Starting /dee2/code/volunteer_pipeline.sh ERR3450083 current disk space = 1542839619584 free memory = 1596908496 ERR3450083 SRAfilesize c97da7f0707579c7d5eea7865a0a289f ERR3450083.sra ERR3450083.sra file validated ERR3450083 is paired end ERR3450083 is conventional basespace ERR3450083 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450083_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.20075 37.0 37.0 37.0 37.0 37.0 2 36.304 37.0 37.0 37.0 37.0 37.0 3 36.3125 37.0 37.0 37.0 37.0 37.0 4 36.481 37.0 37.0 37.0 37.0 37.0 5 36.4995 37.0 37.0 37.0 37.0 37.0 6 36.528 37.0 37.0 37.0 37.0 37.0 7 36.4125 37.0 37.0 37.0 37.0 37.0 8 36.5045 37.0 37.0 37.0 37.0 37.0 9 36.496 37.0 37.0 37.0 37.0 37.0 10-11 36.49925 37.0 37.0 37.0 37.0 37.0 12-13 36.432 37.0 37.0 37.0 37.0 37.0 14-15 36.4875 37.0 37.0 37.0 37.0 37.0 16-17 36.4675 37.0 37.0 37.0 37.0 37.0 18-19 36.39975 37.0 37.0 37.0 37.0 37.0 20-21 36.448499999999996 37.0 37.0 37.0 37.0 37.0 22-23 36.434 37.0 37.0 37.0 37.0 37.0 24-25 36.36025 37.0 37.0 37.0 37.0 37.0 26-27 36.3425 37.0 37.0 37.0 37.0 37.0 28-29 36.336 37.0 37.0 37.0 37.0 37.0 30-31 36.3695 37.0 37.0 37.0 37.0 37.0 32-33 36.25075 37.0 37.0 37.0 37.0 37.0 34-35 36.27075 37.0 37.0 37.0 37.0 37.0 36-37 36.32025 37.0 37.0 37.0 37.0 37.0 38-39 36.224500000000006 37.0 37.0 37.0 37.0 37.0 40-41 36.3155 37.0 37.0 37.0 37.0 37.0 42-43 36.21275 37.0 37.0 37.0 37.0 37.0 44-45 36.16375 37.0 37.0 37.0 37.0 37.0 46-47 36.163 37.0 37.0 37.0 37.0 37.0 48-49 36.08825 37.0 37.0 37.0 37.0 37.0 50-51 36.08 37.0 37.0 37.0 37.0 37.0 52-53 36.09975 37.0 37.0 37.0 37.0 37.0 54-55 36.073750000000004 37.0 37.0 37.0 37.0 37.0 56-57 35.945 37.0 37.0 37.0 37.0 37.0 58-59 36.059 37.0 37.0 37.0 37.0 37.0 60-61 35.94525 37.0 37.0 37.0 37.0 37.0 62-63 36.00575 37.0 37.0 37.0 37.0 37.0 64-65 35.9945 37.0 37.0 37.0 37.0 37.0 66-67 35.984750000000005 37.0 37.0 37.0 37.0 37.0 68-69 35.92375 37.0 37.0 37.0 37.0 37.0 70-71 35.934749999999994 37.0 37.0 37.0 37.0 37.0 72-73 35.9495 37.0 37.0 37.0 37.0 37.0 74-75 36.0245 37.0 37.0 37.0 37.0 37.0 76-77 36.0045 37.0 37.0 37.0 37.0 37.0 78-79 35.9885 37.0 37.0 37.0 37.0 37.0 80-81 36.015249999999995 37.0 37.0 37.0 37.0 37.0 82-83 35.96225 37.0 37.0 37.0 37.0 37.0 84-85 35.91025 37.0 37.0 37.0 37.0 37.0 86-87 35.893249999999995 37.0 37.0 37.0 37.0 37.0 88-89 35.814750000000004 37.0 37.0 37.0 37.0 37.0 90-91 35.8235 37.0 37.0 37.0 37.0 37.0 92-93 35.857 37.0 37.0 37.0 37.0 37.0 94-95 35.78575 37.0 37.0 37.0 37.0 37.0 96-97 35.907 37.0 37.0 37.0 37.0 37.0 98-99 35.8005 37.0 37.0 37.0 37.0 37.0 100-101 35.75075 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 2.0 25 10.0 26 7.0 27 21.0 28 29.0 29 32.0 30 59.0 31 70.0 32 68.0 33 92.0 34 125.0 35 203.0 36 1724.0 37 1556.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.30112923462986 9.585947302383941 11.292346298619824 38.82057716436638 2 22.25 14.475 28.875 34.4 3 21.349999999999998 15.65 24.5 38.5 4 27.55 22.575 18.6 31.275 5 27.125 26.900000000000002 20.825 25.15 6 22.775000000000002 30.4 25.0 21.825 7 19.2 21.95 38.05 20.8 8 21.025 20.349999999999998 31.15 27.474999999999998 9 23.150000000000002 21.0 31.85 24.0 10-11 23.3875 28.599999999999998 22.662499999999998 25.35 12-13 23.849999999999998 22.75 26.575 26.825 14-15 22.625 24.5 26.25 26.625 16-17 23.4375 24.525 26.200000000000003 25.837500000000002 18-19 25.6 23.5625 25.387500000000003 25.45 20-21 23.4625 24.3625 25.624999999999996 26.55 22-23 24.25 24.025 24.5625 27.1625 24-25 24.7375 22.787499999999998 24.7 27.775 26-27 22.8 24.5375 24.5625 28.1 28-29 25.074999999999996 23.962500000000002 24.25 26.7125 30-31 23.7375 24.025 25.2125 27.025 32-33 24.425 22.475 25.324999999999996 27.775 34-35 24.4375 24.1625 24.2375 27.1625 36-37 24.762500000000003 23.4625 24.25 27.525 38-39 24.762500000000003 24.087500000000002 24.837500000000002 26.3125 40-41 24.1125 24.0125 24.6125 27.2625 42-43 25.25 23.849999999999998 25.0375 25.8625 44-45 24.775 23.0375 25.074999999999996 27.1125 46-47 25.124999999999996 23.625 23.599999999999998 27.650000000000002 48-49 24.9875 23.0125 24.099999999999998 27.900000000000002 50-51 23.6375 24.175 24.7375 27.450000000000003 52-53 25.224999999999998 23.962500000000002 23.425 27.3875 54-55 24.4375 22.55 25.4 27.6125 56-57 24.587500000000002 22.7625 24.8625 27.787499999999998 58-59 23.7375 24.9875 24.1375 27.1375 60-61 25.224999999999998 23.45 24.1125 27.212500000000002 62-63 24.887500000000003 23.0625 24.15 27.900000000000002 64-65 24.975 23.425 25.174999999999997 26.424999999999997 66-67 24.0 23.8375 24.474999999999998 27.6875 68-69 24.85 23.5375 25.124999999999996 26.487500000000004 70-71 25.324999999999996 22.787499999999998 24.9 26.987499999999997 72-73 25.924999999999997 23.8625 23.150000000000002 27.0625 74-75 25.0375 24.125 23.5375 27.3 76-77 26.0125 24.025 23.95 26.0125 78-79 25.3 25.137500000000003 22.8125 26.75 80-81 24.8125 23.4375 25.5 26.25 82-83 26.087500000000002 23.849999999999998 23.4375 26.625 84-85 25.55 24.3875 23.599999999999998 26.4625 86-87 24.099999999999998 25.0375 23.974999999999998 26.887499999999996 88-89 26.275 24.462500000000002 22.825 26.437500000000004 90-91 25.224999999999998 24.0125 23.2875 27.474999999999998 92-93 25.587500000000002 24.1125 23.5875 26.7125 94-95 25.074999999999996 24.3875 23.2875 27.250000000000004 96-97 25.662499999999998 24.6625 22.875 26.8 98-99 24.1875 24.6625 23.9875 27.1625 100-101 25.05 24.6 23.75 26.6 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 8.0 1 4.5 2 1.0 3 1.5 4 2.0 5 2.0 6 1.0 7 1.0 8 2.0 9 1.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.5 23 1.5 24 1.5 25 2.5 26 3.5 27 2.5 28 1.5 29 0.5 30 0.5 31 3.5 32 4.5 33 7.0 34 14.0 35 22.5 36 23.5 37 31.5 38 41.5 39 52.5 40 77.0 41 91.5 42 99.5 43 109.5 44 146.0 45 169.0 46 171.5 47 181.5 48 194.0 49 193.0 50 176.0 51 164.0 52 171.5 53 177.5 54 151.5 55 147.5 56 144.5 57 123.5 58 117.5 59 102.0 60 86.0 61 79.5 62 68.0 63 61.5 64 62.5 65 60.5 66 56.5 67 51.5 68 42.0 69 41.5 70 44.0 71 35.5 72 35.0 73 31.5 74 20.5 75 20.5 76 14.5 77 9.0 78 11.5 79 8.5 80 3.0 81 3.0 82 3.0 83 1.0 84 0.5 85 0.5 86 1.5 87 1.5 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 0.375 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 82.525 #Duplication Level Percentage of deduplicated Percentage of total 1 84.5198424719782 69.75 2 11.905483186913058 19.650000000000002 3 2.605271129960618 6.45 4 0.4241139048773099 1.4000000000000001 5 0.3332323538321721 1.375 6 0.060587700696758555 0.3 7 0.060587700696758555 0.35000000000000003 8 0.030293850348379277 0.2 9 0.0 0.0 >10 0.060587700696758555 0.525 >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 CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 11 0.27499999999999997 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGCGAAATCTCGTAT 10 0.25 TruSeq Adapter, Index 6 (97% over 36bp) AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 7 0.17500000000000002 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 7 0.17500000000000002 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 6 0.15 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 6 0.15 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 5 0.125 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 5 0.125 No Hit CCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAA 5 0.125 No Hit GGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCG 5 0.125 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 5 0.125 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 5 0.125 No Hit ATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAATAAATGCGC 5 0.125 No Hit GAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTG 5 0.125 No Hit TACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGAC 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.25 0.0 0.0 0.0 0.0 46-47 0.2625 0.0 0.0 0.0 0.0 48-49 0.30000000000000004 0.0 0.0 0.0 0.0 50-51 0.38749999999999996 0.0 0.0 0.0 0.0 52-53 0.425 0.0 0.0 0.0 0.0 54-55 0.44999999999999996 0.0 0.0 0.0 0.0 56-57 0.5375000000000001 0.0 0.0 0.0 0.0 58-59 0.625 0.0 0.0 0.0 0.0 60-61 0.7375 0.0 0.0 0.0 0.0 62-63 0.9 0.0 0.0 0.0 0.0 64-65 1.15 0.0 0.0 0.0 0.0 66-67 1.3125 0.0 0.0 0.0 0.0 68-69 1.4500000000000002 0.0 0.0 0.0 0.0 70-71 1.65 0.0 0.0 0.0 0.0 72-73 1.925 0.0 0.0 0.0 0.0 74-75 2.4 0.0 0.0 0.0 0.0 76-77 2.7249999999999996 0.0 0.0 0.0 0.0 78-79 3.1125 0.0 0.0 0.0 0.0 80-81 3.3125 0.0 0.0 0.0 0.0 82-83 3.6875 0.0 0.0 0.0 0.0 84-85 3.9875 0.0 0.0 0.0 0.0 86-87 4.4125 0.0 0.0 0.0 0.0 88-89 4.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450083 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450083_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.737 37.0 37.0 37.0 37.0 37.0 2 35.716 37.0 37.0 37.0 37.0 37.0 3 35.8265 37.0 37.0 37.0 37.0 37.0 4 35.9345 37.0 37.0 37.0 37.0 37.0 5 36.0925 37.0 37.0 37.0 37.0 37.0 6 36.095 37.0 37.0 37.0 37.0 37.0 7 35.987 37.0 37.0 37.0 37.0 37.0 8 36.082 37.0 37.0 37.0 37.0 37.0 9 36.1135 37.0 37.0 37.0 37.0 37.0 10-11 36.02325 37.0 37.0 37.0 37.0 37.0 12-13 36.04 37.0 37.0 37.0 37.0 37.0 14-15 35.98725 37.0 37.0 37.0 37.0 37.0 16-17 36.014250000000004 37.0 37.0 37.0 37.0 37.0 18-19 36.0305 37.0 37.0 37.0 37.0 37.0 20-21 35.997 37.0 37.0 37.0 37.0 37.0 22-23 36.040499999999994 37.0 37.0 37.0 37.0 37.0 24-25 35.9495 37.0 37.0 37.0 37.0 37.0 26-27 35.96625 37.0 37.0 37.0 37.0 37.0 28-29 35.935 37.0 37.0 37.0 37.0 37.0 30-31 35.92375 37.0 37.0 37.0 37.0 37.0 32-33 35.823499999999996 37.0 37.0 37.0 37.0 37.0 34-35 35.7905 37.0 37.0 37.0 37.0 37.0 36-37 35.8475 37.0 37.0 37.0 37.0 37.0 38-39 35.82625 37.0 37.0 37.0 37.0 37.0 40-41 35.824 37.0 37.0 37.0 37.0 37.0 42-43 35.829499999999996 37.0 37.0 37.0 37.0 37.0 44-45 35.87375 37.0 37.0 37.0 37.0 37.0 46-47 35.768249999999995 37.0 37.0 37.0 37.0 37.0 48-49 35.775999999999996 37.0 37.0 37.0 37.0 37.0 50-51 35.7445 37.0 37.0 37.0 37.0 37.0 52-53 35.79375 37.0 37.0 37.0 37.0 37.0 54-55 35.854749999999996 37.0 37.0 37.0 37.0 37.0 56-57 35.814750000000004 37.0 37.0 37.0 37.0 37.0 58-59 35.826750000000004 37.0 37.0 37.0 37.0 37.0 60-61 35.708 37.0 37.0 37.0 37.0 37.0 62-63 35.81375 37.0 37.0 37.0 37.0 37.0 64-65 35.7595 37.0 37.0 37.0 37.0 37.0 66-67 35.7655 37.0 37.0 37.0 37.0 37.0 68-69 35.639250000000004 37.0 37.0 37.0 37.0 37.0 70-71 35.6155 37.0 37.0 37.0 37.0 37.0 72-73 35.78175 37.0 37.0 37.0 37.0 37.0 74-75 35.653 37.0 37.0 37.0 37.0 37.0 76-77 35.593999999999994 37.0 37.0 37.0 37.0 37.0 78-79 35.54775 37.0 37.0 37.0 37.0 37.0 80-81 35.574 37.0 37.0 37.0 37.0 37.0 82-83 35.6245 37.0 37.0 37.0 37.0 37.0 84-85 35.701499999999996 37.0 37.0 37.0 37.0 37.0 86-87 35.64125 37.0 37.0 37.0 37.0 37.0 88-89 35.538250000000005 37.0 37.0 37.0 37.0 37.0 90-91 35.588499999999996 37.0 37.0 37.0 37.0 37.0 92-93 35.59375 37.0 37.0 37.0 37.0 37.0 94-95 35.681749999999994 37.0 37.0 37.0 37.0 37.0 96-97 35.601749999999996 37.0 37.0 37.0 37.0 37.0 98-99 35.510999999999996 37.0 37.0 37.0 37.0 37.0 100-101 35.606 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 0.0 15 4.0 16 9.0 17 4.0 18 10.0 19 4.0 20 6.0 21 17.0 22 11.0 23 14.0 24 12.0 25 19.0 26 19.0 27 19.0 28 18.0 29 32.0 30 29.0 31 38.0 32 52.0 33 90.0 34 130.0 35 246.0 36 2067.0 37 1147.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.55 17.375 11.375 28.7 2 27.825 22.775000000000002 25.4 24.0 3 26.700000000000003 24.349999999999998 25.75 23.200000000000003 4 30.275000000000002 28.000000000000004 17.599999999999998 24.125 5 30.2 29.825000000000003 19.425 20.549999999999997 6 24.875 33.275 19.45 22.400000000000002 7 26.625 20.599999999999998 30.225 22.55 8 26.05 22.275 24.0 27.675 9 27.05 21.675 25.3 25.974999999999998 10-11 28.487499999999997 27.1 19.3625 25.05 12-13 28.6875 21.675 23.5125 26.125 14-15 27.4125 25.8125 22.9375 23.8375 16-17 28.749999999999996 23.5875 22.5125 25.15 18-19 28.4 25.387500000000003 21.875 24.337500000000002 20-21 28.000000000000004 26.025 22.7125 23.2625 22-23 27.925 24.962500000000002 21.6125 25.5 24-25 28.3375 24.4125 23.0625 24.1875 26-27 27.737499999999997 25.0375 21.75 25.474999999999998 28-29 28.3125 24.0625 22.9625 24.6625 30-31 28.299999999999997 24.0125 22.15 25.5375 32-33 27.650000000000002 24.3 23.7125 24.337500000000002 34-35 27.6625 24.4875 22.15 25.7 36-37 27.400000000000002 25.5125 21.8 25.2875 38-39 27.187499999999996 24.887500000000003 22.400000000000002 25.525 40-41 27.35 25.637500000000003 22.7625 24.25 42-43 26.775 24.887500000000003 21.8 26.5375 44-45 27.9125 24.8 22.537499999999998 24.75 46-47 27.3125 25.0125 22.0875 25.587500000000002 48-49 26.474999999999998 26.4125 21.8125 25.3 50-51 26.4625 25.7375 22.5875 25.2125 52-53 27.525 24.025 23.1 25.35 54-55 27.8375 24.6625 22.3125 25.1875 56-57 27.474999999999998 23.9125 23.599999999999998 25.0125 58-59 28.9875 24.224999999999998 22.5 24.2875 60-61 27.900000000000002 25.374999999999996 21.9625 24.762500000000003 62-63 28.749999999999996 24.275 22.6875 24.2875 64-65 28.65 24.6875 22.225 24.4375 66-67 28.15 25.575 22.0 24.275 68-69 27.700000000000003 25.337500000000002 21.8125 25.15 70-71 28.575 24.625 22.0125 24.7875 72-73 29.15 24.9375 21.875 24.0375 74-75 27.224999999999998 25.912499999999998 22.5 24.3625 76-77 29.15 23.599999999999998 21.875 25.374999999999996 78-79 28.212500000000002 23.825 22.8875 25.074999999999996 80-81 29.3375 24.3 22.3125 24.05 82-83 29.262500000000003 24.0625 22.55 24.125 84-85 27.5625 24.775 23.175 24.4875 86-87 28.125 25.2875 22.375 24.212500000000002 88-89 29.062500000000004 24.474999999999998 22.3625 24.099999999999998 90-91 28.1375 24.7875 22.225 24.85 92-93 28.749999999999996 25.7625 22.525000000000002 22.9625 94-95 27.8125 26.0375 22.3 23.849999999999998 96-97 29.375 25.6125 22.2125 22.8 98-99 29.049999999999997 24.4 22.35 24.2 100-101 29.5375 24.75 22.6 23.1125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 2 0.0 3 0.0 4 0.5 5 0.5 6 2.0 7 2.0 8 1.0 9 2.0 10 1.0 11 0.0 12 2.0 13 2.0 14 0.5 15 1.5 16 3.5 17 3.5 18 1.0 19 1.0 20 2.0 21 1.5 22 0.5 23 1.0 24 2.5 25 2.0 26 0.5 27 0.0 28 1.5 29 2.5 30 3.5 31 4.0 32 7.0 33 10.0 34 11.0 35 18.5 36 24.0 37 34.5 38 41.5 39 55.5 40 68.0 41 73.5 42 101.5 43 128.5 44 146.5 45 140.5 46 156.0 47 176.5 48 176.5 49 168.0 50 156.0 51 156.5 52 162.5 53 173.0 54 159.5 55 144.5 56 126.5 57 114.0 58 116.5 59 103.0 60 82.5 61 88.5 62 80.5 63 62.5 64 66.0 65 68.0 66 60.0 67 51.0 68 56.5 69 59.0 70 48.5 71 45.0 72 43.0 73 30.0 74 26.0 75 27.0 76 20.0 77 14.5 78 11.5 79 6.0 80 6.0 81 5.0 82 1.0 83 1.5 84 2.5 85 3.0 86 2.5 87 0.5 88 0.0 89 0.0 90 0.5 91 1.5 92 1.5 93 0.5 94 0.0 95 1.5 96 3.0 97 2.5 98 2.5 99 2.5 100 10.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.325 #Duplication Level Percentage of deduplicated Percentage of total 1 85.68040320189742 72.25 2 11.769937740883487 19.85 3 1.7491847020456568 4.425 4 0.5040023717758673 1.7000000000000002 5 0.20753038837829826 0.8750000000000001 6 0.0 0.0 7 0.029647198339756892 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.059294396679513785 0.7250000000000001 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 17 0.42500000000000004 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 12 0.3 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 5 0.125 No Hit CCGGCATCGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCATCGCT 5 0.125 No Hit GGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCA 5 0.125 No Hit GATCATTGCAATTGTTGGTCTTCAACGAGGAATGCCTAGTAAGCGCGAGT 5 0.125 No Hit CGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCA 5 0.125 No Hit CGGGGAGGTAGTGACAATAAATAACAATACCGGGCACATTAGTGTCTGGT 5 0.125 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAGTA 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.21250000000000002 0.0 0.0 0.0 0.0 48-49 0.25 0.0 0.0 0.0 0.0 50-51 0.3375 0.0 0.0 0.0 0.0 52-53 0.375 0.0 0.0 0.0 0.0 54-55 0.4 0.0 0.0 0.0 0.0 56-57 0.4875 0.0 0.0 0.0 0.0 58-59 0.575 0.0 0.0 0.0 0.0 60-61 0.7124999999999999 0.0 0.0 0.0 0.0 62-63 0.875 0.0 0.0 0.0 0.0 64-65 1.1124999999999998 0.0 0.0 0.0 0.0 66-67 1.2875 0.0 0.0 0.0 0.0 68-69 1.4249999999999998 0.0 0.0 0.0 0.0 70-71 1.625 0.0 0.0 0.0 0.0 72-73 1.925 0.0 0.0 0.0 0.0 74-75 2.425 0.0 0.0 0.0 0.0 76-77 2.75 0.0 0.0 0.0 0.0 78-79 3.1500000000000004 0.0 0.0 0.0 0.0 80-81 3.3625 0.0 0.0 0.0 0.0 82-83 3.7375 0.0 0.0 0.0 0.0 84-85 4.025 0.0 0.0 0.0 0.0 86-87 4.4625 0.0 0.0 0.0 0.0 88-89 4.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405666 spots for ERR3450083.sra Written 1405666 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra Read 1405664 spots for ERR3450083.sra Written 1405664 spots for ERR3450083.sra SRR ids: ['ERR3450083.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f7617u4f ERR3450083.sra spots: 28113282 blocks: [[1, 1405664], [1405665, 2811328], [2811329, 4216992], [4216993, 5622656], [5622657, 7028320], [7028321, 8433984], [8433985, 9839648], [9839649, 11245312], [11245313, 12650976], [12650977, 14056640], [14056641, 15462304], [15462305, 16867968], [16867969, 18273632], [18273633, 19679296], [19679297, 21084960], [21084961, 22490624], [22490625, 23896288], [23896289, 25301952], [25301953, 26707616], [26707617, 28113282]] ERR3450083 file size 6759530 ERR3450083 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 ERR3450083 ERR3450083_1.fastq ERR3450083_2.fastq Input file: ERR3450083_1.fastq Paired file: ERR3450083_2.fastq trimmed: ERR3450083-trimmed-pair1.fastq, ERR3450083-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 Sat Dec 7 14:52:56 2024 >> started Sat Dec 7 14:53:23 2024 >> done (27.816s) 28113282 read pairs processed; of these: 150 ( 0.00%) short read pairs filtered out after trimming by size control 76322 ( 0.27%) empty read pairs filtered out after trimming by size control 28036810 (99.73%) read pairs available; of these: 2571574 ( 9.17%) trimmed read pairs available after processing 25465236 (90.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 39 0.00% 19 83 0.00% 20 225 0.00% 21 515 0.00% 22 700 0.00% 23 318 0.00% 24 364 0.00% 25 478 0.00% 26 609 0.00% 27 920 0.00% 28 1160 0.00% 29 1544 0.01% 30 1870 0.01% 31 2283 0.01% 32 2328 0.01% 33 2187 0.01% 34 2260 0.01% 35 2315 0.01% 36 2551 0.01% 37 2797 0.01% 38 3313 0.01% 39 3771 0.01% 40 4544 0.02% 41 5205 0.02% 42 5803 0.02% 43 6407 0.02% 44 5676 0.02% 45 5739 0.02% 46 6054 0.02% 47 6588 0.02% 48 7345 0.03% 49 7964 0.03% 50 8919 0.03% 51 9910 0.04% 52 10851 0.04% 53 11280 0.04% 54 12276 0.04% 55 12855 0.05% 56 13328 0.05% 57 13860 0.05% 58 15203 0.05% 59 16649 0.06% 60 17761 0.06% 61 18808 0.07% 62 21489 0.08% 63 23456 0.08% 64 23996 0.09% 65 24495 0.09% 66 26222 0.09% 67 27089 0.10% 68 28958 0.10% 69 29590 0.11% 70 32347 0.12% 71 34193 0.12% 72 36929 0.13% 73 40020 0.14% 74 41611 0.15% 75 42787 0.15% 76 43684 0.16% 77 46044 0.16% 78 48425 0.17% 79 50662 0.18% 80 52279 0.19% 81 54142 0.19% 82 57864 0.21% 83 59829 0.21% 84 62277 0.22% 85 65604 0.23% 86 67265 0.24% 87 70417 0.25% 88 73381 0.26% 89 75477 0.27% 90 78658 0.28% 91 82172 0.29% 92 87493 0.31% 93 89246 0.32% 94 92427 0.33% 95 95605 0.34% 96 98288 0.35% 97 101540 0.36% 98 102790 0.37% 99 105623 0.38% 100 121545 0.43% 101 25465236 90.83% 28036810 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=35 prefix-density=0.31 prefix-fanout=2.0 sequence=CCCACTTGGAGC criterion=fanout-score sequence-density=0.09 sequence-density-rank=22 fanout-score=43.30 fanout-score-rank=1 prefix-density=1.20 prefix-fanout=3.4 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACGTTCTCCGGCCGTCCTC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=0.29 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.08 sequence-density-rank=27 fanout-score=183.71 fanout-score-rank=1 prefix-density=0.68 prefix-fanout=22.7 sequence=CGGCGGCGGCGA ERR3450083 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:53:52 Started mapping on | Dec 07 14:53:52 Finished on | Dec 07 14:56:06 Mapping speed, Million of reads per hour | 753.23 Number of input reads | 28036810 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 19060895 Uniquely mapped reads % | 67.99% Average mapped length | 198.20 Number of splices: Total | 11669517 Number of splices: Annotated (sjdb) | 11064860 Number of splices: GT/AG | 11515413 Number of splices: GC/AG | 134253 Number of splices: AT/AC | 6186 Number of splices: Non-canonical | 13665 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.96 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1947367 % of reads mapped to multiple loci | 6.95% Number of reads mapped to too many loci | 1164185 % of reads mapped to too many loci | 4.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.39% % of reads unmapped: other | 17.52% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7028548 7028548 7028548 N_multimapping 1947367 1947367 1947367 N_noFeature 856521 18336297 1288747 N_ambiguous 365559 3133 77456 UnstrandedReadsAssigned:17838815 PositiveStrandReadsAssigned:721465 NegativeStrandReadsAssigned:17694692 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450083 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: ERR3450083-trimmed-pair1.fastq ERR3450083-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,036,810 reads, 18,957,037 reads pseudoaligned [quant] estimated average fragment length: 183.328 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,170 rounds 52973 ERR3450083.ke.tsv 35125 ERR3450083.se.tsv 88098 total ==> ERR3450083.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 753.893 0 0 PNS24247 1044 861.672 32.7142 2.90228 PNS24249 1928 1745.67 286.167 12.5315 PNS24246 1044 861.672 32.7142 2.90228 PNS24248 1044 861.672 32.7142 2.90228 PNS24244 1471 1288.67 53.6907 3.18494 PNS24243 293 129.257 0 0 KQK14069 1603 1420.67 5997.73 322.729 KQK14071 474 294.787 226.42 58.7155 ==> ERR3450083.se.tsv <== BRADI_1g14170v3 6329 BRADI_1g53295v3 32 BRADI_1g59795v3 158 BRADI_1g07683v3 0 BRADI_1g00485v3 39 BRADI_1g20270v3 1834 BRADI_1g74790v3 173 BRADI_1g09890v3 13 BRADI_1g77505v3 249 BRADI_1g48960v3 0 ERR3450083 completed mapping pipeline successfully