0.00% 24 0 0.00% 25 1 0.00% 26 4 0.00% 27 4 0.00% 28 1 0.00% 29 2 0.00% 30 5 0.00% 31 4 0.00% 32 9 0.00% 33 15 0.00% 34 15 0.00% 35 18 0.00% 36 19 0.00% 37 27 0.00% 38 39 0.00% 39 36 0.00% 40 44 0.00% 41 53 0.00% 42 60 0.00% 43 76 0.00% 44 71 0.00% 45 83 0.00% 46 96 0.00% 47 119 0.00% 48 147 0.00% 49 153 0.00% 50 184 0.00% 51 218 0.00% 52 241 0.00% 53 278 0.00% 54 294 0.00% 55 339 0.00% 56 350 0.00% 57 413 0.00% 58 482 0.00% 59 555 0.00% 60 704 0.00% 61 799 0.00% 62 826 0.00% 63 966 0.00% 64 1064 0.01% 65 1180 0.01% 66 1313 0.01% 67 1518 0.01% 68 1813 0.01% 69 2038 0.01% 70 2260 0.01% 71 2574 0.01% 72 3015 0.02% 73 3300 0.02% 74 3891 0.02% 75 4330 0.02% 76 4841 0.02% 77 5587 0.03% 78 6208 0.03% 79 7143 0.04% 80 8053 0.04% 81 9067 0.05% 82 10358 0.05% 83 11445 0.06% 84 12972 0.07% 85 14449 0.07% 86 15949 0.08% 87 17704 0.09% 88 19740 0.10% 89 22063 0.11% 90 24350 0.12% 91 27296 0.14% 92 29906 0.15% 93 32292 0.16% 94 35593 0.18% 95 39100 0.20% 96 41743 0.21% 97 47140 0.24% 98 50275 0.25% 99 54637 0.28% 100 58668 0.30% 101 19125122 96.75% 19767754 reads passed initial QC criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=24 prefix-density=0.48 prefix-fanout=2.1 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=85.06 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=8.7 sequence=AAAAAAAAGTATGTTTGCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCC criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=3.56 fanout-score-rank=11 prefix-density=0.51 prefix-fanout=3.3 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.07 sequence-density-rank=32 fanout-score=24.16 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=6.0 sequence=AAGGAGGAGAACCCCCGTGTGCCCATCATCGTCACTGGTAACGATTTCTCCACGCTCTACGCGCCACTCATCCGTGACGGTCGTATGGAGAAGTTCTACTGGGCCCCCACCCGCGAAGACCGTATCGGTGTCTGCAGGGGTATCTTCCAAACTGACAACATCAGCGACGAGTCCGTCATCAAGATCGTAGACACCTTCCCAGGCCAATCCATCGACTTTTTCGGAGCGCTGCGTGCCCGGGTGTACGACGATGAGGTGCGCAAGTGGGTCAGCTCAACCGGAATAGAGAACATCGGCAAGAAGCTGGTGAACTCGAAGGATGGACCGGTGTCCTTTGAGCAGCCAAAGATGACAATCGAGAAGCTCCTGGAGTACGGCCACATGCTCGTCCAAGAGCAGGACAATGTCAAGCGTGTGCAGCTTGCTGACAAGTACATGAGCGAGGCTGCTCTGGGAGATGCTAACTCAGATGCCATGAAGACTGGTTCCTTCTACGGTTAGAACACTCTTC ERR10610862 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 21:41:08 Started mapping on | Dec 06 21:41:10 Finished on | Dec 06 21:49:33 Mapping speed, Million of reads per hour | 141.48 Number of input reads | 19767754 Average input read length | 193 UNIQUE READS: Uniquely mapped reads number | 17229043 Uniquely mapped reads % | 87.16% Average mapped length | 192.07 Number of splices: Total | 9975673 Number of splices: Annotated (sjdb) | 9284809 Number of splices: GT/AG | 9807116 Number of splices: GC/AG | 117631 Number of splices: AT/AC | 3662 Number of splices: Non-canonical | 47264 Mismatch rate per base, % | 0.88% Deletion rate per base | 0.02% Deletion average length | 2.03 Insertion rate per base | 0.01% Insertion average length | 1.94 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 383217 % of reads mapped to multiple loci | 1.94% Number of reads mapped to too many loci | 33732 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.94% % of reads unmapped: other | 0.79% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2155494 2155494 2155494 N_multimapping 383217 383217 383217 N_noFeature 576322 16712234 675029 N_ambiguous 492669 1888 75604 UnstrandedReadsAssigned:16160052 PositiveStrandReadsAssigned:514921 NegativeStrandReadsAssigned:16478410 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR10610862 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: ERR10610862-trimmed-pair1.fastq ERR10610862-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,767,754 reads, 17,644,683 reads pseudoaligned [quant] estimated average fragment length: 160.914 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,169 rounds 52973 ERR10610862.ke.tsv 35125 ERR10610862.se.tsv 88098 total ==> ERR10610862.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 776.179 0 0 PNS24247 1044 884.086 45.9829 4.24153 PNS24249 1928 1768.09 23.2892 1.07417 PNS24246 1044 884.086 45.9829 4.24153 PNS24248 1044 884.086 45.9829 4.24153 PNS24244 1471 1311.09 69.762 4.33918 PNS24243 293 138.608 0 0 KQK14069 1603 1443.09 1097.77 62.0356 KQK14071 474 315.198 47.7757 12.3607 ==> ERR10610862.se.tsv <== BRADI_1g14170v3 1242 BRADI_1g53295v3 200 BRADI_1g59795v3 659 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 384 BRADI_1g74790v3 63 BRADI_1g09890v3 0 BRADI_1g77505v3 273 BRADI_1g48960v3 0 ERR10610862 completed mapping pipeline successfully