Starting /dee2/code/volunteer_pipeline.sh ERR3450060 current disk space = 1543066959872 free memory = 1602370820 ERR3450060 SRAfilesize 885d7a15805fbd03d1f7f431f5cd9e34 ERR3450060.sra ERR3450060.sra file validated ERR3450060 is paired end ERR3450060 is conventional basespace ERR3450060 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450060_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.09075 37.0 37.0 37.0 37.0 37.0 2 36.4345 37.0 37.0 37.0 37.0 37.0 3 36.498 37.0 37.0 37.0 37.0 37.0 4 36.5555 37.0 37.0 37.0 37.0 37.0 5 36.5255 37.0 37.0 37.0 37.0 37.0 6 36.481 37.0 37.0 37.0 37.0 37.0 7 36.454 37.0 37.0 37.0 37.0 37.0 8 36.4855 37.0 37.0 37.0 37.0 37.0 9 36.5 37.0 37.0 37.0 37.0 37.0 10-11 36.501999999999995 37.0 37.0 37.0 37.0 37.0 12-13 36.531 37.0 37.0 37.0 37.0 37.0 14-15 36.53975 37.0 37.0 37.0 37.0 37.0 16-17 36.501999999999995 37.0 37.0 37.0 37.0 37.0 18-19 36.4885 37.0 37.0 37.0 37.0 37.0 20-21 36.503249999999994 37.0 37.0 37.0 37.0 37.0 22-23 36.5165 37.0 37.0 37.0 37.0 37.0 24-25 36.562 37.0 37.0 37.0 37.0 37.0 26-27 36.4345 37.0 37.0 37.0 37.0 37.0 28-29 36.43925 37.0 37.0 37.0 37.0 37.0 30-31 36.4395 37.0 37.0 37.0 37.0 37.0 32-33 36.408 37.0 37.0 37.0 37.0 37.0 34-35 36.36425 37.0 37.0 37.0 37.0 37.0 36-37 36.38875 37.0 37.0 37.0 37.0 37.0 38-39 36.356 37.0 37.0 37.0 37.0 37.0 40-41 36.333 37.0 37.0 37.0 37.0 37.0 42-43 36.287000000000006 37.0 37.0 37.0 37.0 37.0 44-45 36.30175 37.0 37.0 37.0 37.0 37.0 46-47 36.24225 37.0 37.0 37.0 37.0 37.0 48-49 36.317750000000004 37.0 37.0 37.0 37.0 37.0 50-51 36.2815 37.0 37.0 37.0 37.0 37.0 52-53 36.204750000000004 37.0 37.0 37.0 37.0 37.0 54-55 36.1885 37.0 37.0 37.0 37.0 37.0 56-57 36.2025 37.0 37.0 37.0 37.0 37.0 58-59 36.2065 37.0 37.0 37.0 37.0 37.0 60-61 36.14425 37.0 37.0 37.0 37.0 37.0 62-63 36.1425 37.0 37.0 37.0 37.0 37.0 64-65 36.066 37.0 37.0 37.0 37.0 37.0 66-67 36.132999999999996 37.0 37.0 37.0 37.0 37.0 68-69 36.20075 37.0 37.0 37.0 37.0 37.0 70-71 36.132999999999996 37.0 37.0 37.0 37.0 37.0 72-73 36.113749999999996 37.0 37.0 37.0 37.0 37.0 74-75 36.211749999999995 37.0 37.0 37.0 37.0 37.0 76-77 36.18075 37.0 37.0 37.0 37.0 37.0 78-79 36.1145 37.0 37.0 37.0 37.0 37.0 80-81 36.1405 37.0 37.0 37.0 37.0 37.0 82-83 36.13375 37.0 37.0 37.0 37.0 37.0 84-85 36.08125 37.0 37.0 37.0 37.0 37.0 86-87 36.12675 37.0 37.0 37.0 37.0 37.0 88-89 36.09725 37.0 37.0 37.0 37.0 37.0 90-91 36.13 37.0 37.0 37.0 37.0 37.0 92-93 36.0205 37.0 37.0 37.0 37.0 37.0 94-95 36.10725 37.0 37.0 37.0 37.0 37.0 96-97 36.00675 37.0 37.0 37.0 37.0 37.0 98-99 35.94775 37.0 37.0 37.0 37.0 37.0 100-101 36.106 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 3.0 23 0.0 24 1.0 25 12.0 26 11.0 27 14.0 28 22.0 29 34.0 30 48.0 31 44.0 32 50.0 33 69.0 34 106.0 35 172.0 36 1621.0 37 1792.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.28661140416981 9.897010801306203 11.152976639035419 39.66340115548857 2 21.7 13.700000000000001 29.825000000000003 34.775 3 21.925 18.4 24.2 35.475 4 27.3 23.0 18.425 31.275 5 28.7 27.500000000000004 20.0 23.799999999999997 6 23.0 32.025 23.1 21.875 7 20.474999999999998 22.525000000000002 37.075 19.925 8 21.05 21.349999999999998 30.0 27.6 9 22.3 20.225 32.35 25.124999999999996 10-11 23.375 28.962500000000002 21.7875 25.874999999999996 12-13 23.8125 23.0625 24.962500000000002 28.1625 14-15 23.6625 24.525 25.275 26.5375 16-17 24.6125 24.325 25.0125 26.05 18-19 24.6625 24.2625 25.025 26.05 20-21 24.4125 24.825 24.925 25.837500000000002 22-23 23.6125 24.712500000000002 24.95 26.724999999999998 24-25 23.9 23.599999999999998 24.375 28.125 26-27 23.525 24.7 25.112499999999997 26.6625 28-29 24.525 24.4125 23.8875 27.175 30-31 24.175 23.325000000000003 25.4375 27.0625 32-33 24.525 23.375 24.637500000000003 27.462500000000002 34-35 24.9375 24.6875 23.549999999999997 26.825 36-37 24.6625 24.087500000000002 23.6875 27.5625 38-39 23.9 24.4875 25.25 26.3625 40-41 25.412499999999998 25.3 23.525 25.7625 42-43 24.25 24.6625 24.1375 26.950000000000003 44-45 24.25 23.7 24.25 27.800000000000004 46-47 24.4 23.2875 24.887500000000003 27.425 48-49 24.975 23.1375 24.625 27.2625 50-51 24.95 23.8625 24.875 26.3125 52-53 25.224999999999998 23.4125 24.1125 27.250000000000004 54-55 25.0 23.775 23.849999999999998 27.375 56-57 24.887500000000003 23.7875 24.349999999999998 26.974999999999998 58-59 24.75 24.325 24.2375 26.687499999999996 60-61 23.962500000000002 23.474999999999998 25.162499999999998 27.400000000000002 62-63 25.5375 22.45 25.387500000000003 26.625 64-65 24.375 24.349999999999998 23.8125 27.462500000000002 66-67 25.15 23.4875 23.9875 27.375 68-69 24.099999999999998 23.9875 24.45 27.462500000000002 70-71 25.2875 23.7125 24.349999999999998 26.650000000000002 72-73 26.3 23.575 23.75 26.375 74-75 25.7875 23.200000000000003 23.375 27.6375 76-77 26.4125 23.575 23.5625 26.450000000000003 78-79 25.2625 24.175 23.125 27.437499999999996 80-81 25.7875 23.375 22.675 28.1625 82-83 26.85 24.075 22.875 26.200000000000003 84-85 25.650000000000002 23.05 23.3375 27.962500000000002 86-87 25.5 22.55 24.587500000000002 27.3625 88-89 25.275 23.799999999999997 23.3625 27.5625 90-91 24.9875 24.9 23.0625 27.05 92-93 25.275 24.8625 23.7875 26.075 94-95 24.3125 24.65 24.4 26.637499999999996 96-97 25.275 23.4375 23.962500000000002 27.325 98-99 25.224999999999998 24.224999999999998 23.225 27.325 100-101 25.3 24.4875 23.5875 26.625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 5.0 1 2.5 2 1.0 3 1.5 4 1.0 5 0.5 6 0.0 7 2.0 8 2.5 9 0.5 10 0.0 11 1.5 12 1.5 13 0.5 14 1.0 15 1.0 16 0.5 17 0.0 18 1.0 19 1.0 20 0.0 21 0.0 22 0.5 23 0.5 24 0.5 25 1.0 26 0.5 27 0.0 28 0.5 29 0.5 30 0.5 31 4.5 32 7.5 33 9.0 34 10.5 35 17.5 36 31.0 37 33.5 38 35.0 39 53.5 40 78.0 41 102.0 42 119.5 43 135.5 44 145.5 45 152.0 46 167.5 47 186.5 48 181.0 49 174.0 50 175.5 51 165.5 52 160.0 53 157.5 54 157.0 55 150.5 56 143.5 57 131.5 58 110.0 59 95.5 60 88.0 61 80.0 62 62.5 63 59.5 64 70.5 65 71.0 66 64.0 67 47.0 68 45.0 69 40.0 70 34.0 71 36.5 72 34.0 73 36.0 74 27.5 75 20.5 76 19.5 77 12.0 78 8.5 79 9.0 80 7.0 81 5.0 82 3.0 83 0.5 84 1.0 85 1.0 86 0.5 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 0.0 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 0.475 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 88.275 #Duplication Level Percentage of deduplicated Percentage of total 1 90.28603794958934 79.7 2 7.873123760974228 13.900000000000002 3 1.0195412064570943 2.7 4 0.3964882469555367 1.4000000000000001 5 0.22656471254602095 1.0 6 0.05664117813650524 0.3 7 0.05664117813650524 0.35000000000000003 8 0.05664117813650524 0.4 9 0.0 0.0 >10 0.02832058906825262 0.25 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGATAGATCTCGTAT 10 0.25 TruSeq Adapter, Index 1 (97% over 36bp) AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 8 0.2 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 7 0.17500000000000002 No Hit GTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGA 7 0.17500000000000002 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 6 0.15 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 6 0.15 No Hit CTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATC 5 0.125 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 5 0.125 No Hit CCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTA 5 0.125 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 5 0.125 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 5 0.125 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 5 0.125 No Hit CTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAG 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 0.0125 0.0 0.0 0.0 0.0 30-31 0.0875 0.0 0.0 0.0 0.0 32-33 0.15 0.0 0.0 0.0 0.0 34-35 0.175 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 0.25 0.0 0.0 0.0 0.0 42-43 0.2875 0.0 0.0 0.0 0.0 44-45 0.3 0.0 0.0 0.0 0.0 46-47 0.325 0.0 0.0 0.0 0.0 48-49 0.3625 0.0 0.0 0.0 0.0 50-51 0.4375 0.0 0.0 0.0 0.0 52-53 0.5125 0.0 0.0 0.0 0.0 54-55 0.6625 0.0 0.0 0.0 0.0 56-57 0.7124999999999999 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.9 0.0 0.0 0.0 0.0 62-63 1.0375 0.0 0.0 0.0 0.0 64-65 1.1749999999999998 0.0 0.0 0.0 0.0 66-67 1.45 0.0 0.0 0.0 0.0 68-69 1.6875 0.0 0.0 0.0 0.0 70-71 1.875 0.0 0.0 0.0 0.0 72-73 2.25 0.0 0.0 0.0 0.0 74-75 2.4875 0.0 0.0 0.0 0.0 76-77 2.8 0.0 0.0 0.0 0.0 78-79 3.1375 0.0 0.0 0.0 0.0 80-81 3.675 0.0 0.0 0.0 0.0 82-83 4.1875 0.0 0.0 0.0 0.0 84-85 4.75 0.0 0.0 0.0 0.0 86-87 5.0875 0.0 0.0 0.0 0.0 88-89 5.35 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCGGCC 15 0.009957196 47.5 84-85 >>END_MODULE ERR3450060 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450060_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 36.035 37.0 37.0 37.0 37.0 37.0 2 36.0245 37.0 37.0 37.0 37.0 37.0 3 36.009 37.0 37.0 37.0 37.0 37.0 4 36.103 37.0 37.0 37.0 37.0 37.0 5 36.2155 37.0 37.0 37.0 37.0 37.0 6 36.218 37.0 37.0 37.0 37.0 37.0 7 36.15 37.0 37.0 37.0 37.0 37.0 8 36.1455 37.0 37.0 37.0 37.0 37.0 9 36.1775 37.0 37.0 37.0 37.0 37.0 10-11 36.0445 37.0 37.0 37.0 37.0 37.0 12-13 36.130250000000004 37.0 37.0 37.0 37.0 37.0 14-15 36.12675 37.0 37.0 37.0 37.0 37.0 16-17 36.158500000000004 37.0 37.0 37.0 37.0 37.0 18-19 36.1365 37.0 37.0 37.0 37.0 37.0 20-21 36.117000000000004 37.0 37.0 37.0 37.0 37.0 22-23 36.07575 37.0 37.0 37.0 37.0 37.0 24-25 36.075 37.0 37.0 37.0 37.0 37.0 26-27 36.02475 37.0 37.0 37.0 37.0 37.0 28-29 35.99 37.0 37.0 37.0 37.0 37.0 30-31 35.99575 37.0 37.0 37.0 37.0 37.0 32-33 35.9025 37.0 37.0 37.0 37.0 37.0 34-35 35.97475 37.0 37.0 37.0 37.0 37.0 36-37 35.989999999999995 37.0 37.0 37.0 37.0 37.0 38-39 35.977000000000004 37.0 37.0 37.0 37.0 37.0 40-41 35.938 37.0 37.0 37.0 37.0 37.0 42-43 35.86775 37.0 37.0 37.0 37.0 37.0 44-45 35.91375 37.0 37.0 37.0 37.0 37.0 46-47 35.95 37.0 37.0 37.0 37.0 37.0 48-49 35.87325 37.0 37.0 37.0 37.0 37.0 50-51 35.8565 37.0 37.0 37.0 37.0 37.0 52-53 35.942 37.0 37.0 37.0 37.0 37.0 54-55 35.92425 37.0 37.0 37.0 37.0 37.0 56-57 35.802 37.0 37.0 37.0 37.0 37.0 58-59 35.842 37.0 37.0 37.0 37.0 37.0 60-61 35.70825 37.0 37.0 37.0 37.0 37.0 62-63 35.689499999999995 37.0 37.0 37.0 37.0 37.0 64-65 35.76475 37.0 37.0 37.0 37.0 37.0 66-67 35.72525 37.0 37.0 37.0 37.0 37.0 68-69 35.733999999999995 37.0 37.0 37.0 37.0 37.0 70-71 35.63975000000001 37.0 37.0 37.0 37.0 37.0 72-73 35.609750000000005 37.0 37.0 37.0 37.0 37.0 74-75 35.63075 37.0 37.0 37.0 37.0 37.0 76-77 35.671499999999995 37.0 37.0 37.0 37.0 37.0 78-79 35.7405 37.0 37.0 37.0 37.0 37.0 80-81 35.72625 37.0 37.0 37.0 37.0 37.0 82-83 35.588499999999996 37.0 37.0 37.0 37.0 37.0 84-85 35.6695 37.0 37.0 37.0 37.0 37.0 86-87 35.81325 37.0 37.0 37.0 37.0 37.0 88-89 35.8375 37.0 37.0 37.0 37.0 37.0 90-91 35.81075 37.0 37.0 37.0 37.0 37.0 92-93 35.8485 37.0 37.0 37.0 37.0 37.0 94-95 35.8735 37.0 37.0 37.0 37.0 37.0 96-97 35.78375 37.0 37.0 37.0 37.0 37.0 98-99 35.795 37.0 37.0 37.0 37.0 37.0 100-101 35.688 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 5.0 15 3.0 16 1.0 17 7.0 18 5.0 19 5.0 20 5.0 21 13.0 22 11.0 23 9.0 24 18.0 25 9.0 26 12.0 27 24.0 28 24.0 29 27.0 30 35.0 31 48.0 32 57.0 33 72.0 34 123.0 35 217.0 36 2030.0 37 1240.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.075 16.75 12.049999999999999 30.125 2 26.6 23.35 25.8 24.25 3 25.525 24.525 26.474999999999998 23.474999999999998 4 30.75 26.375 18.6 24.275 5 31.724999999999998 28.175 17.925 22.175 6 24.224999999999998 34.025 19.2 22.55 7 26.0 19.025 31.474999999999998 23.5 8 24.975 20.8 24.224999999999998 30.0 9 26.650000000000002 22.475 25.15 25.724999999999998 10-11 28.462500000000002 27.125 19.225 25.1875 12-13 28.9375 22.075 22.9375 26.05 14-15 28.012500000000003 24.65 22.6125 24.725 16-17 28.225 24.45 21.912499999999998 25.412499999999998 18-19 28.5625 24.175 22.9875 24.275 20-21 28.262500000000003 24.637500000000003 21.8625 25.2375 22-23 27.975 24.7375 22.125 25.162499999999998 24-25 27.737499999999997 24.65 22.275 25.337500000000002 26-27 27.1375 25.025 23.0125 24.825 28-29 28.499999999999996 24.775 22.225 24.5 30-31 27.487499999999997 25.2875 22.325 24.9 32-33 27.725 25.337500000000002 22.3375 24.6 34-35 27.487499999999997 24.587500000000002 22.275 25.650000000000002 36-37 27.1375 24.65 22.787499999999998 25.424999999999997 38-39 26.637499999999996 25.3 22.8625 25.2 40-41 27.037499999999998 25.112499999999997 22.5 25.35 42-43 26.650000000000002 24.0375 23.3125 26.0 44-45 26.724999999999998 25.5625 23.2875 24.425 46-47 27.275 24.087500000000002 23.0625 25.575 48-49 27.125 25.0 23.0 24.875 50-51 26.887499999999996 24.875 23.5875 24.65 52-53 27.3625 24.125 23.2125 25.3 54-55 26.375 23.825 23.65 26.150000000000002 56-57 26.674999999999997 25.2625 23.525 24.5375 58-59 26.437500000000004 25.1 23.45 25.0125 60-61 26.5125 25.087500000000002 23.1875 25.2125 62-63 26.637499999999996 24.675 23.775 24.9125 64-65 27.400000000000002 24.15 23.200000000000003 25.25 66-67 27.3375 24.25 23.8875 24.525 68-69 26.987499999999997 24.3 23.175 25.5375 70-71 29.175 23.95 22.825 24.05 72-73 26.625 24.375 24.6875 24.3125 74-75 26.525 25.0625 24.325 24.087500000000002 76-77 27.3875 24.2375 22.900000000000002 25.474999999999998 78-79 28.050000000000004 24.275 22.8125 24.8625 80-81 26.875 25.4625 22.85 24.8125 82-83 27.975 24.425 23.05 24.55 84-85 28.075 24.55 23.400000000000002 23.974999999999998 86-87 28.375 25.2125 22.125 24.2875 88-89 28.575 23.65 22.75 25.025 90-91 28.012500000000003 24.887500000000003 22.900000000000002 24.2 92-93 29.0875 25.674999999999997 22.1875 23.05 94-95 28.475 25.05 21.5625 24.9125 96-97 28.95 24.6 22.6125 23.8375 98-99 28.3125 25.837500000000002 22.3625 23.4875 100-101 28.7 25.2 22.237499999999997 23.8625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 1.0 5 1.0 6 0.5 7 0.5 8 0.0 9 2.0 10 3.0 11 2.0 12 1.0 13 1.0 14 2.5 15 2.0 16 1.0 17 1.0 18 2.5 19 4.5 20 3.0 21 1.0 22 2.0 23 2.0 24 0.5 25 1.5 26 4.0 27 4.0 28 3.0 29 1.5 30 2.5 31 4.0 32 4.0 33 8.5 34 12.5 35 18.5 36 33.5 37 37.5 38 46.5 39 61.0 40 66.0 41 85.0 42 112.5 43 127.5 44 133.0 45 143.5 46 149.0 47 166.5 48 179.0 49 171.0 50 168.5 51 151.0 52 142.0 53 156.5 54 153.0 55 156.5 56 149.0 57 115.5 58 100.0 59 87.5 60 88.0 61 81.5 62 65.0 63 62.5 64 67.5 65 67.5 66 66.5 67 74.0 68 65.0 69 56.0 70 57.5 71 47.5 72 35.5 73 37.5 74 30.0 75 22.0 76 22.5 77 15.5 78 11.5 79 8.0 80 4.5 81 5.0 82 4.0 83 2.0 84 1.0 85 1.0 86 1.5 87 1.5 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.5 97 0.5 98 0.0 99 0.5 100 4.0 >>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 89.3 #Duplication Level Percentage of deduplicated Percentage of total 1 91.0414333706607 81.3 2 7.3348264277715565 13.100000000000001 3 1.0358342665173572 2.775 4 0.2799552071668533 1.0 5 0.08398656215005598 0.375 6 0.08398656215005598 0.44999999999999996 7 0.055991041433370664 0.35000000000000003 8 0.027995520716685332 0.2 9 0.055991041433370664 0.44999999999999996 >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 CCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGT 9 0.22499999999999998 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 9 0.22499999999999998 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTT 7 0.17500000000000002 No Hit GTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGTCGGGGGCA 6 0.15 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 6 0.15 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 5 0.125 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 5 0.125 No Hit CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACC 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 0.0125 0.0 0.0 0.0 0.0 30-31 0.0875 0.0 0.0 0.0 0.0 32-33 0.15 0.0 0.0 0.0 0.0 34-35 0.175 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 0.25 0.0 0.0 0.0 0.0 42-43 0.2875 0.0 0.0 0.0 0.0 44-45 0.3 0.0 0.0 0.0 0.0 46-47 0.325 0.0 0.0 0.0 0.0 48-49 0.3625 0.0 0.0 0.0 0.0 50-51 0.4375 0.0 0.0 0.0 0.0 52-53 0.5125 0.0 0.0 0.0 0.0 54-55 0.6625 0.0 0.0 0.0 0.0 56-57 0.7124999999999999 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.9 0.0 0.0 0.0 0.0 62-63 1.0625 0.0 0.0 0.0 0.0 64-65 1.2000000000000002 0.0 0.0 0.0 0.0 66-67 1.475 0.0 0.0 0.0 0.0 68-69 1.6875 0.0 0.0 0.0 0.0 70-71 1.85 0.0 0.0 0.0 0.0 72-73 2.2249999999999996 0.0 0.0 0.0 0.0 74-75 2.4375 0.0 0.0 0.0 0.0 76-77 2.75 0.0 0.0 0.0 0.0 78-79 3.0875000000000004 0.0 0.0 0.0 0.0 80-81 3.6125 0.0 0.0 0.0 0.0 82-83 4.1375 0.0 0.0 0.0 0.0 84-85 4.699999999999999 0.0 0.0 0.0 0.0 86-87 5.0125 0.0 0.0 0.0 0.0 88-89 5.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164982 spots for ERR3450060.sra Written 2164982 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra Read 2164979 spots for ERR3450060.sra Written 2164979 spots for ERR3450060.sra SRR ids: ['ERR3450060.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_h5nqt4sl ERR3450060.sra spots: 43299583 blocks: [[1, 2164979], [2164980, 4329958], [4329959, 6494937], [6494938, 8659916], [8659917, 10824895], [10824896, 12989874], [12989875, 15154853], [15154854, 17319832], [17319833, 19484811], [19484812, 21649790], [21649791, 23814769], [23814770, 25979748], [25979749, 28144727], [28144728, 30309706], [30309707, 32474685], [32474686, 34639664], [34639665, 36804643], [36804644, 38969622], [38969623, 41134601], [41134602, 43299583]] ERR3450060 file size 10422632 ERR3450060 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 ERR3450060 ERR3450060_1.fastq ERR3450060_2.fastq Input file: ERR3450060_1.fastq Paired file: ERR3450060_2.fastq trimmed: ERR3450060-trimmed-pair1.fastq, ERR3450060-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 14:19:29 2024 >> started Sat Dec 7 14:20:13 2024 >> done (43.914s) 43299583 read pairs processed; of these: 304 ( 0.00%) short read pairs filtered out after trimming by size control 63709 ( 0.15%) empty read pairs filtered out after trimming by size control 43235570 (99.85%) read pairs available; of these: 4008039 ( 9.27%) trimmed read pairs available after processing 39227531 (90.73%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 70 0.00% 19 109 0.00% 20 368 0.00% 21 919 0.00% 22 1138 0.00% 23 510 0.00% 24 527 0.00% 25 724 0.00% 26 1108 0.00% 27 1481 0.00% 28 1934 0.00% 29 2674 0.01% 30 3233 0.01% 31 3829 0.01% 32 4005 0.01% 33 3691 0.01% 34 3776 0.01% 35 3821 0.01% 36 4355 0.01% 37 4757 0.01% 38 5483 0.01% 39 6369 0.01% 40 7318 0.02% 41 8500 0.02% 42 9766 0.02% 43 9909 0.02% 44 9285 0.02% 45 9083 0.02% 46 9842 0.02% 47 11066 0.03% 48 12057 0.03% 49 12989 0.03% 50 14446 0.03% 51 16249 0.04% 52 17818 0.04% 53 18786 0.04% 54 19689 0.05% 55 20595 0.05% 56 21471 0.05% 57 22026 0.05% 58 24153 0.06% 59 26751 0.06% 60 28229 0.07% 61 31678 0.07% 62 34154 0.08% 63 36537 0.08% 64 38315 0.09% 65 39419 0.09% 66 41662 0.10% 67 43182 0.10% 68 45719 0.11% 69 47370 0.11% 70 50727 0.12% 71 54051 0.13% 72 58483 0.14% 73 61575 0.14% 74 64976 0.15% 75 67193 0.16% 76 69590 0.16% 77 71332 0.16% 78 75094 0.17% 79 78415 0.18% 80 82117 0.19% 81 84655 0.20% 82 91183 0.21% 83 93288 0.22% 84 97341 0.23% 85 101983 0.24% 86 104946 0.24% 87 109352 0.25% 88 112830 0.26% 89 116705 0.27% 90 121506 0.28% 91 128144 0.30% 92 134193 0.31% 93 138111 0.32% 94 142653 0.33% 95 147518 0.34% 96 149653 0.35% 97 154711 0.36% 98 158014 0.37% 99 161663 0.37% 100 183092 0.42% 101 39227531 90.73% 43235570 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=30 prefix-density=0.34 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=167.30 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=21.0 sequence=CGCCGCCGCCGCG criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=31 prefix-density=0.25 prefix-fanout=2.0 sequence=CAAGTGTTGGATTTAAAGCTGGTGTTAAAGATTATAGATTGACTTACTACACCCCGGAGTATGAAACCAAGGATACTGATATCTTGGCAGCATTCCGAGTATCTCCTCAACCTGGGGTTCCGCCCGAAGAAGCAGGGGCTGCAGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTTTGGACTGATGGACTTACTAGTCTTGATCGTTACAAAGGACGATGCTATCACATCGAGCCTGTTCCTGGGGAAGACAGTCAATGGATCTGTTATGTAGCTTATCCATTAGATCTATTTGAAGAGGGTTCCGTTACTAACATGTTTACTTCCATTGTAGGTAACGTATTTGGTTTCAAAGCCCTACGTGCTCTACGTCTGGAGGATCTACGAATTCCCCCTACTTATTCAAAAACTTTCCAAGGCCCGCCTCACGGTATCCAAGTGGAAAGAGATAAGTTGAACAAGTATGGTCGTCCTTTATTGGGATGTACTATTAAGCCAAAATTGGG criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=211.87 fanout-score-rank=1 prefix-density=0.75 prefix-fanout=22.1 sequence=CGGCGGCGGCGC ERR3450060 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:20:52 Started mapping on | Dec 07 14:20:52 Finished on | Dec 07 14:23:53 Mapping speed, Million of reads per hour | 859.93 Number of input reads | 43235570 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 31162035 Uniquely mapped reads % | 72.07% Average mapped length | 198.08 Number of splices: Total | 19300303 Number of splices: Annotated (sjdb) | 18284131 Number of splices: GT/AG | 19048221 Number of splices: GC/AG | 218133 Number of splices: AT/AC | 11828 Number of splices: Non-canonical | 22121 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.15 Insertion rate per base | 0.01% Insertion average length | 1.97 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2291243 % of reads mapped to multiple loci | 5.30% Number of reads mapped to too many loci | 1676089 % of reads mapped to too many loci | 3.88% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.21% % of reads unmapped: other | 15.54% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9782292 9782292 9782292 N_multimapping 2291243 2291243 2291243 N_noFeature 1086672 30045549 1741447 N_ambiguous 565436 4444 108931 UnstrandedReadsAssigned:29509927 PositiveStrandReadsAssigned:1112042 NegativeStrandReadsAssigned:29311657 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450060 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: ERR3450060-trimmed-pair1.fastq ERR3450060-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 43,235,570 reads, 31,047,366 reads pseudoaligned [quant] estimated average fragment length: 188.077 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,335 rounds 52973 ERR3450060.ke.tsv 35125 ERR3450060.se.tsv 88098 total ==> ERR3450060.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 749.028 0 0 PNS24247 1044 856.923 57.7227 3.24026 PNS24249 1928 1740.92 345.465 9.54553 PNS24246 1044 856.923 57.7227 3.24026 PNS24248 1044 856.923 57.7227 3.24026 PNS24244 1471 1283.92 88.3665 3.31073 PNS24243 293 128.537 0 0 KQK14069 1603 1415.92 9452.79 321.141 KQK14071 474 291.393 534.202 88.1865 ==> ERR3450060.se.tsv <== BRADI_1g14170v3 10378 BRADI_1g53295v3 40 BRADI_1g59795v3 353 BRADI_1g07683v3 0 BRADI_1g00485v3 63 BRADI_1g20270v3 3461 BRADI_1g74790v3 331 BRADI_1g09890v3 41 BRADI_1g77505v3 372 BRADI_1g48960v3 2 ERR3450060 completed mapping pipeline successfully