Starting /dee2/code/volunteer_pipeline.sh SRR10225140 current disk space = 3052057374720 free memory = 1574539580 SRR10225140 SRAfilesize f255f32c885c73b89b7b9e6515f032e5 SRR10225140.sra SRR10225140.sra file validated SRR10225140 is paired end SRR10225140 is conventional basespace SRR10225140 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225140_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.834 34.0 31.0 34.0 31.0 34.0 2 33.05375 34.0 33.0 34.0 31.0 34.0 3 33.125 34.0 33.0 34.0 31.0 34.0 4 36.46525 37.0 37.0 37.0 35.0 37.0 5 36.39675 37.0 37.0 37.0 35.0 37.0 6 36.33875 37.0 37.0 37.0 35.0 37.0 7 36.39125 37.0 37.0 37.0 35.0 37.0 8 36.421 37.0 37.0 37.0 35.0 37.0 9 38.28475 39.0 39.0 39.0 37.0 39.0 10-11 38.212374999999994 39.0 39.0 39.0 37.0 39.0 12-13 38.22775 39.0 39.0 39.0 37.0 39.0 14-15 39.809 41.0 40.0 41.0 37.5 41.0 16-17 39.761624999999995 41.0 40.0 41.0 37.0 41.0 18-19 39.679500000000004 41.0 40.0 41.0 37.0 41.0 20-21 39.6385 41.0 40.0 41.0 37.0 41.0 22-23 39.61775 41.0 40.0 41.0 37.0 41.0 24-25 39.56725 41.0 40.0 41.0 37.0 41.0 26-27 39.471374999999995 41.0 40.0 41.0 37.0 41.0 28-29 39.382875 41.0 40.0 41.0 36.0 41.0 30-31 39.288375 41.0 39.0 41.0 36.0 41.0 32-33 39.06575 40.5 39.0 41.0 35.5 41.0 34-35 38.920625 40.0 38.5 41.0 35.0 41.0 36-37 38.708749999999995 40.0 38.0 41.0 35.0 41.0 38-39 38.701 40.0 38.0 41.0 35.0 41.0 40-41 38.492125 40.0 38.0 41.0 34.5 41.0 42-43 38.121624999999995 40.0 38.0 41.0 33.5 41.0 44-45 38.55075 40.0 38.0 41.0 34.5 41.0 46-47 38.62375 41.0 38.0 41.0 35.0 41.0 48-49 38.622875 40.5 38.0 41.0 35.0 41.0 50-51 38.488875 40.0 38.0 41.0 34.5 41.0 52-53 38.376875 40.0 38.0 41.0 34.0 41.0 54-55 38.074625 40.0 37.0 41.0 33.5 41.0 56-57 37.935874999999996 40.0 37.0 41.0 33.5 41.0 58-59 37.635625000000005 40.0 36.0 41.0 33.0 41.0 60-61 37.371 39.0 36.0 41.0 33.0 41.0 62-63 37.09675 39.0 35.0 41.0 33.0 41.0 64-65 36.7245 38.5 35.0 40.5 32.0 41.0 66-67 36.401624999999996 37.0 35.0 40.0 32.0 41.0 68-69 36.063125 37.0 35.0 39.0 32.0 41.0 70-71 35.622749999999996 36.5 35.0 39.0 32.0 41.0 72-73 35.158 36.0 35.0 39.0 31.0 40.0 74-75 34.16775 35.5 35.0 37.0 29.5 39.0 76-77 33.74912500000001 35.0 35.0 37.0 29.5 39.0 78-79 33.528125 35.0 34.5 36.5 30.0 38.0 80-81 33.20825 35.0 34.0 36.0 29.5 37.0 82-83 32.970124999999996 35.0 34.0 36.0 29.5 37.0 84-85 32.831 35.0 34.0 35.0 29.0 36.5 86-87 32.54925 35.0 34.0 35.0 29.0 36.0 88-89 32.393 35.0 34.0 35.0 29.0 36.0 90-91 32.2615 35.0 34.0 35.0 29.0 36.0 92-93 32.152375000000006 35.0 34.0 35.0 29.0 35.0 94-95 31.9665 35.0 34.0 35.0 27.0 35.0 96-97 31.845625 35.0 34.0 35.0 27.0 35.0 98-99 31.8015 35.0 34.0 35.0 27.0 35.0 100 31.697 35.0 34.0 35.0 25.0 35.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 2.0 9 1.0 10 3.0 11 3.0 12 2.0 13 5.0 14 3.0 15 6.0 16 9.0 17 3.0 18 4.0 19 9.0 20 4.0 21 7.0 22 13.0 23 14.0 24 14.0 25 13.0 26 21.0 27 42.0 28 59.0 29 63.0 30 42.0 31 55.0 32 62.0 33 90.0 34 126.0 35 183.0 36 351.0 37 916.0 38 1553.0 39 322.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 28.227021597187342 37.21747865394274 21.848317428427926 12.70718232044199 2 33.975 32.975 18.125 14.924999999999999 3 29.75 33.7 22.05 14.499999999999998 4 28.225 30.15 24.375 17.25 5 26.450000000000003 31.624999999999996 22.075 19.85 6 31.125000000000004 27.150000000000002 23.375 18.35 7 26.700000000000003 29.525000000000002 23.95 19.825 8 22.45 32.800000000000004 26.35 18.4 9 24.325 32.475 25.8 17.4 10-11 25.6 30.5125 25.1875 18.7 12-13 23.9875 30.075000000000003 25.4375 20.5 14-15 22.75 30.012499999999996 26.737499999999997 20.5 16-17 22.725 30.2625 25.4375 21.575 18-19 24.349999999999998 27.1 27.750000000000004 20.8 20-21 23.35 27.900000000000002 27.700000000000003 21.05 22-23 25.224999999999998 29.6375 26.0125 19.125 24-25 23.5625 29.049999999999997 25.25 22.1375 26-27 22.375 29.1125 27.6 20.9125 28-29 23.2875 29.725 25.85 21.1375 30-31 24.825 27.537499999999998 27.962500000000002 19.675 32-33 22.925 29.825000000000003 26.0375 21.212500000000002 34-35 22.650000000000002 29.012500000000003 26.825 21.512500000000003 36-37 23.2375 28.9 26.7625 21.099999999999998 38-39 23.5875 29.825000000000003 25.2875 21.3 40-41 24.1625 29.5375 26.674999999999997 19.625 42-43 23.3625 29.512500000000003 25.8125 21.3125 44-45 23.575 27.712500000000002 27.437499999999996 21.275 46-47 24.7 27.750000000000004 27.675 19.875 48-49 23.7 29.375 27.037499999999998 19.8875 50-51 24.1625 27.825 26.3125 21.7 52-53 24.928116014501814 27.990998874859358 26.328291036379547 20.75259407425928 54-55 23.69046130766346 26.815851981497683 28.003500437554695 21.49018627328416 56-57 22.75 27.2625 29.25 20.7375 58-59 23.1 27.925 28.1875 20.7875 60-61 24.224999999999998 28.4125 26.474999999999998 20.8875 62-63 23.090386298287285 28.528566070758842 28.89111138892362 19.489936242030254 64-65 24.3125 28.9 26.2875 20.5 66-67 22.75 31.3125 26.525 19.412499999999998 68-69 22.877859732466558 30.966370796349548 25.978247280910118 20.177522190273784 70-71 23.62135800925347 30.43641365512067 26.30986619982493 19.632362135800925 72-73 23.15289411176397 31.003875484435557 26.078259782472806 19.764970621327667 74-75 23.6875 29.875 26.7125 19.725 76-77 23.525 29.549999999999997 26.487500000000004 20.4375 78-79 24.775 28.012500000000003 26.775 20.4375 80-81 23.55294411801475 28.403550443805475 28.091011376422053 19.95249406175772 82-83 24.087500000000002 28.000000000000004 27.6375 20.275000000000002 84-85 23.4125 28.449999999999996 27.6875 20.45 86-87 23.7375 28.512500000000003 27.375 20.375 88-89 23.8125 28.3125 27.1375 20.7375 90-91 24.62807850981373 28.391048881110137 27.50343792974122 19.47743467933492 92-93 23.7 28.299999999999997 27.200000000000003 20.8 94-95 24.1875 28.1375 27.6625 20.0125 96-97 24.224999999999998 29.6875 26.75 19.3375 98-99 22.877859732466558 27.815976997124643 28.50356294536817 20.80260032504063 100 23.875 28.275 26.400000000000002 21.45 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 1.0 3 0.5 4 0.0 5 0.0 6 0.5 7 1.0 8 1.0 9 1.0 10 1.5 11 1.0 12 0.0 13 0.5 14 0.5 15 0.5 16 1.0 17 2.5 18 2.5 19 4.0 20 5.5 21 7.0 22 6.5 23 5.5 24 5.5 25 7.5 26 9.0 27 10.5 28 15.5 29 15.0 30 13.5 31 20.0 32 26.0 33 33.0 34 43.5 35 53.0 36 76.5 37 104.0 38 142.0 39 171.0 40 191.5 41 221.5 42 243.5 43 251.5 44 277.0 45 281.5 46 247.0 47 230.5 48 222.5 49 190.5 50 151.0 51 125.5 52 90.5 53 82.0 54 82.0 55 61.0 56 42.5 57 33.0 58 32.5 59 28.5 60 22.5 61 18.0 62 15.0 63 13.0 64 8.5 65 4.5 66 4.0 67 2.5 68 2.0 69 5.0 70 5.0 71 5.0 72 5.0 73 4.5 74 3.5 75 1.5 76 2.0 77 2.5 78 1.0 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 0.44999999999999996 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 0.0125 54-55 0.0125 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0125 64-65 0.0 66-67 0.0 68-69 0.0125 70-71 0.0375 72-73 0.0125 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0125 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0125 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0125 100 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.92500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.24420119885326 95.19999999999999 2 0.49517852488923636 0.95 3 0.07818608287724785 0.22499999999999998 4 0.07818608287724785 0.3 5 0.026062027625749284 0.125 6 0.0 0.0 7 0.026062027625749284 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.026062027625749284 0.44999999999999996 >50 0.0 0.0 >100 0.026062027625749284 2.5749999999999997 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATG 103 2.5749999999999997 TruSeq Adapter, Index 1 (100% over 49bp) CAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTG 18 0.44999999999999996 No Hit AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAAC 7 0.17500000000000002 No Hit AGATCGGAAGAGCACACGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) >>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 3.2 0.0 0.0 0.0 0.0 2 3.225 0.0 0.0 0.0 0.0 3 3.225 0.0 0.0 0.0 0.0 4 3.225 0.0 0.0 0.0 0.0 5 3.225 0.0 0.0 0.0 0.0 6 3.225 0.0 0.0 0.0 0.0 7 3.225 0.0 0.0 0.0 0.0 8 3.225 0.0 0.0 0.0 0.0 9 3.225 0.0 0.0 0.0 0.0 10-11 3.2375 0.0 0.0 0.0 0.0 12-13 3.325 0.0 0.0 0.0 0.0 14-15 3.325 0.0 0.0 0.0 0.0 16-17 3.325 0.0 0.0 0.0 0.0 18-19 3.325 0.0 0.0 0.0 0.0 20-21 3.3625 0.0 0.0 0.0 0.0 22-23 3.375 0.0 0.0 0.0 0.0 24-25 3.375 0.0 0.0 0.0 0.0 26-27 3.3875 0.0 0.0 0.0 0.0 28-29 3.4 0.0 0.0 0.0 0.0 30-31 3.4 0.0 0.0 0.0 0.0 32-33 3.4 0.0 0.0 0.0 0.0 34-35 3.4 0.0 0.0 0.0 0.0 36-37 3.4 0.0 0.0 0.0 0.0 38-39 3.4 0.0 0.0 0.0 0.0 40-41 3.4 0.0 0.0 0.0 0.0 42-43 3.4124999999999996 0.0 0.0 0.0 0.0 44-45 3.45 0.0 0.0 0.0 0.0 46-47 3.45 0.0 0.0 0.0 0.0 48-49 3.45 0.0 0.0 0.0 0.0 50-51 3.45 0.0 0.0 0.0 0.0 52-53 3.4625000000000004 0.0 0.0 0.0 0.0 54-55 3.475 0.0 0.0 0.0 0.0 56-57 3.4875 0.0 0.0 0.0 0.0 58-59 3.5 0.0 0.0 0.0 0.0 60-61 3.5 0.0 0.0 0.0 0.0 62-63 3.5 0.0 0.0 0.0 0.0 64-65 3.5 0.0 0.0 0.0 0.0 66-67 3.5 0.0 0.0 0.0 0.0 68-69 3.5 0.0 0.0 0.0 0.0 70-71 3.5 0.0 0.0 0.0 0.0 72-73 3.5 0.0 0.0 0.0 0.0 74-75 3.5 0.0 0.0 0.0 0.0 76-77 3.5 0.0 0.0 0.0 0.0 78-79 3.5 0.0 0.0 0.0 0.0 80-81 3.525 0.0 0.0 0.0 0.0 82-83 3.575 0.0 0.0 0.0 0.0 84-85 3.575 0.0 0.0 0.0 0.0 86-87 3.575 0.0 0.0 0.0 0.0 88 3.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAGAGC 15 6.4061093E-4 94.0 7 AGAGCAC 15 6.4061093E-4 94.0 9 AGATCGG 15 6.4061093E-4 94.0 1 AAGAGCA 20 0.0020083564 70.5 8 GATCGGA 20 0.0020083564 70.5 2 CGGAAGA 20 0.0020083564 70.5 5 ATCGGAA 20 0.0020083564 70.5 3 TCGGAAG 25 0.0048637707 56.4 4 GGAAGAG 25 0.0048637707 56.4 6 AAAAAAA 85 0.001703774 16.588234 66-67 >>END_MODULE SRR10225140 read2 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225140_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.24925 34.0 31.0 34.0 30.0 34.0 2 32.461 34.0 31.0 34.0 31.0 34.0 3 32.43 34.0 31.0 34.0 30.0 34.0 4 35.807 37.0 37.0 37.0 35.0 37.0 5 35.75075 37.0 37.0 37.0 35.0 37.0 6 35.78425 37.0 37.0 37.0 35.0 37.0 7 35.69675 37.0 37.0 37.0 35.0 37.0 8 35.73975 37.0 37.0 37.0 35.0 37.0 9 37.5255 39.0 39.0 39.0 35.0 39.0 10-11 37.483000000000004 39.0 39.0 39.0 35.0 39.0 12-13 37.476749999999996 39.0 39.0 39.0 35.0 39.0 14-15 38.976124999999996 41.0 39.5 41.0 36.0 41.0 16-17 38.825375 41.0 39.5 41.0 35.5 41.0 18-19 38.6455 41.0 39.0 41.0 34.5 41.0 20-21 38.49425 41.0 39.0 41.0 35.0 41.0 22-23 38.384 41.0 39.0 41.0 34.0 41.0 24-25 38.245875 41.0 39.0 41.0 34.0 41.0 26-27 38.15675 41.0 39.0 41.0 34.0 41.0 28-29 37.989375 40.5 38.5 41.0 33.5 41.0 30-31 37.754999999999995 40.0 38.0 41.0 33.0 41.0 32-33 37.68075 40.0 38.0 41.0 33.0 41.0 34-35 37.563625 40.0 38.0 41.0 33.0 41.0 36-37 37.445625 40.0 38.0 41.0 32.0 41.0 38-39 37.3605 40.0 38.0 41.0 31.5 41.0 40-41 37.42175 40.0 38.0 41.0 32.5 41.0 42-43 37.204875 40.0 38.0 41.0 31.5 41.0 44-45 37.22475 40.0 37.5 41.0 32.0 41.0 46-47 37.454625 40.0 38.0 41.0 32.0 41.0 48-49 37.369749999999996 40.0 38.0 41.0 32.0 41.0 50-51 37.292125 40.0 37.5 41.0 32.0 41.0 52-53 37.076 40.0 37.0 41.0 32.0 41.0 54-55 36.951750000000004 40.0 37.0 41.0 31.5 41.0 56-57 36.673 40.0 36.0 41.0 31.0 41.0 58-59 36.5105 39.5 36.0 41.0 31.5 41.0 60-61 36.284000000000006 39.0 35.0 41.0 31.0 41.0 62-63 36.061499999999995 39.0 35.0 41.0 31.0 41.0 64-65 35.594875 38.0 35.0 40.5 30.0 41.0 66-67 34.872749999999996 37.0 35.0 40.0 28.5 41.0 68-69 34.1935 37.0 35.0 39.5 26.0 41.0 70-71 33.81425 36.5 35.0 39.0 26.0 41.0 72-73 33.4815 36.0 34.0 39.0 26.0 40.5 74-75 33.128 35.5 34.0 37.5 26.0 39.5 76-77 32.75975 35.0 34.0 37.0 25.0 39.0 78-79 32.430875 35.0 34.0 37.0 25.0 39.0 80-81 32.143125 35.0 34.0 36.0 24.5 37.5 82-83 31.841124999999998 35.0 34.0 36.0 24.5 37.0 84-85 31.5865 35.0 33.5 35.5 23.5 37.0 86-87 31.36325 35.0 33.5 35.0 21.5 36.0 88-89 31.145000000000003 35.0 33.0 35.0 19.0 36.0 90-91 30.935499999999998 35.0 33.0 35.0 17.0 36.0 92-93 30.796125 35.0 33.0 35.0 13.0 35.5 94-95 30.617125 35.0 33.0 35.0 4.5 35.0 96-97 30.430500000000002 35.0 33.0 35.0 2.0 35.0 98-99 30.273 35.0 33.0 35.0 2.0 35.0 100 30.19475 35.0 33.0 35.0 2.0 35.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 31.0 3 10.0 4 6.0 5 9.0 6 13.0 7 17.0 8 11.0 9 5.0 10 3.0 11 14.0 12 6.0 13 8.0 14 7.0 15 7.0 16 7.0 17 11.0 18 7.0 19 8.0 20 18.0 21 12.0 22 16.0 23 11.0 24 36.0 25 59.0 26 42.0 27 29.0 28 31.0 29 33.0 30 49.0 31 45.0 32 60.0 33 79.0 34 131.0 35 205.0 36 340.0 37 792.0 38 1443.0 39 388.0 40 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.0 17.4 15.5 28.1 2 30.975 6.5 19.375 43.15 3 17.349999999999998 9.15 21.375 52.125 4 20.825 7.775 22.475 48.925000000000004 5 23.125 11.0 23.25 42.625 6 31.55 11.05 27.775 29.625 7 20.200000000000003 26.55 33.4 19.85 8 14.875 30.95 34.599999999999994 19.575 9 16.0 31.75 33.324999999999996 18.925 10-11 17.75 31.25 31.125000000000004 19.875 12-13 18.675 28.1625 30.562499999999996 22.6 14-15 18.0125 28.037499999999998 32.087500000000006 21.8625 16-17 19.75 28.299999999999997 29.9625 21.987499999999997 18-19 18.337500000000002 30.112499999999997 31.175000000000004 20.375 20-21 17.849999999999998 30.175 30.349999999999998 21.625 22-23 21.8875 28.725 27.925 21.462500000000002 24-25 19.5875 31.4625 27.875 21.075 26-27 18.85 31.9875 27.575 21.587500000000002 28-29 19.875 30.9 27.6375 21.587500000000002 30-31 19.85 29.2375 28.575 22.3375 32-33 19.400000000000002 28.787499999999998 29.275000000000002 22.537499999999998 34-35 19.7625 29.6625 27.825 22.75 36-37 18.387500000000003 29.775000000000002 28.8625 22.975 38-39 19.787499999999998 28.3375 28.425 23.45 40-41 19.85 28.762500000000003 28.075 23.3125 42-43 20.275000000000002 30.162499999999998 28.6625 20.9 44-45 21.6125 29.2875 27.6 21.5 46-47 19.125 28.425 28.7375 23.7125 48-49 19.8625 29.299999999999997 27.150000000000002 23.6875 50-51 19.275000000000002 28.499999999999996 27.6375 24.587500000000002 52-53 18.525 31.45 27.800000000000004 22.225 54-55 18.75 29.275000000000002 28.925 23.05 56-57 18.0375 30.425 29.525000000000002 22.0125 58-59 18.925 29.912499999999998 29.4125 21.75 60-61 18.475 32.125 27.287499999999998 22.112499999999997 62-63 18.95 31.25 27.150000000000002 22.650000000000002 64-65 18.712500000000002 30.662499999999998 28.075 22.55 66-67 19.75 30.3 27.037499999999998 22.912499999999998 68-69 18.475 31.087500000000002 27.537499999999998 22.900000000000002 70-71 18.875 31.2625 27.487499999999997 22.375 72-73 20.2625 29.8875 27.6 22.25 74-75 20.125 30.025000000000002 26.875 22.975 76-77 19.775000000000002 30.362499999999997 26.974999999999998 22.8875 78-79 20.25 29.037499999999998 27.5125 23.200000000000003 80-81 20.0875 29.5875 26.8125 23.5125 82-83 20.3875 29.2375 27.1 23.275000000000002 84-85 19.675 28.749999999999996 28.849999999999998 22.725 86-87 19.9625 29.912499999999998 27.4125 22.7125 88-89 20.275000000000002 29.762499999999996 27.237499999999997 22.725 90-91 20.3125 29.1625 27.375 23.150000000000002 92-93 22.15 29.4125 26.125 22.3125 94-95 20.8 29.049999999999997 27.425 22.725 96-97 19.9375 29.1875 27.8625 23.0125 98-99 20.6125 29.025000000000002 27.625 22.7375 100 20.150000000000002 30.125 26.55 23.175 >>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 0.5 10 1.5 11 1.0 12 0.5 13 2.5 14 2.5 15 2.5 16 3.5 17 2.5 18 3.0 19 4.0 20 4.5 21 3.5 22 6.5 23 12.5 24 11.0 25 10.5 26 15.0 27 19.5 28 23.5 29 24.5 30 29.5 31 43.0 32 61.0 33 71.5 34 72.0 35 101.0 36 125.0 37 127.5 38 150.5 39 181.0 40 203.5 41 206.0 42 206.5 43 223.0 44 216.0 45 216.0 46 219.0 47 200.5 48 181.5 49 159.5 50 134.5 51 112.5 52 91.5 53 77.0 54 67.5 55 49.0 56 39.0 57 35.0 58 34.5 59 36.5 60 35.5 61 29.0 62 19.5 63 13.5 64 13.5 65 11.5 66 9.0 67 6.5 68 5.5 69 5.0 70 4.5 71 3.5 72 1.5 73 3.5 74 5.0 75 2.0 76 0.0 77 0.0 78 0.5 79 1.0 80 0.5 81 0.5 82 0.5 83 0.0 84 0.0 85 0.5 86 0.5 87 0.0 88 0.5 89 0.5 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 0.5 >>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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.1 #Duplication Level Percentage of deduplicated Percentage of total 1 98.00210304942166 93.2 2 1.5772870662460567 3.0 3 0.2103049421661409 0.6 4 0.07886435331230283 0.3 5 0.10515247108307045 0.5 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 0.026288117770767613 2.4 >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 fail #Sequence Count Percentage Possible Source AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 96 2.4 Illumina Single End PCR Primer 1 (100% over 50bp) CGTGTGCTCTTCCGATCTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTG 5 0.125 Illumina Single End PCR Primer 1 (100% over 32bp) GCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCC 5 0.125 No Hit CCCCTCTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCA 5 0.125 No Hit GCCACCATCTACCATCTATACATACATCCCATCATCCCACCATGACCATC 5 0.125 No Hit >>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 2.8 0.0 0.0 0.0 0.0 2 2.825 0.0 0.0 0.0 0.0 3 2.825 0.0 0.0 0.0 0.0 4 2.825 0.0 0.0 0.0 0.0 5 2.825 0.0 0.0 0.0 0.0 6 2.825 0.0 0.0 0.0 0.0 7 2.825 0.0 0.0 0.0 0.0 8 2.825 0.0 0.0 0.0 0.0 9 2.825 0.0 0.0 0.0 0.0 10-11 2.8375000000000004 0.0 0.0 0.0 0.0 12-13 2.925 0.0 0.0 0.0 0.0 14-15 2.925 0.0 0.0 0.0 0.0 16-17 2.9375 0.0 0.0 0.0 0.0 18-19 3.0125 0.0 0.0 0.0 0.0 20-21 3.1 0.0 0.0 0.0 0.0 22-23 3.1 0.0 0.0 0.0 0.0 24-25 3.1125 0.0 0.0 0.0 0.0 26-27 3.1375 0.0 0.0 0.0 0.0 28-29 3.15 0.0 0.0 0.0 0.0 30-31 3.175 0.0 0.0 0.0 0.0 32-33 3.175 0.0 0.0 0.0 0.0 34-35 3.175 0.0 0.0 0.0 0.0 36-37 3.175 0.0 0.0 0.0 0.0 38-39 3.175 0.0 0.0 0.0 0.0 40-41 3.175 0.0 0.0 0.0 0.0 42-43 3.175 0.0 0.0 0.0 0.0 44-45 3.2 0.0 0.0 0.0 0.0 46-47 3.2 0.0 0.0 0.0 0.0 48-49 3.2 0.0 0.0 0.0 0.0 50-51 3.2 0.0 0.0 0.0 0.0 52-53 3.2125000000000004 0.0 0.0 0.0 0.0 54-55 3.225 0.0 0.0 0.0 0.0 56-57 3.225 0.0 0.0 0.0 0.0 58-59 3.225 0.0 0.0 0.0 0.0 60-61 3.225 0.0 0.0 0.0 0.0 62-63 3.225 0.0 0.0 0.0 0.0 64-65 3.225 0.0 0.0 0.0 0.0 66-67 3.225 0.0 0.0 0.0 0.0 68-69 3.225 0.0 0.0 0.0 0.0 70-71 3.225 0.0 0.0 0.0 0.0 72-73 3.225 0.0 0.0 0.0 0.0 74-75 3.225 0.0 0.0 0.0 0.0 76-77 3.225 0.0 0.0 0.0 0.0 78-79 3.225 0.0 0.0 0.0 0.0 80-81 3.2375 0.0 0.0 0.0 0.0 82-83 3.275 0.0 0.0 0.0 0.0 84-85 3.275 0.0 0.0 0.0 0.0 86-87 3.275 0.0 0.0 0.0 0.0 88 3.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGATCGG 20 0.0020083564 70.5 1 >>END_MODULE Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762162 spots for SRR10225140.sra Written 3762162 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra Read 3762146 spots for SRR10225140.sra Written 3762146 spots for SRR10225140.sra SRR ids: ['SRR10225140.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dto1k0qb SRR10225140.sra spots: 75242936 blocks: [[1, 3762146], [3762147, 7524292], [7524293, 11286438], [11286439, 15048584], [15048585, 18810730], [18810731, 22572876], [22572877, 26335022], [26335023, 30097168], [30097169, 33859314], [33859315, 37621460], [37621461, 41383606], [41383607, 45145752], [45145753, 48907898], [48907899, 52670044], [52670045, 56432190], [56432191, 60194336], [60194337, 63956482], [63956483, 67718628], [67718629, 71480774], [71480775, 75242936]] SRR10225140 file size 20574471 SRR10225140 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 SRR10225140 SRR10225140_1.fastq SRR10225140_2.fastq Input file: SRR10225140_1.fastq Paired file: SRR10225140_2.fastq trimmed: SRR10225140-trimmed-pair1.fastq, SRR10225140-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 23:53:44 2025 >> started Tue Feb 11 23:54:53 2025 >> done (69.758s) 75242936 read pairs processed; of these: 580124 ( 0.77%) short read pairs filtered out after trimming by size control 3767137 ( 5.01%) empty read pairs filtered out after trimming by size control 70895675 (94.22%) read pairs available; of these: 9914928 (13.99%) trimmed read pairs available after processing 60980747 (86.01%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 46544 0.07% 19 27388 0.04% 20 37846 0.05% 21 16176 0.02% 22 11214 0.02% 23 11602 0.02% 24 25142 0.04% 25 28843 0.04% 26 21365 0.03% 27 15960 0.02% 28 10225 0.01% 29 12651 0.02% 30 12896 0.02% 31 8675 0.01% 32 9133 0.01% 33 5917 0.01% 34 3758 0.01% 35 4080 0.01% 36 4237 0.01% 37 4595 0.01% 38 4973 0.01% 39 5321 0.01% 40 6141 0.01% 41 6194 0.01% 42 6373 0.01% 43 7511 0.01% 44 7508 0.01% 45 8244 0.01% 46 8420 0.01% 47 8623 0.01% 48 9454 0.01% 49 9985 0.01% 50 10810 0.02% 51 11820 0.02% 52 12135 0.02% 53 12921 0.02% 54 14954 0.02% 55 17353 0.02% 56 16751 0.02% 57 18002 0.03% 58 19415 0.03% 59 153613 0.22% 60 161232 0.23% 61 81979 0.12% 62 87495 0.12% 63 93459 0.13% 64 93555 0.13% 65 96215 0.14% 66 103276 0.15% 67 108523 0.15% 68 105911 0.15% 69 106125 0.15% 70 107235 0.15% 71 104565 0.15% 72 106302 0.15% 73 113268 0.16% 74 112604 0.16% 75 117290 0.17% 76 126676 0.18% 77 118900 0.17% 78 119184 0.17% 79 121885 0.17% 80 125645 0.18% 81 134461 0.19% 82 138949 0.20% 83 150014 0.21% 84 155874 0.22% 85 157323 0.22% 86 150410 0.21% 87 167614 0.24% 88 178011 0.25% 89 199349 0.28% 90 233820 0.33% 91 349834 0.49% 92 246509 0.35% 93 291005 0.41% 94 302334 0.43% 95 1245546 1.76% 96 401589 0.57% 97 509866 0.72% 98 721680 1.02% 99 1174648 1.66% 100 60980747 86.01% 70895675 reads passed initial QC criterion=sequence-density sequence-density=1.12 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=23 prefix-density=1.11 prefix-fanout=2.0 sequence=GATTCCCCTAGTAAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=108.87 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=11.4 sequence=GAGAAGATGATCCAGGAGAAAAAGGCTAAGCAACAGCAGCTCAAGAAACAGGTGTGGGATGGAAAGCCATGTGAAGAAAAGAAAGA criterion=sequence-density sequence-density=1.32 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=21 prefix-density=1.35 prefix-fanout=2.0 sequence=GCTATCGGTCTCTCGCC criterion=fanout-score sequence-density=0.11 sequence-density-rank=12 fanout-score=142.90 fanout-score-rank=1 prefix-density=0.71 prefix-fanout=23.0 sequence=CTTCTTCTTTTT SRR10225140 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 23:55:33 Started mapping on | Feb 11 23:55:33 Finished on | Feb 12 00:05:14 Mapping speed, Million of reads per hour | 439.28 Number of input reads | 70895675 Average input read length | 195 UNIQUE READS: Uniquely mapped reads number | 56787964 Uniquely mapped reads % | 80.10% Average mapped length | 194.57 Number of splices: Total | 22460990 Number of splices: Annotated (sjdb) | 21791879 Number of splices: GT/AG | 21955608 Number of splices: GC/AG | 331462 Number of splices: AT/AC | 30703 Number of splices: Non-canonical | 143217 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 2.47 Insertion rate per base | 0.03% Insertion average length | 2.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2366014 % of reads mapped to multiple loci | 3.34% Number of reads mapped to too many loci | 3837287 % of reads mapped to too many loci | 5.41% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 10.41% % of reads unmapped: other | 0.74% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 12190201 12190201 12190201 N_multimapping 2366014 2366014 2366014 N_noFeature 2781759 3426685 55643643 N_ambiguous 976514 467768 12759 UnstrandedReadsAssigned:53029691 PositiveStrandReadsAssigned:52893511 NegativeStrandReadsAssigned:1131562 Dataset is classified positive stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR10225140 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: SRR10225140-trimmed-pair1.fastq SRR10225140-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 70,895,675 reads, 56,134,501 reads pseudoaligned [quant] estimated average fragment length: 265.71 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,211 rounds 52401 SRR10225140.ke.tsv 34699 SRR10225140.se.tsv 87100 total ==> SRR10225140.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1753.29 13159.5 91.4677 Potri.005G024800.1.v4.1 1035 770.29 902 14.2704 Potri.004G059700.1.v4.1 961 696.304 1407 24.6251 Potri.007G009000.2.v4.1 1416 1151.29 0 0 Potri.003G141000.2.v4.1 2943 2678.29 2175 9.89657 Potri.016G087400.1.v4.1 270 58.4682 3913.35 815.665 Potri.015G069301.1.v4.1 564 299.98 0 0 Potri.010G195200.1.v4.1 1773 1508.29 168 1.3574 Potri.012G127500.1.v4.1 977 712.297 6871 117.555 ==> SRR10225140.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 91 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 906 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 15 Potri.001G416900.v4.1 5 Potri.001G452600.v4.1 1122 SRR10225140 completed mapping pipeline successfully