Starting /dee2/code/volunteer_pipeline.sh SRR7169841 current disk space = 3052433248256 free memory = 1576925588 SRR7169841 SRAfilesize e77bbc1d4e38cf83ba68392d70dbf7c5 SRR7169841.sra SRR7169841.sra file validated SRR7169841 is paired end SRR7169841 is conventional basespace SRR7169841 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169841_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 28.20225 31.0 25.0 32.0 18.0 33.0 2 31.94925 33.0 31.0 33.0 29.0 33.0 3 32.256 33.0 33.0 33.0 31.0 34.0 4 32.66275 33.0 33.0 34.0 31.0 34.0 5 33.299 34.0 33.0 34.0 33.0 34.0 6 37.26625 38.0 37.0 38.0 36.0 38.0 7 37.54625 38.0 38.0 38.0 37.0 38.0 8 37.625 38.0 38.0 38.0 38.0 38.0 9 37.64275 38.0 38.0 38.0 38.0 38.0 10-14 37.6309 38.0 38.0 38.0 38.0 38.0 15-19 37.65 38.0 38.0 38.0 38.0 38.0 20-24 37.55 38.0 38.0 38.0 38.0 38.0 25-29 37.56185 38.0 38.0 38.0 38.0 38.0 30-34 37.52875 38.0 38.0 38.0 38.0 38.0 35-39 37.534099999999995 38.0 38.0 38.0 38.0 38.0 40-44 37.48055 38.0 38.0 38.0 37.4 38.0 45-49 37.46335 38.0 38.0 38.0 37.0 38.0 50-54 37.3661 38.0 38.0 38.0 37.0 38.0 55-59 37.30525 38.0 38.0 38.0 37.0 38.0 60-64 37.25345 38.0 38.0 38.0 37.0 38.0 65-69 37.215250000000005 38.0 38.0 38.0 36.4 38.0 70-74 37.1241 38.0 38.0 38.0 36.0 38.0 75-79 36.98175 38.0 38.0 38.0 36.0 38.0 80-84 36.86905 38.0 38.0 38.0 35.8 38.0 85-89 36.81805 38.0 38.0 38.0 35.2 38.0 90-94 36.7732 38.0 38.0 38.0 35.2 38.0 95-99 36.617 38.0 38.0 38.0 34.6 38.0 100-104 36.477250000000005 38.0 38.0 38.0 34.2 38.0 105-109 36.1898 38.0 37.8 38.0 33.4 38.0 110-114 36.063 38.0 37.0 38.0 33.2 38.0 115-119 35.98525 38.0 37.0 38.0 32.8 38.0 120-124 35.65505 38.0 36.8 38.0 31.2 38.0 125-129 35.25935 38.0 36.0 38.0 29.0 38.0 130-134 35.177550000000004 38.0 36.0 38.0 29.4 38.0 135-139 34.912150000000004 38.0 35.6 38.0 28.0 38.0 140-144 34.427800000000005 38.0 35.0 38.0 26.0 38.0 145-149 34.0671 38.0 35.0 38.0 24.6 38.0 150-151 30.543750000000003 36.5 29.5 38.0 8.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 1.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 0.0 15 1.0 16 4.0 17 1.0 18 4.0 19 13.0 20 2.0 21 2.0 22 6.0 23 4.0 24 6.0 25 8.0 26 16.0 27 23.0 28 16.0 29 29.0 30 39.0 31 56.0 32 69.0 33 86.0 34 145.0 35 230.0 36 702.0 37 2535.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.346876587100056 12.87455561198578 9.522600304723209 34.25596749619096 2 22.275 13.675 31.2 32.85 3 18.925 16.775000000000002 27.625 36.675000000000004 4 21.825 22.875 24.75 30.55 5 23.849999999999998 28.675 24.2 23.275000000000002 6 21.099999999999998 33.0 23.625 22.275 7 16.25 27.85 38.574999999999996 17.325 8 16.150000000000002 29.625 29.775000000000002 24.45 9 17.724999999999998 26.525 32.175 23.575 10-14 19.564999999999998 30.255 27.644999999999996 22.535 15-19 20.06 28.73 27.63 23.580000000000002 20-24 20.31 29.675 26.979999999999997 23.035 25-29 19.415 30.240000000000002 26.240000000000002 24.104999999999997 30-34 19.64 29.875 27.169999999999998 23.315 35-39 19.8 28.83 27.205000000000002 24.165 40-44 20.275000000000002 29.459999999999997 26.924999999999997 23.34 45-49 20.080000000000002 28.835 27.315 23.77 50-54 19.93 29.299999999999997 27.034999999999997 23.735 55-59 20.225 28.615000000000002 27.075 24.085 60-64 19.585 28.17 27.72 24.525 65-69 20.085 28.585 27.62 23.71 70-74 20.0 28.585 27.49 23.925 75-79 19.89 28.055000000000003 27.47 24.585 80-84 20.21 28.51 27.529999999999998 23.75 85-89 19.885 28.165000000000003 27.38 24.57 90-94 20.419999999999998 28.22 27.35 24.01 95-99 20.69 28.29 27.02 24.0 100-104 20.599999999999998 28.715000000000003 26.729999999999997 23.955000000000002 105-109 20.974999999999998 28.205000000000002 27.04 23.78 110-114 21.325 28.494999999999997 26.035000000000004 24.145 115-119 20.715 27.71 27.295 24.279999999999998 120-124 20.44 28.16 26.724999999999998 24.675 125-129 20.44 27.405 27.139999999999997 25.014999999999997 130-134 20.785 27.82 27.33 24.065 135-139 20.005 28.37 26.945000000000004 24.68 140-144 20.830000000000002 27.889999999999997 26.924999999999997 24.355 145-149 20.735 27.529999999999998 27.445000000000004 24.29 150-151 20.724999999999998 27.675 26.987499999999997 24.6125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 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 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 0.0 22 1.0 23 2.0 24 1.5 25 4.0 26 6.5 27 5.0 28 7.0 29 13.5 30 23.5 31 40.0 32 42.5 33 47.5 34 66.0 35 79.5 36 94.5 37 107.0 38 122.0 39 146.5 40 169.0 41 180.0 42 205.5 43 233.5 44 256.0 45 266.0 46 261.5 47 267.0 48 236.5 49 193.0 50 176.0 51 149.5 52 129.5 53 107.0 54 86.0 55 66.0 56 38.5 57 37.0 58 36.5 59 28.5 60 18.5 61 12.0 62 10.0 63 6.5 64 5.5 65 3.5 66 1.5 67 1.0 68 2.0 69 2.5 70 1.0 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 1.55 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.125 #Duplication Level Percentage of deduplicated Percentage of total 1 99.34426229508196 98.475 2 0.6305170239596469 1.25 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 0.025220680958385876 0.27499999999999997 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGTAT 11 0.27499999999999997 TruSeq Adapter, Index 6 (97% over 36bp) >>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 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.0625 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 0.175 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2625 0.0 0.0 0.0 0.0 80-81 0.3375 0.0 0.0 0.0 0.0 82-83 0.4375 0.0 0.0 0.0 0.0 84-85 0.525 0.0 0.0 0.0 0.0 86-87 0.625 0.0 0.0 0.0 0.0 88-89 0.7875 0.0 0.0 0.0 0.0 90-91 0.8875 0.0 0.0 0.0 0.0 92-93 0.9875 0.0 0.0 0.0 0.0 94-95 1.1875 0.0 0.0 0.0 0.0 96-97 1.425 0.0 0.0 0.0 0.0 98-99 1.65 0.0 0.0 0.0 0.0 100-101 1.8375 0.0 0.0 0.0 0.0 102-103 2.0875 0.0 0.0 0.0 0.0 104-105 2.45 0.0 0.0 0.0 0.0 106-107 2.8375 0.0 0.0 0.0 0.0 108-109 3.2375 0.0 0.0 0.0 0.0 110-111 3.4749999999999996 0.0 0.0 0.0 0.0 112-113 3.8 0.0 0.0 0.0 0.0 114-115 4.15 0.0 0.0 0.0 0.0 116-117 4.5625 0.0 0.0 0.0 0.0 118-119 4.7875 0.0 0.0 0.0 0.0 120-121 5.050000000000001 0.0 0.0 0.0 0.0 122-123 5.487500000000001 0.0 0.0 0.0 0.0 124-125 5.9125 0.0 0.0 0.0 0.0 126-127 6.3 0.0 0.0 0.0 0.0 128-129 6.637499999999999 0.0 0.0 0.0 0.0 130-131 7.125 0.0 0.0 0.0 0.0 132-133 7.475 0.0 0.0 0.0 0.0 134-135 7.824999999999999 0.0 0.0 0.0 0.0 136-137 8.0875 0.0 0.0 0.0 0.0 138-139 8.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTCATG 10 0.006830828 145.0 1 CCCAACC 10 0.006830828 145.0 2 >>END_MODULE SRR7169841 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169841_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.80175 33.0 33.0 34.0 32.0 34.0 2 32.91675 34.0 33.0 34.0 32.0 34.0 3 32.8925 34.0 33.0 34.0 33.0 34.0 4 32.86675 34.0 33.0 34.0 32.0 34.0 5 32.797 34.0 33.0 34.0 32.0 34.0 6 37.0975 38.0 38.0 38.0 37.0 38.0 7 37.067 38.0 38.0 38.0 37.0 38.0 8 37.1325 38.0 38.0 38.0 37.0 38.0 9 37.0385 38.0 38.0 38.0 37.0 38.0 10-14 37.05535 38.0 38.0 38.0 37.0 38.0 15-19 37.0268 38.0 38.0 38.0 37.0 38.0 20-24 37.022749999999995 38.0 38.0 38.0 37.0 38.0 25-29 37.003 38.0 38.0 38.0 37.0 38.0 30-34 36.97495 38.0 38.0 38.0 37.0 38.0 35-39 36.90465 38.0 38.0 38.0 36.8 38.0 40-44 36.88555 38.0 38.0 38.0 37.0 38.0 45-49 36.853300000000004 38.0 38.0 38.0 36.8 38.0 50-54 36.87585 38.0 38.0 38.0 37.0 38.0 55-59 36.81245 38.0 38.0 38.0 36.2 38.0 60-64 36.763400000000004 38.0 38.0 38.0 36.0 38.0 65-69 36.70674999999999 38.0 38.0 38.0 36.0 38.0 70-74 36.6012 38.0 38.0 38.0 36.0 38.0 75-79 36.49485 38.0 38.0 38.0 35.4 38.0 80-84 36.41844999999999 38.0 38.0 38.0 35.2 38.0 85-89 36.31145 38.0 38.0 38.0 34.6 38.0 90-94 36.2391 38.0 38.0 38.0 34.4 38.0 95-99 36.162400000000005 38.0 38.0 38.0 34.4 38.0 100-104 36.080650000000006 38.0 38.0 38.0 34.0 38.0 105-109 36.019400000000005 38.0 38.0 38.0 34.0 38.0 110-114 35.829750000000004 38.0 38.0 38.0 33.8 38.0 115-119 35.658899999999996 38.0 38.0 38.0 33.0 38.0 120-124 35.4437 38.0 37.6 38.0 31.6 38.0 125-129 35.26185 38.0 36.8 38.0 30.8 38.0 130-134 34.878400000000006 38.0 36.0 38.0 28.2 38.0 135-139 34.64305 38.0 35.8 38.0 27.4 38.0 140-144 34.2193 38.0 35.6 38.0 24.2 38.0 145-149 33.57260000000001 38.0 35.0 38.0 20.0 38.0 150-151 29.447875 35.5 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 29.0 3 4.0 4 1.0 5 1.0 6 3.0 7 3.0 8 1.0 9 1.0 10 3.0 11 1.0 12 2.0 13 6.0 14 5.0 15 4.0 16 7.0 17 2.0 18 4.0 19 5.0 20 12.0 21 7.0 22 8.0 23 10.0 24 11.0 25 12.0 26 16.0 27 22.0 28 29.0 29 36.0 30 27.0 31 47.0 32 63.0 33 69.0 34 102.0 35 192.0 36 467.0 37 2788.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.03450862715679 21.980495123780948 14.053513378344586 25.93148287071768 2 28.08339613162522 25.79753830695805 28.48530519969857 17.633760361718164 3 21.423183303997988 29.067136032185065 30.52552175006286 18.984158913754086 4 24.182184197282336 32.284851534977356 24.13185707096125 19.401107196779062 5 25.415198792148967 35.83291394061399 21.615500754906893 17.136386512330144 6 21.577493092187893 37.30218538055765 22.180356694297913 18.939964832956544 7 20.89927153981412 23.335845265008793 36.850037678975134 18.914845516201957 8 22.481788495352927 25.67194172318513 27.530771163024365 24.315498618437577 9 23.31072594825421 25.42074855563929 28.560663149962323 22.707862346144182 10-14 23.90616366102376 28.552770382277593 26.096348018285028 21.444717938413625 15-19 23.652348656116555 28.078372268274304 27.289625722180354 20.979653353428787 20-24 24.079377040944486 28.500376789751318 26.83245415724692 20.58779201205727 25-29 24.677216779703592 28.359708615925648 26.26475759859332 20.69831700577744 30-34 23.602110022607384 28.4652097462949 26.731976890228587 21.20070334086913 35-39 24.02913840743532 27.902537050992215 27.0936950514946 20.97462949007787 40-44 24.245164531524743 27.591057523235367 27.269530268776688 20.894247676463202 45-49 23.463799427222025 28.146510576295032 27.211978093754713 21.177711902728234 50-54 23.905943827563682 27.930462744309903 27.272270511983116 20.891322916143295 55-59 24.667169053001757 27.942727957799544 26.772167797035923 20.617935192162772 60-64 23.376036171816125 28.585782466716907 27.651343883446373 20.3868374780206 65-69 24.046434494195687 28.08181315644002 27.951153324287652 19.920599025076637 70-74 23.8930492033975 27.76800522691863 27.948937025682262 20.39000854400161 75-79 23.312390047750693 27.816034179442074 27.770796682583565 21.10077909022367 80-84 23.949326362356725 27.810174944701387 27.277297405992357 20.963201286949527 85-89 24.02071705134007 28.144013677276615 27.414894151958563 20.42037511942475 90-94 24.484665661136248 27.169431875314228 27.9587732528909 20.38712921065862 95-99 23.80186069901936 27.684184058335426 27.568518984158914 20.945436258486296 100-104 24.26725654818762 27.856819667186166 27.756271680659594 20.11965210396662 105-109 24.547374773687388 27.20277610138805 27.217863608931804 21.03198551599276 110-114 24.44545043005885 27.433227704843823 27.986519792766963 20.134802072330366 115-119 25.35841843151064 27.511444237637704 27.134161678152825 19.995975652698828 120-124 24.962254655259184 27.75541016607952 26.89481630598893 20.38751887267237 125-129 24.918214303689165 27.86753233680608 26.9968292314661 20.21742412803865 130-134 25.25293199778527 27.67403231489405 26.873710172648106 20.199325514672573 135-139 25.932450797805405 27.744500931192427 26.61700307041828 19.706045200583883 140-144 25.71486105517519 27.87958115183246 26.923076923076923 19.482480869915424 145-149 25.106982832401954 27.644363892664753 27.87595025927604 19.37270301565725 150-151 26.22373222599723 28.287404051843463 26.63898326412483 18.84988045803448 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 9.0 1 9.5 2 5.0 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 1.0 21 2.0 22 1.0 23 0.0 24 1.0 25 3.0 26 3.5 27 3.5 28 5.5 29 7.5 30 10.5 31 11.0 32 14.0 33 24.5 34 31.0 35 41.5 36 57.5 37 78.0 38 102.5 39 135.5 40 182.5 41 218.0 42 270.0 43 298.5 44 303.0 45 327.0 46 304.5 47 253.5 48 228.0 49 215.0 50 181.5 51 145.5 52 122.5 53 93.5 54 69.5 55 60.5 56 47.5 57 34.5 58 26.5 59 17.5 60 13.5 61 11.5 62 6.0 63 2.5 64 3.0 65 4.0 66 3.0 67 1.0 68 1.0 69 0.5 70 0.5 71 0.5 72 0.5 73 0.5 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 0.025 2 0.475 3 0.575 4 0.65 5 0.65 6 0.475 7 0.475 8 0.475 9 0.475 10-14 0.46499999999999997 15-19 0.475 20-24 0.475 25-29 0.475 30-34 0.475 35-39 0.475 40-44 0.475 45-49 0.485 50-54 0.485 55-59 0.475 60-64 0.475 65-69 0.505 70-74 0.515 75-79 0.525 80-84 0.54 85-89 0.565 90-94 0.5499999999999999 95-99 0.575 100-104 0.545 105-109 0.58 110-114 0.5950000000000001 115-119 0.605 120-124 0.65 125-129 0.655 130-134 0.6649999999999999 135-139 0.6649999999999999 140-144 0.6799999999999999 145-149 0.685 150-151 0.6625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.875 #Duplication Level Percentage of deduplicated Percentage of total 1 99.3426042983565 98.225 2 0.5056890012642226 1.0 3 0.025284450063211124 0.075 4 0.07585335018963338 0.3 5 0.025284450063211124 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.025284450063211124 0.27499999999999997 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGGCTATAGTGTAGATCT 11 0.27499999999999997 Illumina Single End PCR Primer 1 (97% over 34bp) CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 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 0.0 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 0.037500000000000006 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.21250000000000002 0.0 0.0 0.0 0.0 80-81 0.275 0.0 0.0 0.0 0.0 82-83 0.36250000000000004 0.0 0.0 0.0 0.0 84-85 0.45 0.0 0.0 0.0 0.0 86-87 0.55 0.0 0.0 0.0 0.0 88-89 0.7125 0.0 0.0 0.0 0.0 90-91 0.8125 0.0 0.0 0.0 0.0 92-93 0.9125000000000001 0.0 0.0 0.0 0.0 94-95 1.1125 0.0 0.0 0.0 0.0 96-97 1.35 0.0 0.0 0.0 0.0 98-99 1.5875 0.0 0.0 0.0 0.0 100-101 1.7875 0.0 0.0 0.0 0.0 102-103 2.025 0.0 0.0 0.0 0.0 104-105 2.375 0.0 0.0 0.0 0.0 106-107 2.775 0.0 0.0 0.0 0.0 108-109 3.1875 0.0 0.0 0.0 0.0 110-111 3.425 0.0 0.0 0.0 0.0 112-113 3.75 0.0 0.0 0.0 0.0 114-115 4.1 0.0 0.0 0.0 0.0 116-117 4.487500000000001 0.0 0.0 0.0 0.0 118-119 4.7125 0.0 0.0 0.0 0.0 120-121 5.0 0.0 0.0 0.0 0.0 122-123 5.4375 0.0 0.0 0.0 0.0 124-125 5.8875 0.0 0.0 0.0 0.0 126-127 6.25 0.0 0.0 0.0 0.0 128-129 6.612500000000001 0.0 0.0 0.0 0.0 130-131 7.1 0.0 0.0 0.0 0.0 132-133 7.449999999999999 0.0 0.0 0.0 0.0 134-135 7.762499999999999 0.0 0.0 0.0 0.0 136-137 8.0125 0.0 0.0 0.0 0.0 138-139 8.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGTGAT 10 0.006830828 145.0 8 >>END_MODULE Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596213 spots for SRR7169841.sra Written 596213 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra Read 596197 spots for SRR7169841.sra Written 596197 spots for SRR7169841.sra SRR ids: ['SRR7169841.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1kqma16v SRR7169841.sra spots: 11923956 blocks: [[1, 596197], [596198, 1192394], [1192395, 1788591], [1788592, 2384788], [2384789, 2980985], [2980986, 3577182], [3577183, 4173379], [4173380, 4769576], [4769577, 5365773], [5365774, 5961970], [5961971, 6558167], [6558168, 7154364], [7154365, 7750561], [7750562, 8346758], [8346759, 8942955], [8942956, 9539152], [9539153, 10135349], [10135350, 10731546], [10731547, 11327743], [11327744, 11923956]] SRR7169841 file size 4018937 SRR7169841 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 SRR7169841 SRR7169841_1.fastq SRR7169841_2.fastq Input file: SRR7169841_1.fastq Paired file: SRR7169841_2.fastq trimmed: SRR7169841-trimmed-pair1.fastq, SRR7169841-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 22:58:16 2025 >> started Tue Feb 11 22:58:30 2025 >> done (14.042s) 11923956 read pairs processed; of these: 25851 ( 0.22%) short read pairs filtered out after trimming by size control 87207 ( 0.73%) empty read pairs filtered out after trimming by size control 11810898 (99.05%) read pairs available; of these: 5103624 (43.21%) trimmed read pairs available after processing 6707274 (56.79%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 8 0.00% 20 7 0.00% 21 8 0.00% 22 7 0.00% 23 5 0.00% 24 12 0.00% 25 3 0.00% 26 5 0.00% 27 7 0.00% 28 6 0.00% 29 7 0.00% 30 13 0.00% 31 12 0.00% 32 11 0.00% 33 11 0.00% 34 21 0.00% 35 13 0.00% 36 18 0.00% 37 22 0.00% 38 25 0.00% 39 25 0.00% 40 28 0.00% 41 39 0.00% 42 39 0.00% 43 40 0.00% 44 33 0.00% 45 63 0.00% 46 77 0.00% 47 91 0.00% 48 98 0.00% 49 120 0.00% 50 147 0.00% 51 153 0.00% 52 183 0.00% 53 205 0.00% 54 236 0.00% 55 261 0.00% 56 293 0.00% 57 386 0.00% 58 403 0.00% 59 431 0.00% 60 513 0.00% 61 647 0.01% 62 688 0.01% 63 768 0.01% 64 934 0.01% 65 1028 0.01% 66 1129 0.01% 67 1298 0.01% 68 1429 0.01% 69 1642 0.01% 70 1946 0.02% 71 2153 0.02% 72 2397 0.02% 73 2817 0.02% 74 3041 0.03% 75 3501 0.03% 76 3983 0.03% 77 4168 0.04% 78 4389 0.04% 79 4752 0.04% 80 5173 0.04% 81 5762 0.05% 82 6202 0.05% 83 6968 0.06% 84 8583 0.07% 85 9417 0.08% 86 9894 0.08% 87 10374 0.09% 88 11204 0.09% 89 11098 0.09% 90 11527 0.10% 91 12025 0.10% 92 12561 0.11% 93 13470 0.11% 94 14042 0.12% 95 15177 0.13% 96 15800 0.13% 97 16183 0.14% 98 16340 0.14% 99 16142 0.14% 100 16975 0.14% 101 17041 0.14% 102 17832 0.15% 103 18066 0.15% 104 18752 0.16% 105 19929 0.17% 106 20470 0.17% 107 20751 0.18% 108 20960 0.18% 109 21249 0.18% 110 21017 0.18% 111 20983 0.18% 112 21750 0.18% 113 22298 0.19% 114 23366 0.20% 115 24268 0.21% 116 24607 0.21% 117 25130 0.21% 118 25446 0.22% 119 25725 0.22% 120 25584 0.22% 121 26756 0.23% 122 26436 0.22% 123 27128 0.23% 124 28486 0.24% 125 29052 0.25% 126 30179 0.26% 127 30620 0.26% 128 31429 0.27% 129 32009 0.27% 130 32948 0.28% 131 33845 0.29% 132 34744 0.29% 133 35560 0.30% 134 37521 0.32% 135 39000 0.33% 136 40102 0.34% 137 42829 0.36% 138 45277 0.38% 139 48428 0.41% 140 50956 0.43% 141 55034 0.47% 142 59743 0.51% 143 65792 0.56% 144 74686 0.63% 145 87287 0.74% 146 107649 0.91% 147 143496 1.21% 148 214897 1.82% 149 458422 3.88% 150 2406371 20.37% 151 6707274 56.79% 11810898 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=2.58 fanout-score-rank=35 prefix-density=0.25 prefix-fanout=2.3 sequence=CCAACATACCAGTGCACAAACGCACGCTTGGCATACATGAGATCAAACTTGTGGTCAATGCGAGAGAAGACTTCTGCAACACTTGTGGAATTGGAAATCATGCAAACAGCCCTCTGAACCTTAGCAAGGTCGCCTCCTGGAACAACAGTTGGTGGCTGGTAGTTGATGCCACACTTGAACCCAGTTGGGCACCAGTCAACGAACTGGATTGTGCGCTTGGTCTTGATGGTAGCCACAGCTGCATTCACATCCTTGGGCACAACATCACCTCTATACATCAGGCAGCAAGCCATGTACTTGCCATGACGTGGGTCACACTTGGCCATCATGGATGATGGCTCAAAAGCACTGTTGGTTATCTCAGCCACAGAGAGCTGCTCATGGTATGCCTTCTCTGCGGAGATGACAGGGGCATAAGAGGAAAGCATGAAATGGATCCTGGGGTATGGAACCAAGTTGGTTTGGAACTCAGTAACATCCACATTAAGAGCTCCATCAAACCTTAATGAGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=47.10 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=4.9 sequence=AACATATTCATCATAACTCAATTACATTATTCTCACCCAGAACATCTCTTCCAGCAATAGATACAAACCATGGCAATTAACTAGAGCAGAACATCATTTCACAAGGTTTATAAGGAAAGAGACCTCCTTGACTTGGACAAACACTCGTCTATAAGAAACACCCAAATTTCCAACTATTCGGCTGTTTATTTCATTAATAACTGGAGAGCAGGAGATGCCAGTGCCTCAGACAAACTGATCAAGGTACTCTTCCACGGTGGTATATTTGACATCTGGATATAGCTCAGAGGCCTCAAGCCCCCATGATGGGTCAATCTCAAAGTTGGTCATGTCACCATTAACGAGGGCTGAGTGGTTGATTGACAGAACAATATTAATCGGAATCGGAGACTCTTGGATGTCCTTCAGAAGTTTCTCTTCAGGAACAAAGGTTTTTTCGAGGGTTTTGCCAATCTTTTTCTCCCATAGATCAATAAGCTCATTGAATGAGTAGGTGTTTTTAGGAGGCTTG criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=6.43 fanout-score-rank=18 prefix-density=0.40 prefix-fanout=3.6 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.03 sequence-density-rank=41 fanout-score=111.26 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=12.6 sequence=GAGGAGAAGGAACACGAGGATACTAGTGTTCCTGTCGAGGTAGTCCATACAGAGACACCCCATGAACCAGAGGATAAGAAGGGTTTCCTTGACAAAATCAAGGAGAAATTGCCAGGACATAAGAAAGCTGACGAGGTCCCTCCTCCAGCTCCTGAACATGTTTCCCCTGAAGCTGCAGTTTCCCATGAAGGAGATG SRR7169841 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 22:59:16 Started mapping on | Feb 11 22:59:16 Finished on | Feb 11 23:00:23 Mapping speed, Million of reads per hour | 634.62 Number of input reads | 11810898 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 11194622 Uniquely mapped reads % | 94.78% Average mapped length | 292.10 Number of splices: Total | 9823676 Number of splices: Annotated (sjdb) | 9662594 Number of splices: GT/AG | 9682214 Number of splices: GC/AG | 111495 Number of splices: AT/AC | 8144 Number of splices: Non-canonical | 21823 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.74 Insertion rate per base | 0.02% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 210254 % of reads mapped to multiple loci | 1.78% Number of reads mapped to too many loci | 16471 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.26% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 417766 417766 417766 N_multimapping 210254 210254 210254 N_noFeature 208471 11058681 252197 N_ambiguous 141341 613 48988 UnstrandedReadsAssigned:10844810 PositiveStrandReadsAssigned:135328 NegativeStrandReadsAssigned:10893437 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7169841 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: SRR7169841-trimmed-pair1.fastq SRR7169841-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,810,898 reads, 10,826,902 reads pseudoaligned [quant] estimated average fragment length: 253.075 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,210 rounds 52401 SRR7169841.ke.tsv 34699 SRR7169841.se.tsv 87100 total ==> SRR7169841.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1765.93 172 8.13583 Potri.005G024800.1.v4.1 1035 782.925 19 2.02712 Potri.004G059700.1.v4.1 961 708.937 2 0.23565 Potri.007G009000.2.v4.1 1416 1163.93 0 0 Potri.003G141000.2.v4.1 2943 2690.93 177 5.49437 Potri.016G087400.1.v4.1 270 84.6171 1057 1043.43 Potri.015G069301.1.v4.1 564 315.591 0 0 Potri.010G195200.1.v4.1 1773 1520.93 14 0.768893 Potri.012G127500.1.v4.1 977 724.937 4709 542.593 ==> SRR7169841.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 955 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 211 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 16 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 1 SRR7169841 completed mapping pipeline successfully