Starting /dee2/code/volunteer_pipeline.sh SRR6958330 current disk space = 1549460307968 free memory = 1596801220 SRR6958330 SRAfilesize 1bb836504f84717bfe157c65231066ba SRR6958330.sra SRR6958330.sra file validated SRR6958330 is paired end SRR6958330 is conventional basespace SRR6958330 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958330_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.8885 33.0 33.0 34.0 32.0 34.0 2 33.24725 34.0 33.0 34.0 33.0 34.0 3 31.78875 33.0 31.0 33.0 31.0 34.0 4 32.14575 33.0 32.0 33.0 31.0 34.0 5 32.793 33.0 33.0 33.0 32.0 34.0 6 36.773 38.0 37.0 38.0 34.0 38.0 7 37.354 38.0 38.0 38.0 36.0 38.0 8 37.46875 38.0 38.0 38.0 37.0 38.0 9 37.5905 38.0 38.0 38.0 38.0 38.0 10-14 37.637550000000005 38.0 38.0 38.0 38.0 38.0 15-19 37.56635 38.0 38.0 38.0 38.0 38.0 20-24 37.6297 38.0 38.0 38.0 38.0 38.0 25-29 37.60045 38.0 38.0 38.0 38.0 38.0 30-34 37.57599999999999 38.0 38.0 38.0 38.0 38.0 35-39 37.5499 38.0 38.0 38.0 38.0 38.0 40-44 37.565 38.0 38.0 38.0 38.0 38.0 45-49 37.49825 38.0 38.0 38.0 37.4 38.0 50-54 37.4574 38.0 38.0 38.0 37.2 38.0 55-59 37.2971 38.0 38.0 38.0 37.0 38.0 60-64 37.18725 38.0 38.0 38.0 36.6 38.0 65-69 37.2858 38.0 38.0 38.0 36.8 38.0 70-74 37.25865 38.0 38.0 38.0 36.4 38.0 75-79 37.10655 38.0 38.0 38.0 35.8 38.0 80-84 37.12465 38.0 38.0 38.0 36.0 38.0 85-89 37.02720000000001 38.0 38.0 38.0 36.0 38.0 90-94 36.9384 38.0 38.0 38.0 35.4 38.0 95-99 36.710699999999996 38.0 38.0 38.0 34.4 38.0 100-104 36.3698 38.0 37.8 38.0 32.8 38.0 105-109 36.28685 38.0 37.8 38.0 33.2 38.0 110-114 36.121 38.0 37.8 38.0 32.8 38.0 115-119 35.71775 38.0 37.2 38.0 31.8 38.0 120-124 35.6069 38.0 37.0 38.0 30.8 38.0 125-129 35.399 38.0 36.8 38.0 30.2 38.0 130-134 34.96585 38.0 36.0 38.0 28.0 38.0 135-139 34.18185 38.0 34.0 38.0 24.8 38.0 140-144 34.043 38.0 33.4 38.0 25.4 38.0 145-149 33.4099 38.0 33.2 38.0 21.4 38.0 150-151 26.872374999999998 32.5 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 0.0 10 1.0 11 1.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 1.0 18 6.0 19 6.0 20 3.0 21 4.0 22 4.0 23 5.0 24 12.0 25 11.0 26 13.0 27 22.0 28 24.0 29 29.0 30 35.0 31 35.0 32 63.0 33 85.0 34 153.0 35 317.0 36 786.0 37 2382.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.75 9.85 9.525 37.875 2 22.975 11.825 34.150000000000006 31.05 3 21.275 17.4 26.450000000000003 34.875 4 25.45 23.625 23.275000000000002 27.650000000000002 5 25.525 28.675 23.175 22.625 6 22.825 31.75 24.025 21.4 7 17.75 24.3 38.224999999999994 19.725 8 20.4 23.799999999999997 29.099999999999998 26.700000000000003 9 19.6 21.975 33.475 24.95 10-14 22.564999999999998 26.064999999999998 26.155 25.215 15-19 22.564025610244098 25.690276110444177 25.8703481392557 25.875350140056025 20-24 22.395 25.825 26.11 25.669999999999998 25-29 22.830000000000002 25.44 25.935000000000002 25.795 30-34 22.74 25.679999999999996 25.95 25.629999999999995 35-39 22.830000000000002 25.785000000000004 25.564999999999998 25.82 40-44 22.814999999999998 25.480000000000004 25.885 25.82 45-49 22.855 25.345000000000002 25.319999999999997 26.479999999999997 50-54 22.49 25.540000000000003 25.729999999999997 26.240000000000002 55-59 23.16 25.295 26.07 25.474999999999998 60-64 22.91102417494232 25.6344668472264 25.60938910622931 25.84511987160197 65-69 22.720000000000002 26.115 25.900000000000002 25.264999999999997 70-74 22.7 25.585 25.990000000000002 25.724999999999998 75-79 23.05730573057306 25.477547754775475 25.902590259025903 25.562556255625562 80-84 23.125 24.915000000000003 26.025 25.935000000000002 85-89 22.686134306715335 25.336266813340668 25.83629181459073 26.14130706535327 90-94 23.175 25.275 26.0 25.55 95-99 23.31 25.055 26.135 25.5 100-104 23.150000000000002 25.365 25.569999999999997 25.915 105-109 23.106155307765388 25.28626431321566 25.346267313365665 26.26131306565328 110-114 22.585 25.290000000000003 25.759999999999998 26.365 115-119 23.22 25.169999999999998 25.44 26.169999999999998 120-124 23.674999999999997 25.290000000000003 25.224999999999998 25.81 125-129 23.50735073507351 24.34743474347435 26.347634763476346 25.797579757975797 130-134 23.305 25.319999999999997 25.2 26.174999999999997 135-139 23.71 25.105 25.2 25.985000000000003 140-144 23.575 25.25 25.405 25.77 145-149 23.875 25.319999999999997 25.580000000000002 25.224999999999998 150-151 24.2375 24.4875 25.5125 25.7625 >>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 0.0 21 0.5 22 0.5 23 0.0 24 0.0 25 0.0 26 1.0 27 1.5 28 2.5 29 6.5 30 6.0 31 7.5 32 13.0 33 16.5 34 22.5 35 33.5 36 46.0 37 65.5 38 86.0 39 114.0 40 138.5 41 156.0 42 179.0 43 202.5 44 218.5 45 209.5 46 209.5 47 211.0 48 191.5 49 166.5 50 161.0 51 159.5 52 143.0 53 116.5 54 96.5 55 98.5 56 90.0 57 81.0 58 76.5 59 76.0 60 76.5 61 67.0 62 58.5 63 52.5 64 44.0 65 42.5 66 42.0 67 37.0 68 32.0 69 26.5 70 29.0 71 26.5 72 21.5 73 14.5 74 7.5 75 7.5 76 6.0 77 3.0 78 1.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.04 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.31 65-69 0.0 70-74 0.0 75-79 0.01 80-84 0.0 85-89 0.005 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.005 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.01 130-134 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 99.75 #Duplication Level Percentage of deduplicated Percentage of total 1 99.74937343358395 99.5 2 0.2506265664160401 0.5 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 0.0 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 0.025 0.0 0.0 0.0 0.0 88-89 0.037500000000000006 0.0 0.0 0.0 0.0 90-91 0.05 0.0 0.0 0.0 0.0 92-93 0.05 0.0 0.0 0.0 0.0 94-95 0.07500000000000001 0.0 0.0 0.0 0.0 96-97 0.1125 0.0 0.0 0.0 0.0 98-99 0.15 0.0 0.0 0.0 0.0 100-101 0.16249999999999998 0.0 0.0 0.0 0.0 102-103 0.225 0.0 0.0 0.0 0.0 104-105 0.25 0.0 0.0 0.0 0.0 106-107 0.3375 0.0 0.0 0.0 0.0 108-109 0.4375 0.0 0.0 0.0 0.0 110-111 0.4875 0.0 0.0 0.0 0.0 112-113 0.55 0.0 0.0 0.0 0.0 114-115 0.6625000000000001 0.0 0.0 0.0 0.0 116-117 0.725 0.0 0.0 0.0 0.0 118-119 0.8999999999999999 0.0 0.0 0.0 0.0 120-121 1.0499999999999998 0.0 0.0 0.0 0.0 122-123 1.1375000000000002 0.0 0.0 0.0 0.0 124-125 1.2875 0.0 0.0 0.0 0.0 126-127 1.4874999999999998 0.0 0.0 0.0 0.0 128-129 1.6625 0.0 0.0 0.0 0.0 130-131 1.875 0.0 0.0 0.0 0.0 132-133 1.9875 0.0 0.0 0.0 0.0 134-135 2.25 0.0 0.0 0.0 0.0 136-137 2.4625 0.0 0.0 0.0 0.0 138-139 2.6624999999999996 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6958330 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958330_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.96625 33.0 33.0 34.0 32.0 34.0 2 33.0505 34.0 33.0 34.0 32.0 34.0 3 33.129 34.0 33.0 34.0 33.0 34.0 4 33.07875 34.0 33.0 34.0 33.0 34.0 5 33.06825 34.0 33.0 34.0 33.0 34.0 6 37.26375 38.0 38.0 38.0 37.0 38.0 7 37.28375 38.0 38.0 38.0 37.0 38.0 8 37.31825 38.0 38.0 38.0 37.0 38.0 9 37.2895 38.0 38.0 38.0 38.0 38.0 10-14 37.2675 38.0 38.0 38.0 37.0 38.0 15-19 37.2471 38.0 38.0 38.0 37.0 38.0 20-24 37.2395 38.0 38.0 38.0 37.0 38.0 25-29 37.125299999999996 38.0 38.0 38.0 37.0 38.0 30-34 37.1541 38.0 38.0 38.0 37.0 38.0 35-39 37.1683 38.0 38.0 38.0 37.0 38.0 40-44 37.11255 38.0 38.0 38.0 37.0 38.0 45-49 37.0979 38.0 38.0 38.0 36.8 38.0 50-54 37.0589 38.0 38.0 38.0 36.6 38.0 55-59 36.975350000000006 38.0 38.0 38.0 36.2 38.0 60-64 36.97085 38.0 38.0 38.0 36.0 38.0 65-69 36.89905 38.0 38.0 38.0 36.0 38.0 70-74 36.866949999999996 38.0 38.0 38.0 36.0 38.0 75-79 36.9276 38.0 38.0 38.0 36.0 38.0 80-84 36.84365 38.0 38.0 38.0 35.8 38.0 85-89 36.6711 38.0 38.0 38.0 35.2 38.0 90-94 36.57135 38.0 38.0 38.0 34.8 38.0 95-99 36.472950000000004 38.0 38.0 38.0 34.4 38.0 100-104 36.4852 38.0 38.0 38.0 34.6 38.0 105-109 36.276650000000004 38.0 38.0 38.0 33.8 38.0 110-114 36.08925 38.0 38.0 38.0 33.6 38.0 115-119 35.9265 38.0 38.0 38.0 33.2 38.0 120-124 35.91215 38.0 38.0 38.0 33.2 38.0 125-129 35.80765 38.0 37.4 38.0 32.8 38.0 130-134 35.61805 38.0 36.8 38.0 32.0 38.0 135-139 35.488099999999996 38.0 36.4 38.0 32.2 38.0 140-144 35.07055 38.0 36.0 38.0 31.0 38.0 145-149 34.4397 38.0 35.6 38.0 27.6 38.0 150-151 30.58775 35.5 29.0 38.0 14.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 16.0 3 1.0 4 0.0 5 1.0 6 0.0 7 1.0 8 1.0 9 1.0 10 1.0 11 3.0 12 1.0 13 0.0 14 2.0 15 0.0 16 1.0 17 3.0 18 5.0 19 4.0 20 6.0 21 5.0 22 6.0 23 6.0 24 15.0 25 13.0 26 15.0 27 21.0 28 21.0 29 21.0 30 30.0 31 49.0 32 50.0 33 82.0 34 104.0 35 195.0 36 514.0 37 2806.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.875 17.25 13.3 31.574999999999996 2 28.564269606614882 22.149837133550488 27.536958155850666 21.748935103983964 3 22.94383149448345 23.495486459378135 29.13741223671013 24.423269809428287 4 26.71679197994987 30.32581453634085 19.548872180451127 23.408521303258144 5 27.662240040090204 32.44800801804059 18.59183162114758 21.297920320721627 6 23.50288148333751 34.97870207967928 19.894763217238786 21.623653219744423 7 21.67376597344024 20.095214232022048 35.20420947131045 23.026810323227263 8 24.630418441493358 23.653219744424955 23.477825106489604 28.238536707592083 9 23.277374091706342 23.25231771485843 27.0107742420446 26.45953395139063 10-14 25.86448832314323 26.04490327753834 23.12318332163977 24.967425077678662 15-19 25.41998896745399 25.565417983049997 24.407000651923173 24.607592397572837 20-24 25.325781876503612 25.265637530072173 24.759422614274257 24.64915797914996 25-29 25.666733507118504 25.300782033286545 24.50872267896531 24.523761780629638 30-34 25.89697334135097 24.94487873321307 24.76949288434556 24.3886550410904 35-39 25.42721122525683 25.69782009521423 24.640440992232524 24.234527687296417 40-44 26.0510096707922 25.82552487848875 23.93646339630205 24.187002054416997 45-49 25.526157546602523 25.571256764882744 24.669272399278412 24.233313289236317 50-54 26.289150588824857 25.74793284891005 24.359809571535955 23.60310699072914 55-59 25.846863098817398 25.190418921627582 24.73441571457206 24.22830226498296 60-64 25.91330493610624 25.84815835630168 24.27461789025307 23.963918817339014 65-69 25.987171777911406 25.32070555221487 24.969933854479855 23.722188815393867 70-74 26.06494938358224 25.729177107346896 23.96511977548361 24.24075373358725 75-79 26.589508492409443 25.05636554937622 24.620471967533444 23.733653990680896 80-84 26.188686807956312 25.547372112831308 24.575379528032467 23.68856155117992 85-89 26.00350789275871 25.47231270358306 24.359809571535955 24.164369832122276 90-94 25.776708759270395 25.741631589496894 24.78953698135899 23.692122669873722 95-99 26.531021349102936 25.538739099929842 24.887240653503056 23.042998897464166 100-104 26.59984966173891 25.742921573540468 24.159358556752693 23.497870207967928 105-109 26.171268226687378 25.20418900636368 24.808337926542066 23.816204840406876 110-114 26.875469807065897 25.452267602104733 24.585316963167124 23.08694562766224 115-119 26.523351373020642 25.846863098817398 24.268390459009822 23.361395069152135 120-124 25.53500726707763 25.70540770811407 25.134065052874256 23.625519971934043 125-129 25.955804980708525 26.17627899984968 24.537756175777922 23.33015984366388 130-134 26.35165606053014 25.945783434383923 24.562810041589415 23.139750463496515 135-139 26.37803166967328 26.35297654840649 24.53898576869112 22.730006013229104 140-144 26.87681667836023 26.28545655006515 24.170592362433595 22.667134409141024 145-149 26.42076776586148 25.744211686879826 24.997494236744515 22.837526310514182 150-151 26.196441994487596 26.359308443998998 23.92883988975194 23.515409671761464 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 4.0 2 3.0 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 0.5 17 0.5 18 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 1.5 25 2.0 26 1.5 27 2.0 28 2.0 29 4.0 30 7.0 31 10.0 32 16.0 33 18.0 34 19.5 35 27.5 36 40.0 37 53.0 38 71.5 39 97.5 40 125.5 41 143.5 42 158.0 43 179.0 44 191.5 45 187.0 46 183.0 47 197.0 48 202.5 49 177.5 50 139.5 51 134.0 52 130.0 53 127.0 54 111.5 55 94.5 56 95.5 57 87.0 58 81.0 59 79.0 60 81.5 61 74.5 62 68.5 63 67.5 64 72.5 65 74.0 66 60.5 67 46.0 68 54.5 69 56.5 70 41.0 71 25.5 72 18.5 73 17.0 74 13.5 75 11.0 76 5.5 77 3.0 78 1.5 79 0.0 80 0.5 81 0.5 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 0.0 2 0.22499999999999998 3 0.3 4 0.25 5 0.22499999999999998 6 0.22499999999999998 7 0.22499999999999998 8 0.22499999999999998 9 0.22499999999999998 10-14 0.22999999999999998 15-19 0.295 20-24 0.24 25-29 0.26 30-34 0.22 35-39 0.22499999999999998 40-44 0.215 45-49 0.22 50-54 0.22499999999999998 55-59 0.22 60-64 0.22499999999999998 65-69 0.22 70-74 0.22999999999999998 75-79 0.20500000000000002 80-84 0.20500000000000002 85-89 0.22499999999999998 90-94 0.22 95-99 0.22999999999999998 100-104 0.22499999999999998 105-109 0.215 110-114 0.22499999999999998 115-119 0.22 120-124 0.23500000000000001 125-129 0.215 130-134 0.215 135-139 0.22 140-144 0.22999999999999998 145-149 0.22999999999999998 150-151 0.22499999999999998 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.45 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57264957264957 99.02499999999999 2 0.32679738562091504 0.65 3 0.07541478129713425 0.22499999999999998 4 0.025138260432378077 0.1 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 90-91 0.025 0.0 0.0 0.0 0.0 92-93 0.025 0.0 0.0 0.0 0.0 94-95 0.05 0.0 0.0 0.0 0.0 96-97 0.0875 0.0 0.0 0.0 0.0 98-99 0.125 0.0 0.0 0.0 0.0 100-101 0.1375 0.0 0.0 0.0 0.0 102-103 0.2 0.0 0.0 0.0 0.0 104-105 0.225 0.0 0.0 0.0 0.0 106-107 0.3125 0.0 0.0 0.0 0.0 108-109 0.4125 0.0 0.0 0.0 0.0 110-111 0.4625 0.0 0.0 0.0 0.0 112-113 0.525 0.0 0.0 0.0 0.0 114-115 0.6375 0.0 0.0 0.0 0.0 116-117 0.7 0.0 0.0 0.0 0.0 118-119 0.875 0.0 0.0 0.0 0.0 120-121 1.025 0.0 0.0 0.0 0.0 122-123 1.1124999999999998 0.0 0.0 0.0 0.0 124-125 1.2625 0.0 0.0 0.0 0.0 126-127 1.4625 0.0 0.0 0.0 0.0 128-129 1.6375 0.0 0.0 0.0 0.0 130-131 1.85 0.0 0.0 0.0 0.0 132-133 1.975 0.0 0.0 0.0 0.0 134-135 2.25 0.0 0.0 0.0 0.0 136-137 2.4625 0.0 0.0 0.0 0.0 138-139 2.6624999999999996 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra Read 1255285 spots for SRR6958330.sra Written 1255285 spots for SRR6958330.sra SRR ids: ['SRR6958330.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hw03jqp1 SRR6958330.sra spots: 25105700 blocks: [[1, 1255285], [1255286, 2510570], [2510571, 3765855], [3765856, 5021140], [5021141, 6276425], [6276426, 7531710], [7531711, 8786995], [8786996, 10042280], [10042281, 11297565], [11297566, 12552850], [12552851, 13808135], [13808136, 15063420], [15063421, 16318705], [16318706, 17573990], [17573991, 18829275], [18829276, 20084560], [20084561, 21339845], [21339846, 22595130], [22595131, 23850415], [23850416, 25105700]] SRR6958330 file size 8485797 SRR6958330 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 SRR6958330 SRR6958330_1.fastq SRR6958330_2.fastq Input file: SRR6958330_1.fastq Paired file: SRR6958330_2.fastq trimmed: SRR6958330-trimmed-pair1.fastq, SRR6958330-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 20:05:19 2024 >> started Fri Dec 6 20:05:49 2024 >> done (30.281s) 25105700 read pairs processed; of these: 22599 ( 0.09%) short read pairs filtered out after trimming by size control 73716 ( 0.29%) empty read pairs filtered out after trimming by size control 25009385 (99.62%) read pairs available; of these: 10885380 (43.53%) trimmed read pairs available after processing 14124005 (56.47%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 2 0.00% 20 3 0.00% 21 3 0.00% 22 5 0.00% 23 5 0.00% 24 4 0.00% 25 9 0.00% 26 9 0.00% 27 6 0.00% 28 5 0.00% 29 8 0.00% 30 7 0.00% 31 8 0.00% 32 5 0.00% 33 4 0.00% 34 5 0.00% 35 8 0.00% 36 8 0.00% 37 2 0.00% 38 7 0.00% 39 12 0.00% 40 11 0.00% 41 10 0.00% 42 14 0.00% 43 20 0.00% 44 12 0.00% 45 15 0.00% 46 17 0.00% 47 28 0.00% 48 30 0.00% 49 37 0.00% 50 36 0.00% 51 34 0.00% 52 39 0.00% 53 51 0.00% 54 47 0.00% 55 64 0.00% 56 54 0.00% 57 82 0.00% 58 87 0.00% 59 90 0.00% 60 109 0.00% 61 108 0.00% 62 142 0.00% 63 158 0.00% 64 149 0.00% 65 208 0.00% 66 184 0.00% 67 221 0.00% 68 220 0.00% 69 303 0.00% 70 363 0.00% 71 456 0.00% 72 460 0.00% 73 546 0.00% 74 613 0.00% 75 633 0.00% 76 754 0.00% 77 805 0.00% 78 912 0.00% 79 1032 0.00% 80 1207 0.00% 81 1284 0.01% 82 1546 0.01% 83 1741 0.01% 84 2671 0.01% 85 3204 0.01% 86 3298 0.01% 87 3732 0.01% 88 3994 0.02% 89 4153 0.02% 90 4411 0.02% 91 4567 0.02% 92 4933 0.02% 93 5108 0.02% 94 5619 0.02% 95 5914 0.02% 96 6326 0.03% 97 6554 0.03% 98 6993 0.03% 99 7521 0.03% 100 8085 0.03% 101 8492 0.03% 102 9299 0.04% 103 9694 0.04% 104 10209 0.04% 105 10867 0.04% 106 11480 0.05% 107 11881 0.05% 108 12527 0.05% 109 13599 0.05% 110 14147 0.06% 111 14928 0.06% 112 15879 0.06% 113 16912 0.07% 114 17878 0.07% 115 19262 0.08% 116 19917 0.08% 117 21261 0.09% 118 21756 0.09% 119 22704 0.09% 120 24211 0.10% 121 25725 0.10% 122 27300 0.11% 123 28416 0.11% 124 30466 0.12% 125 31879 0.13% 126 32942 0.13% 127 35192 0.14% 128 36225 0.14% 129 38682 0.15% 130 40406 0.16% 131 42518 0.17% 132 44970 0.18% 133 47917 0.19% 134 50595 0.20% 135 52952 0.21% 136 56830 0.23% 137 59908 0.24% 138 63787 0.26% 139 69405 0.28% 140 74447 0.30% 141 81709 0.33% 142 90490 0.36% 143 102297 0.41% 144 118291 0.47% 145 143836 0.58% 146 183074 0.73% 147 257326 1.03% 148 406479 1.63% 149 915503 3.66% 150 7286766 29.14% 151 14124005 56.47% 25009385 reads passed initial QC criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=3.12 fanout-score-rank=26 prefix-density=0.40 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=38 fanout-score=213.39 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=8.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=4.48 fanout-score-rank=21 prefix-density=0.37 prefix-fanout=3.3 sequence=AAGATGTACCCAGA criterion=fanout-score sequence-density=0.10 sequence-density-rank=26 fanout-score=145.22 fanout-score-rank=1 prefix-density=0.72 prefix-fanout=20.9 sequence=CAAGAAGAAGGTGCAGACCGAGTGCGCCTCCATGCCTTTCGATGACCAATGCGCCGTCTTGGAAAAGGAGGCCGTGAACGTGTCCCTCGAGAACCTCAAGACCTACCCGTTCGTCAAGGAAGGCGTCGCCAACGGAACCCTCAAGCT SRR6958330 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 20:06:33 Started mapping on | Dec 06 20:06:33 Finished on | Dec 06 20:08:33 Mapping speed, Million of reads per hour | 750.28 Number of input reads | 25009385 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 24060250 Uniquely mapped reads % | 96.20% Average mapped length | 297.52 Number of splices: Total | 26268224 Number of splices: Annotated (sjdb) | 24654729 Number of splices: GT/AG | 25917836 Number of splices: GC/AG | 293414 Number of splices: AT/AC | 13421 Number of splices: Non-canonical | 43553 Mismatch rate per base, % | 0.18% Deletion rate per base | 0.01% Deletion average length | 2.53 Insertion rate per base | 0.01% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 213860 % of reads mapped to multiple loci | 0.86% Number of reads mapped to too many loci | 28575 % of reads mapped to too many loci | 0.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.02% % of reads unmapped: other | 0.80% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 748949 748949 748949 N_multimapping 213860 213860 213860 N_noFeature 1014895 23400995 1235006 N_ambiguous 531725 3662 93881 UnstrandedReadsAssigned:22513630 PositiveStrandReadsAssigned:655593 NegativeStrandReadsAssigned:22731363 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR6958330 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: SRR6958330-trimmed-pair1.fastq SRR6958330-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,009,385 reads, 22,716,639 reads pseudoaligned [quant] estimated average fragment length: 275.564 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,165 rounds 52973 SRR6958330.ke.tsv 35125 SRR6958330.se.tsv 88098 total ==> SRR6958330.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 661.976 26.715 2.59903 PNS24247 1044 769.436 85.4179 7.14949 PNS24249 1928 1653.44 112.177 4.36935 PNS24246 1044 769.436 85.4179 7.14949 PNS24248 1044 769.436 85.4179 7.14949 PNS24244 1471 1196.44 102.854 5.53643 PNS24243 293 78.743 1 0.817875 KQK14069 1603 1328.44 1256.24 60.9019 KQK14071 474 216.461 27.0704 8.05402 ==> SRR6958330.se.tsv <== BRADI_1g14170v3 1432 BRADI_1g53295v3 709 BRADI_1g59795v3 315 BRADI_1g07683v3 0 BRADI_1g00485v3 15 BRADI_1g20270v3 607 BRADI_1g74790v3 656 BRADI_1g09890v3 0 BRADI_1g77505v3 306 BRADI_1g48960v3 1 SRR6958330 completed mapping pipeline successfully