Starting /dee2/code/volunteer_pipeline.sh ERR3317461 current disk space = 1524938162176 free memory = 1378730920 ERR3317461 SRAfilesize 44ff783e9985b240064896b2fd618b85 ERR3317461.sra ERR3317461.sra file validated ERR3317461 is paired end ERR3317461 is conventional basespace ERR3317461 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317461_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.14025 34.0 31.0 34.0 30.0 34.0 2 32.144 34.0 31.0 34.0 30.0 34.0 3 32.7665 34.0 31.0 34.0 30.0 34.0 4 36.365 37.0 37.0 37.0 35.0 37.0 5 36.37525 37.0 37.0 37.0 35.0 37.0 6 36.3935 37.0 37.0 37.0 35.0 37.0 7 36.36575 37.0 37.0 37.0 35.0 37.0 8 36.4165 37.0 37.0 37.0 35.0 37.0 9 38.2285 39.0 39.0 39.0 37.0 39.0 10-11 38.2055 39.0 39.0 39.0 37.0 39.0 12-13 38.1575 39.0 39.0 39.0 37.0 39.0 14-15 39.655375 41.0 40.0 41.0 37.0 41.0 16-17 39.647875 41.0 40.0 41.0 37.0 41.0 18-19 39.577875 41.0 40.0 41.0 36.5 41.0 20-21 39.56175 41.0 40.0 41.0 37.0 41.0 22-23 39.485375000000005 41.0 39.0 41.0 36.0 41.0 24-25 39.367875 41.0 39.0 41.0 36.0 41.0 26-27 39.220625 41.0 39.0 41.0 36.0 41.0 28-29 38.964 40.0 39.0 41.0 35.5 41.0 30-31 38.79225 40.0 38.5 41.0 35.0 41.0 32-33 38.6435 40.0 38.0 41.0 34.5 41.0 34-35 38.407624999999996 40.0 38.0 41.0 34.0 41.0 36-37 38.103 40.0 38.0 41.0 33.5 41.0 38-39 37.882999999999996 40.0 38.0 41.0 33.0 41.0 40-41 37.66325 40.0 37.5 41.0 32.5 41.0 42-43 37.69325 40.0 38.0 41.0 33.0 41.0 44-45 37.487125000000006 40.0 37.0 41.0 32.5 41.0 46-47 37.265875 40.0 36.5 41.0 32.0 41.0 48-49 36.97375 39.5 35.5 41.0 31.0 41.0 50-51 37.237625 40.0 36.0 41.0 32.0 41.0 52-53 37.123625 40.0 36.0 41.0 32.5 41.0 54-55 36.877125 39.0 35.0 41.0 32.0 41.0 56-57 36.547 39.0 35.0 41.0 31.0 41.0 58-59 36.196 38.5 35.0 41.0 31.0 41.0 60-61 35.831625 37.5 35.0 40.5 30.0 41.0 62-63 35.412875 37.0 35.0 40.0 29.5 41.0 64-65 35.073875 36.5 35.0 39.5 29.0 41.0 66-67 34.567 36.0 34.0 39.0 28.5 41.0 68-69 34.203 35.5 34.0 39.0 27.5 41.0 70-71 33.691625 35.0 34.0 38.0 26.0 40.0 72-73 33.272 35.0 33.0 37.0 26.0 39.0 74-75 32.88575 35.0 33.0 37.0 25.5 39.0 76-77 31.639875 34.5 31.5 35.5 24.5 37.0 78-79 32.1435 35.0 33.0 36.0 25.0 37.0 80-81 31.93525 35.0 33.0 35.0 25.0 37.0 82-83 31.563375 35.0 33.0 35.0 23.5 36.5 84-85 31.2475 35.0 32.0 35.0 22.5 36.0 86-87 31.040875 35.0 32.0 35.0 20.0 36.0 88-89 30.767875 35.0 32.0 35.0 19.5 35.5 90-91 30.4475 35.0 31.5 35.0 18.0 35.0 92-93 30.197499999999998 35.0 31.0 35.0 12.0 35.0 94-95 29.815875 34.5 31.0 35.0 2.0 35.0 96-97 29.44625 34.0 31.0 35.0 2.0 35.0 98-99 29.0805 34.0 30.5 35.0 2.0 35.0 100-101 26.4065 32.0 24.5 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 3.0 9 3.0 10 9.0 11 12.0 12 6.0 13 10.0 14 7.0 15 11.0 16 13.0 17 8.0 18 14.0 19 9.0 20 13.0 21 17.0 22 30.0 23 23.0 24 17.0 25 38.0 26 33.0 27 35.0 28 49.0 29 61.0 30 76.0 31 83.0 32 109.0 33 131.0 34 205.0 35 288.0 36 587.0 37 1003.0 38 963.0 39 131.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.276054097056488 25.351365685494564 17.899761336515514 27.472818880933442 2 28.4 24.474999999999998 17.974999999999998 29.15 3 28.4 24.325 18.675 28.599999999999998 4 30.425 23.125 15.975 30.475 5 28.225 25.124999999999996 15.825 30.825000000000003 6 28.599999999999998 27.825 19.625 23.95 7 30.9 24.474999999999998 20.8 23.825 8 31.0 25.1 25.374999999999996 18.525 9 33.300000000000004 26.424999999999997 24.75 15.525 10-11 32.0125 27.425 22.325 18.2375 12-13 29.15 26.825 23.6375 20.3875 14-15 27.6875 26.200000000000003 25.825 20.2875 16-17 25.4375 25.8 26.275 22.4875 18-19 25.924999999999997 26.974999999999998 26.1625 20.9375 20-21 25.8125 26.0125 26.5125 21.6625 22-23 25.324999999999996 26.424999999999997 26.1625 22.0875 24-25 24.825 26.087500000000002 25.900000000000002 23.1875 26-27 25.650000000000002 26.337500000000002 25.374999999999996 22.6375 28-29 25.900000000000002 25.7875 24.675 23.6375 30-31 26.5 25.5375 25.75 22.2125 32-33 24.825 26.05 24.9375 24.1875 34-35 25.624999999999996 26.2625 24.3125 23.799999999999997 36-37 25.6125 26.987499999999997 25.2625 22.1375 38-39 26.237500000000004 25.724999999999998 25.25 22.787499999999998 40-41 26.087500000000002 25.937500000000004 25.074999999999996 22.900000000000002 42-43 25.224999999999998 26.887499999999996 25.5375 22.35 44-45 26.1 26.1625 25.1 22.6375 46-47 25.137500000000003 25.887500000000003 25.112499999999997 23.8625 48-49 25.474999999999998 27.125 24.8625 22.537499999999998 50-51 25.4375 25.937500000000004 26.1125 22.5125 52-53 26.5625 26.25 24.525 22.662499999999998 54-55 27.537499999999998 25.55 24.8125 22.1 56-57 25.6125 26.625 24.8 22.9625 58-59 25.5375 26.737499999999997 24.5375 23.1875 60-61 25.912499999999998 26.275 24.6 23.2125 62-63 25.587500000000002 27.5875 24.4125 22.412499999999998 64-65 26.6 25.5 24.525 23.375 66-67 26.200000000000003 26.325 25.0375 22.4375 68-69 25.900000000000002 26.4125 24.637500000000003 23.05 70-71 26.525 26.05 24.275 23.150000000000002 72-73 25.362499999999997 26.125 25.074999999999996 23.4375 74-75 25.7875 25.974999999999998 25.224999999999998 23.0125 76-77 26.237500000000004 26.6 24.0125 23.150000000000002 78-79 26.200000000000003 26.2125 24.6625 22.925 80-81 26.0625 26.5125 24.5 22.925 82-83 26.55 26.5125 24.462500000000002 22.475 84-85 26.275 26.200000000000003 24.4125 23.1125 86-87 25.7125 26.0625 24.587500000000002 23.6375 88-89 25.924999999999997 26.6 23.7125 23.7625 90-91 25.85 27.237499999999997 24.4875 22.425 92-93 26.5125 26.974999999999998 23.1375 23.375 94-95 25.575 26.8375 23.6625 23.925 96-97 25.825 25.724999999999998 25.1875 23.2625 98-99 25.6125 26.4625 23.962500000000002 23.962500000000002 100-101 25.85 26.924999999999997 23.9 23.325000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 3.0 1 1.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 1.0 8 1.0 9 0.0 10 0.5 11 1.0 12 1.0 13 1.0 14 0.5 15 3.0 16 3.0 17 0.5 18 1.5 19 1.5 20 1.5 21 1.5 22 0.5 23 0.5 24 2.0 25 2.5 26 5.5 27 8.0 28 9.5 29 13.0 30 13.0 31 14.0 32 15.0 33 16.5 34 24.0 35 31.0 36 37.0 37 50.0 38 70.0 39 88.5 40 117.0 41 151.5 42 163.0 43 179.5 44 197.5 45 190.5 46 191.0 47 203.0 48 187.0 49 173.5 50 190.0 51 177.5 52 152.5 53 132.0 54 111.5 55 106.5 56 93.0 57 81.0 58 71.5 59 62.0 60 65.0 61 61.5 62 47.5 63 39.5 64 45.5 65 43.5 66 41.5 67 39.5 68 29.0 69 35.5 70 37.0 71 23.5 72 20.0 73 17.0 74 15.5 75 17.0 76 15.5 77 12.5 78 5.5 79 6.0 80 6.5 81 3.0 82 4.0 83 5.5 84 3.0 85 1.5 86 2.0 87 2.0 88 1.0 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 0.5 99 0.5 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 5.7250000000000005 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 97.925 #Duplication Level Percentage of deduplicated Percentage of total 1 98.39162624457492 96.35000000000001 2 1.2764871074802144 2.5 3 0.17870819504723004 0.525 4 0.12764871074802145 0.5 5 0.025529742149604292 0.125 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 warn #Sequence Count Percentage Possible Source TGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTG 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 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 0.037500000000000006 0.0 0.0 0.0 0.0 30-31 0.07500000000000001 0.0 0.0 0.0 0.0 32-33 0.15 0.0 0.0 0.0 0.0 34-35 0.1875 0.0 0.0 0.0 0.0 36-37 0.2 0.0 0.0 0.0 0.0 38-39 0.2 0.0 0.0 0.0 0.0 40-41 0.21250000000000002 0.0 0.0 0.0 0.0 42-43 0.225 0.0 0.0 0.0 0.0 44-45 0.30000000000000004 0.0 0.0 0.0 0.0 46-47 0.3875 0.0 0.0 0.0 0.0 48-49 0.4625 0.0 0.0 0.0 0.0 50-51 0.5 0.0 0.0 0.0 0.0 52-53 0.625 0.0 0.0 0.0 0.0 54-55 0.7875000000000001 0.0 0.0 0.0 0.0 56-57 0.85 0.0 0.0 0.0 0.0 58-59 0.875 0.0 0.0 0.0 0.0 60-61 0.975 0.0 0.0 0.0 0.0 62-63 1.1375000000000002 0.0 0.0 0.0 0.0 64-65 1.225 0.0 0.0 0.0 0.0 66-67 1.4 0.0 0.0 0.0 0.0 68-69 1.5625 0.0 0.0 0.0 0.0 70-71 1.6749999999999998 0.0 0.0 0.0 0.0 72-73 1.9375 0.0 0.0 0.0 0.0 74-75 2.2125 0.0 0.0 0.0 0.0 76-77 2.575 0.0 0.0 0.0 0.0 78-79 2.8499999999999996 0.0 0.0 0.0 0.0 80-81 3.2249999999999996 0.0 0.0 0.0 0.0 82-83 3.55 0.0 0.0 0.0 0.0 84-85 4.0375 0.0 0.0 0.0 0.0 86-87 4.325 0.0 0.0 0.0 0.0 88-89 4.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3317461 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317461_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.94675 33.0 31.0 34.0 28.0 34.0 2 31.32675 33.0 31.0 34.0 28.0 34.0 3 31.6625 34.0 31.0 34.0 30.0 34.0 4 35.0835 37.0 35.0 37.0 33.0 37.0 5 34.2595 37.0 35.0 37.0 32.0 37.0 6 34.72625 37.0 35.0 37.0 32.0 37.0 7 35.15625 37.0 35.0 37.0 32.0 37.0 8 35.295 37.0 36.0 37.0 35.0 37.0 9 37.11675 39.0 38.0 39.0 35.0 39.0 10-11 37.02425 39.0 38.0 39.0 35.0 39.0 12-13 37.090875 39.0 38.0 39.0 35.0 39.0 14-15 38.4955 41.0 39.5 41.0 35.5 41.0 16-17 38.454375 41.0 39.0 41.0 35.0 41.0 18-19 38.397000000000006 41.0 39.0 41.0 35.0 41.0 20-21 38.37225 41.0 39.0 41.0 35.0 41.0 22-23 38.2705 41.0 39.0 41.0 35.0 41.0 24-25 38.145875000000004 41.0 39.0 41.0 34.0 41.0 26-27 38.052125000000004 41.0 38.5 41.0 34.0 41.0 28-29 37.888374999999996 40.5 38.0 41.0 33.5 41.0 30-31 37.730625 40.0 38.0 41.0 33.0 41.0 32-33 37.59 40.0 38.0 41.0 33.0 41.0 34-35 37.478875 40.0 38.0 41.0 33.0 41.0 36-37 37.426875 40.0 38.0 41.0 33.0 41.0 38-39 37.366749999999996 40.0 38.0 41.0 33.0 41.0 40-41 37.394999999999996 40.0 38.0 41.0 33.0 41.0 42-43 37.303 40.0 38.0 41.0 33.0 41.0 44-45 37.202875 40.0 37.5 41.0 33.0 41.0 46-47 37.086875 40.0 37.0 41.0 32.0 41.0 48-49 36.795249999999996 40.0 36.5 41.0 31.0 41.0 50-51 36.028625000000005 39.0 35.5 40.5 30.0 40.5 52-53 35.937250000000006 39.0 35.0 40.5 30.0 41.0 54-55 36.162375 39.0 35.0 41.0 31.0 41.0 56-57 35.994625 39.0 35.0 41.0 30.0 41.0 58-59 35.8125 39.0 35.0 41.0 30.0 41.0 60-61 35.462375 38.5 35.0 41.0 28.5 41.0 62-63 35.00075 38.0 35.0 40.0 27.5 41.0 64-65 34.73375 37.0 34.5 40.0 28.0 41.0 66-67 34.86875 37.0 35.0 40.0 29.0 41.0 68-69 34.43925 36.0 35.0 39.0 29.0 41.0 70-71 34.184 36.0 35.0 39.0 28.5 41.0 72-73 33.748125 35.5 34.5 38.5 28.0 40.5 74-75 33.29175 35.0 34.0 37.0 27.0 39.0 76-77 33.06275 35.0 34.0 37.0 27.0 39.0 78-79 32.713875 35.0 34.0 36.0 26.5 39.0 80-81 32.415 35.0 34.0 36.0 26.5 37.0 82-83 32.154375 35.0 34.0 35.5 26.0 37.0 84-85 31.904125 35.0 34.0 35.0 25.0 36.5 86-87 31.665374999999997 35.0 33.0 35.0 24.0 36.0 88-89 31.59275 35.0 33.0 35.0 25.0 36.0 90-91 31.418999999999997 35.0 33.0 35.0 24.0 36.0 92-93 31.253875 35.0 33.0 35.0 24.0 35.0 94-95 30.985125 35.0 33.0 35.0 21.5 35.0 96-97 30.866875 35.0 33.0 35.0 20.0 35.0 98-99 30.608375000000002 35.0 33.0 35.0 10.0 35.0 100-101 28.652625 33.5 29.0 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 89.0 3 3.0 4 3.0 5 3.0 6 9.0 7 4.0 8 10.0 9 7.0 10 5.0 11 10.0 12 8.0 13 7.0 14 7.0 15 13.0 16 11.0 17 9.0 18 13.0 19 12.0 20 9.0 21 14.0 22 10.0 23 8.0 24 16.0 25 16.0 26 17.0 27 20.0 28 33.0 29 35.0 30 44.0 31 54.0 32 71.0 33 118.0 34 162.0 35 275.0 36 455.0 37 937.0 38 1261.0 39 222.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.09757317988491 10.457843382536902 28.946710032524393 30.497873405053788 2 26.025 11.375 26.35 36.25 3 22.225 12.8 30.625000000000004 34.35 4 24.25 11.475 27.500000000000004 36.775000000000006 5 25.199280020570843 14.55386988943173 24.247878632039086 35.99897145795835 6 24.2 19.625 30.475 25.7 7 18.45 24.7 39.475 17.375 8 17.275 25.624999999999996 35.949999999999996 21.15 9 17.5 28.925 34.0 19.575 10-11 18.875 27.150000000000002 32.6625 21.3125 12-13 19.075 27.462500000000002 32.925 20.5375 14-15 20.200000000000003 26.700000000000003 31.0 22.1 16-17 20.2375 27.150000000000002 29.0875 23.525 18-19 20.0125 27.675 29.6375 22.675 20-21 20.325 25.9625 29.762499999999996 23.95 22-23 20.9875 25.35 28.549999999999997 25.112499999999997 24-25 19.8375 26.325 30.4375 23.400000000000002 26-27 21.0375 26.75 28.15 24.0625 28-29 20.6375 25.6 27.975 25.7875 30-31 20.225 26.375 29.6375 23.7625 32-33 21.375 25.4875 28.1125 25.025 34-35 21.5625 25.624999999999996 27.325 25.4875 36-37 20.3375 26.3125 28.5625 24.7875 38-39 21.6875 26.5625 26.637499999999996 25.112499999999997 40-41 21.087500000000002 24.675 28.275 25.9625 42-43 21.224999999999998 26.1125 28.1 24.5625 44-45 21.7375 26.887499999999996 27.1 24.275 46-47 21.075 25.224999999999998 27.5875 26.1125 48-49 20.4375 26.224999999999998 28.012500000000003 25.324999999999996 50-51 21.349999999999998 26.2875 27.5875 24.775 52-53 21.0375 26.424999999999997 27.4125 25.124999999999996 54-55 21.212500000000002 25.0625 29.65 24.075 56-57 21.125 25.687500000000004 28.012500000000003 25.174999999999997 58-59 20.8 25.6 27.575 26.025 60-61 21.462500000000002 25.9625 28.0625 24.5125 62-63 21.8 26.1125 27.275 24.8125 64-65 21.325 25.374999999999996 28.349999999999998 24.95 66-67 21.7375 26.0125 28.3875 23.8625 68-69 21.6 25.775 28.1 24.525 70-71 21.8875 26.05 26.887499999999996 25.174999999999997 72-73 21.975 24.8125 28.325 24.887500000000003 74-75 22.75 25.674999999999997 26.75 24.825 76-77 22.575 25.224999999999998 26.7125 25.4875 78-79 21.1375 27.037499999999998 25.8 26.025 80-81 21.375 26.05 27.3125 25.2625 82-83 22.412499999999998 25.674999999999997 26.5875 25.324999999999996 84-85 22.425 26.487500000000004 26.75 24.337500000000002 86-87 23.225 26.5125 26.05 24.212500000000002 88-89 21.175 26.174999999999997 27.200000000000003 25.45 90-91 23.45 26.5875 26.4625 23.5 92-93 23.549999999999997 27.0875 25.9875 23.375 94-95 23.2125 25.4 26.3125 25.074999999999996 96-97 23.3625 26.337500000000002 26.2875 24.0125 98-99 23.1 25.35 26.825 24.725 100-101 23.8125 24.9375 25.5 25.75 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 27.0 1 20.0 2 11.0 3 6.0 4 2.0 5 3.0 6 4.5 7 5.5 8 4.0 9 3.5 10 3.5 11 1.0 12 2.5 13 3.0 14 1.5 15 1.0 16 1.0 17 2.5 18 2.5 19 2.5 20 4.5 21 3.5 22 2.0 23 1.5 24 3.5 25 5.5 26 6.5 27 9.0 28 8.5 29 8.0 30 13.5 31 16.5 32 22.0 33 28.0 34 44.0 35 58.5 36 63.5 37 90.0 38 103.5 39 109.5 40 132.0 41 159.0 42 204.5 43 229.5 44 228.0 45 201.0 46 175.5 47 177.5 48 168.5 49 161.5 50 162.5 51 158.5 52 131.0 53 111.0 54 104.5 55 89.5 56 75.0 57 67.0 58 68.5 59 61.5 60 45.0 61 34.5 62 41.5 63 48.0 64 39.5 65 31.5 66 30.5 67 27.0 68 22.0 69 20.0 70 17.0 71 17.0 72 13.0 73 9.0 74 7.0 75 4.0 76 3.5 77 6.0 78 7.0 79 4.5 80 3.5 81 2.0 82 0.5 83 0.5 84 1.0 85 1.0 86 1.0 87 0.5 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.075 2 0.0 3 0.0 4 0.0 5 2.775 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 97.32499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 99.07526329309016 96.42500000000001 2 0.565116876444901 1.0999999999999999 3 0.12843565373747753 0.375 4 0.025687130747495505 0.1 5 0.12843565373747753 0.625 6 0.05137426149499101 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.025687130747495505 1.075 >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 fail #Sequence Count Percentage Possible Source TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 1.075 No Hit TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit TGGGGGTGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 6 0.15 No Hit TCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 5 0.125 No Hit CCACCAAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTGG 5 0.125 No Hit TGGGGATGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 5 0.125 No Hit TCTTCGTATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 5 0.125 No Hit TGTATTATAAGAAATCAACTTGCTTAGGCCTTGCCGGACTCCTCACAACC 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 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 0.0125 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.16249999999999998 0.0 0.0 0.0 0.0 36-37 0.175 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.1875 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.275 0.0 0.0 0.0 0.0 46-47 0.3875 0.0 0.0 0.0 0.0 48-49 0.4625 0.0 0.0 0.0 0.0 50-51 0.5 0.0 0.0 0.0 0.0 52-53 0.5874999999999999 0.0 0.0 0.0 0.0 54-55 0.7375 0.0 0.0 0.0 0.0 56-57 0.8 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.925 0.0 0.0 0.0 0.0 62-63 1.0625 0.0 0.0 0.0 0.0 64-65 1.15 0.0 0.0 0.0 0.0 66-67 1.3 0.0 0.0 0.0 0.0 68-69 1.4625 0.0 0.0 0.0 0.0 70-71 1.5750000000000002 0.0 0.0 0.0 0.0 72-73 1.8375 0.0 0.0 0.0 0.0 74-75 2.0999999999999996 0.0 0.0 0.0 0.0 76-77 2.5 0.0 0.0 0.0 0.0 78-79 2.8 0.0 0.0 0.0 0.0 80-81 3.1500000000000004 0.0 0.0 0.0 0.0 82-83 3.5 0.0 0.0 0.0 0.0 84-85 4.012499999999999 0.0 0.0 0.0 0.0 86-87 4.3 0.0 0.0 0.0 0.0 88-89 4.487500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964468 spots for ERR3317461.sra Written 1964468 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra Read 1964455 spots for ERR3317461.sra Written 1964455 spots for ERR3317461.sra SRR ids: ['ERR3317461.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r9tb5hcd ERR3317461.sra spots: 39289113 blocks: [[1, 1964455], [1964456, 3928910], [3928911, 5893365], [5893366, 7857820], [7857821, 9822275], [9822276, 11786730], [11786731, 13751185], [13751186, 15715640], [15715641, 17680095], [17680096, 19644550], [19644551, 21609005], [21609006, 23573460], [23573461, 25537915], [25537916, 27502370], [27502371, 29466825], [29466826, 31431280], [31431281, 33395735], [33395736, 35360190], [35360191, 37324645], [37324646, 39289113]] ERR3317461 file size 9455263 ERR3317461 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 ERR3317461 ERR3317461_1.fastq ERR3317461_2.fastq Input file: ERR3317461_1.fastq Paired file: ERR3317461_2.fastq trimmed: ERR3317461-trimmed-pair1.fastq, ERR3317461-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Dec 10 10:03:43 2024 >> started Tue Dec 10 10:06:07 2024 >> done (143.886s) 39289113 read pairs processed; of these: 294935 ( 0.75%) short read pairs filtered out after trimming by size control 849682 ( 2.16%) empty read pairs filtered out after trimming by size control 38144496 (97.09%) read pairs available; of these: 10330483 (27.08%) trimmed read pairs available after processing 27814013 (72.92%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 559 0.00% 19 532 0.00% 20 739 0.00% 21 918 0.00% 22 1347 0.00% 23 1829 0.00% 24 2223 0.01% 25 2661 0.01% 26 3048 0.01% 27 3653 0.01% 28 3988 0.01% 29 4377 0.01% 30 4689 0.01% 31 6279 0.02% 32 6518 0.02% 33 7022 0.02% 34 7948 0.02% 35 8204 0.02% 36 9459 0.02% 37 9758 0.03% 38 11252 0.03% 39 11951 0.03% 40 12643 0.03% 41 13986 0.04% 42 14766 0.04% 43 15752 0.04% 44 16986 0.04% 45 17804 0.05% 46 19034 0.05% 47 21108 0.06% 48 22198 0.06% 49 22675 0.06% 50 25450 0.07% 51 25941 0.07% 52 27310 0.07% 53 29735 0.08% 54 34597 0.09% 55 36894 0.10% 56 36170 0.09% 57 40405 0.11% 58 41760 0.11% 59 60114 0.16% 60 71668 0.19% 61 77044 0.20% 62 83560 0.22% 63 89409 0.23% 64 93254 0.24% 65 99230 0.26% 66 107887 0.28% 67 108823 0.29% 68 110699 0.29% 69 113364 0.30% 70 117651 0.31% 71 124453 0.33% 72 134880 0.35% 73 133509 0.35% 74 133020 0.35% 75 133333 0.35% 76 132967 0.35% 77 137174 0.36% 78 152502 0.40% 79 145509 0.38% 80 149376 0.39% 81 155731 0.41% 82 152752 0.40% 83 164584 0.43% 84 165731 0.43% 85 178368 0.47% 86 184081 0.48% 87 192412 0.50% 88 195160 0.51% 89 218765 0.57% 90 211354 0.55% 91 221541 0.58% 92 233040 0.61% 93 253788 0.67% 94 274928 0.72% 95 300218 0.79% 96 339788 0.89% 97 410439 1.08% 98 577295 1.51% 99 751371 1.97% 100 2055543 5.39% 101 27814013 72.92% 38144496 reads passed initial QC criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=0.44 prefix-fanout=2.0 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCC criterion=fanout-score sequence-density=0.07 sequence-density-rank=24 fanout-score=48.24 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=10.5 sequence=GAGGAGAAGAAACTTACAAGGATTCCCCTAGTAACGGCGAGCGAACCGGGAGCAGCCCAGCTTGAGAATCGGGCGG criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=25 prefix-density=0.42 prefix-fanout=2.1 sequence=GTGGCGTCGGTGCACCCGAACATGGGCAGCTTCCACATTGTCCAGTACCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=55.46 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=6.7 sequence=AGCTTCCTCTGTAATGTACATACCAATCACATCCACTCCTCGATCCACCATGCATCCATACACATAGCATGCATAACACTAGCACGGAGTAGTACTTTACAACACAAATTAAGTGCATTGTCGACCATTTCAACTAGAGAGACATATCGTCCCATCAATCAATTTTACATGCATGCA ERR3317461 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 10:06:52 Started mapping on | Dec 10 10:06:52 Finished on | Dec 10 10:11:13 Mapping speed, Million of reads per hour | 526.13 Number of input reads | 38144496 Average input read length | 194 UNIQUE READS: Uniquely mapped reads number | 33981308 Uniquely mapped reads % | 89.09% Average mapped length | 192.89 Number of splices: Total | 21079547 Number of splices: Annotated (sjdb) | 20050529 Number of splices: GT/AG | 20770922 Number of splices: GC/AG | 272342 Number of splices: AT/AC | 18128 Number of splices: Non-canonical | 18155 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.00% Deletion average length | 1.19 Insertion rate per base | 0.00% Insertion average length | 1.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2288507 % of reads mapped to multiple loci | 6.00% Number of reads mapped to too many loci | 123255 % of reads mapped to too many loci | 0.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.48% % of reads unmapped: other | 2.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2124457 2124457 2124457 N_multimapping 2288507 2288507 2288507 N_noFeature 1308522 3557835 31006805 N_ambiguous 1050148 358236 24839 UnstrandedReadsAssigned:31622638 PositiveStrandReadsAssigned:30065237 NegativeStrandReadsAssigned:2949664 Dataset is classified positive stranded MeadianReadLen=101 20thPercentileLength=100 echo kmer=95 ERR3317461 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: ERR3317461-trimmed-pair1.fastq ERR3317461-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,144,496 reads, 31,817,721 reads pseudoaligned [quant] estimated average fragment length: 216.893 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,279 rounds 52973 ERR3317461.ke.tsv 35125 ERR3317461.se.tsv 88098 total ==> ERR3317461.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 720.282 0 0 PNS24247 1044 828.107 53.3275 2.99169 PNS24249 1928 1712.11 77.8284 2.11183 PNS24246 1044 828.107 53.3275 2.99169 PNS24248 1044 828.107 53.3275 2.99169 PNS24244 1471 1255.11 240.189 8.89048 PNS24243 293 117.963 0 0 KQK14069 1603 1387.11 3605.74 120.764 KQK14071 474 269.85 26.9902 4.64661 ==> ERR3317461.se.tsv <== BRADI_1g14170v3 4265 BRADI_1g53295v3 254 BRADI_1g59795v3 876 BRADI_1g07683v3 0 BRADI_1g00485v3 116 BRADI_1g20270v3 2461 BRADI_1g74790v3 325 BRADI_1g09890v3 8 BRADI_1g77505v3 417 BRADI_1g48960v3 1 ERR3317461 completed mapping pipeline successfully