Starting /dee2/code/volunteer_pipeline.sh ERR3450081 current disk space = 1542844329984 free memory = 1597398176 ERR3450081 SRAfilesize c09d618d182d9be9e9052eb9519c6a02 ERR3450081.sra ERR3450081.sra file validated ERR3450081 is paired end ERR3450081 is conventional basespace ERR3450081 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450081_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 36.13275 37.0 37.0 37.0 37.0 37.0 2 36.352 37.0 37.0 37.0 37.0 37.0 3 36.408 37.0 37.0 37.0 37.0 37.0 4 36.481 37.0 37.0 37.0 37.0 37.0 5 36.477 37.0 37.0 37.0 37.0 37.0 6 36.5785 37.0 37.0 37.0 37.0 37.0 7 36.4785 37.0 37.0 37.0 37.0 37.0 8 36.533 37.0 37.0 37.0 37.0 37.0 9 36.48 37.0 37.0 37.0 37.0 37.0 10-11 36.448750000000004 37.0 37.0 37.0 37.0 37.0 12-13 36.4715 37.0 37.0 37.0 37.0 37.0 14-15 36.485 37.0 37.0 37.0 37.0 37.0 16-17 36.3885 37.0 37.0 37.0 37.0 37.0 18-19 36.4765 37.0 37.0 37.0 37.0 37.0 20-21 36.45725 37.0 37.0 37.0 37.0 37.0 22-23 36.39925 37.0 37.0 37.0 37.0 37.0 24-25 36.4075 37.0 37.0 37.0 37.0 37.0 26-27 36.454750000000004 37.0 37.0 37.0 37.0 37.0 28-29 36.324749999999995 37.0 37.0 37.0 37.0 37.0 30-31 36.321250000000006 37.0 37.0 37.0 37.0 37.0 32-33 36.283249999999995 37.0 37.0 37.0 37.0 37.0 34-35 36.27725 37.0 37.0 37.0 37.0 37.0 36-37 36.30825 37.0 37.0 37.0 37.0 37.0 38-39 36.228750000000005 37.0 37.0 37.0 37.0 37.0 40-41 36.234 37.0 37.0 37.0 37.0 37.0 42-43 36.235749999999996 37.0 37.0 37.0 37.0 37.0 44-45 36.1605 37.0 37.0 37.0 37.0 37.0 46-47 36.12525 37.0 37.0 37.0 37.0 37.0 48-49 36.1535 37.0 37.0 37.0 37.0 37.0 50-51 36.15375 37.0 37.0 37.0 37.0 37.0 52-53 36.154250000000005 37.0 37.0 37.0 37.0 37.0 54-55 36.16225 37.0 37.0 37.0 37.0 37.0 56-57 36.05575 37.0 37.0 37.0 37.0 37.0 58-59 36.09725 37.0 37.0 37.0 37.0 37.0 60-61 36.072500000000005 37.0 37.0 37.0 37.0 37.0 62-63 36.04675 37.0 37.0 37.0 37.0 37.0 64-65 36.064 37.0 37.0 37.0 37.0 37.0 66-67 35.98275 37.0 37.0 37.0 37.0 37.0 68-69 36.02475 37.0 37.0 37.0 37.0 37.0 70-71 35.924499999999995 37.0 37.0 37.0 37.0 37.0 72-73 36.007999999999996 37.0 37.0 37.0 37.0 37.0 74-75 35.9835 37.0 37.0 37.0 37.0 37.0 76-77 35.9875 37.0 37.0 37.0 37.0 37.0 78-79 35.92125 37.0 37.0 37.0 37.0 37.0 80-81 35.9245 37.0 37.0 37.0 37.0 37.0 82-83 35.92775 37.0 37.0 37.0 37.0 37.0 84-85 35.946 37.0 37.0 37.0 37.0 37.0 86-87 35.8705 37.0 37.0 37.0 37.0 37.0 88-89 35.917249999999996 37.0 37.0 37.0 37.0 37.0 90-91 35.9255 37.0 37.0 37.0 37.0 37.0 92-93 35.8505 37.0 37.0 37.0 37.0 37.0 94-95 35.8275 37.0 37.0 37.0 37.0 37.0 96-97 35.872749999999996 37.0 37.0 37.0 37.0 37.0 98-99 35.83175 37.0 37.0 37.0 37.0 37.0 100-101 35.8705 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 1.0 23 3.0 24 7.0 25 4.0 26 12.0 27 21.0 28 29.0 29 29.0 30 39.0 31 59.0 32 76.0 33 97.0 34 126.0 35 183.0 36 1770.0 37 1541.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.683932612522 9.580085491576565 10.93789288408348 38.79808901181796 2 21.325 13.600000000000001 29.4 35.675000000000004 3 21.875 17.525 25.374999999999996 35.225 4 27.55 23.0 18.75 30.7 5 27.200000000000003 26.575 21.425 24.8 6 23.325000000000003 31.424999999999997 24.099999999999998 21.15 7 19.5 23.825 36.375 20.3 8 22.275 20.525 30.349999999999998 26.85 9 22.125 20.549999999999997 31.674999999999997 25.650000000000002 10-11 22.6875 28.425 23.962500000000002 24.925 12-13 23.35 23.625 25.937500000000004 27.0875 14-15 22.662499999999998 24.275 26.75 26.3125 16-17 23.75 24.5125 25.4625 26.275 18-19 24.1875 25.35 25.15 25.3125 20-21 23.75 25.15 25.85 25.25 22-23 25.412499999999998 24.2 23.9125 26.474999999999998 24-25 23.275000000000002 23.875 26.35 26.5 26-27 24.9375 24.1625 24.425 26.474999999999998 28-29 24.212500000000002 23.3125 24.45 28.025 30-31 24.5125 22.775000000000002 24.587500000000002 28.125 32-33 24.275 23.4375 24.525 27.762500000000003 34-35 23.3625 24.087500000000002 24.587500000000002 27.962500000000002 36-37 23.599999999999998 24.775 24.4 27.224999999999998 38-39 24.375 24.7375 24.6625 26.224999999999998 40-41 24.2375 23.7625 24.625 27.375 42-43 24.375 23.1 24.9125 27.6125 44-45 24.6625 23.8375 25.35 26.150000000000002 46-47 23.4625 24.337500000000002 25.362499999999997 26.8375 48-49 24.875 23.125 24.95 27.05 50-51 23.7875 24.0 25.324999999999996 26.887499999999996 52-53 24.637500000000003 24.25 24.375 26.737499999999997 54-55 23.4625 23.5375 25.15 27.85 56-57 23.7125 24.1875 25.1875 26.9125 58-59 23.724999999999998 23.5 24.762500000000003 28.012500000000003 60-61 24.775 24.1875 24.95 26.087500000000002 62-63 24.637500000000003 23.65 25.362499999999997 26.35 64-65 24.2 24.6625 24.9125 26.224999999999998 66-67 24.7375 24.0375 25.0 26.224999999999998 68-69 24.474999999999998 23.425 25.2875 26.8125 70-71 24.6125 24.05 24.45 26.887499999999996 72-73 24.3125 24.1875 24.525 26.974999999999998 74-75 24.7875 23.7 24.962500000000002 26.55 76-77 25.275 24.375 23.799999999999997 26.55 78-79 24.825 24.887500000000003 23.7 26.5875 80-81 25.0 24.2375 24.5125 26.25 82-83 24.6875 23.7125 24.337500000000002 27.2625 84-85 25.174999999999997 24.1375 23.3875 27.3 86-87 25.275 24.4375 23.3125 26.974999999999998 88-89 24.775 24.0625 24.125 27.037499999999998 90-91 24.2625 23.75 23.9 28.0875 92-93 25.9625 24.025 23.7 26.3125 94-95 26.05 24.025 23.9375 25.9875 96-97 25.174999999999997 24.337500000000002 23.025000000000002 27.462500000000002 98-99 24.05 26.05 23.9 26.0 100-101 24.0 24.3875 24.125 27.487499999999997 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 3.0 1 1.5 2 0.0 3 1.0 4 1.5 5 1.0 6 0.5 7 0.5 8 2.0 9 1.5 10 0.5 11 1.5 12 1.0 13 0.0 14 0.5 15 1.0 16 0.5 17 0.0 18 0.5 19 0.5 20 0.0 21 0.0 22 0.5 23 2.0 24 2.0 25 1.5 26 1.5 27 3.0 28 3.0 29 1.0 30 3.0 31 7.5 32 9.0 33 13.0 34 14.0 35 21.0 36 31.5 37 40.0 38 53.5 39 63.0 40 81.5 41 106.5 42 126.0 43 137.5 44 142.0 45 159.0 46 171.0 47 172.5 48 173.0 49 171.5 50 179.5 51 181.0 52 181.5 53 168.5 54 156.0 55 157.5 56 140.5 57 130.0 58 111.0 59 87.0 60 70.5 61 60.5 62 69.5 63 59.5 64 44.5 65 53.5 66 55.5 67 48.0 68 48.5 69 40.0 70 29.5 71 33.0 72 36.0 73 27.5 74 21.0 75 18.0 76 16.0 77 14.5 78 10.5 79 11.0 80 8.0 81 1.5 82 1.0 83 0.5 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 1.0 96 1.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.575 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 85.25 #Duplication Level Percentage of deduplicated Percentage of total 1 87.03812316715542 74.2 2 10.381231671554252 17.7 3 1.8181818181818181 4.65 4 0.3519061583577713 1.2 5 0.17595307917888564 0.75 6 0.02932551319648094 0.15 7 0.05865102639296188 0.35000000000000003 8 0.1466275659824047 1.0 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 GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 8 0.2 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 8 0.2 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 8 0.2 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 8 0.2 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 8 0.2 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 3 (97% over 36bp) GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 7 0.17500000000000002 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 6 0.15 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 5 0.125 No Hit GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 5 0.125 No Hit CTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATC 5 0.125 No Hit GTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTC 5 0.125 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 5 0.125 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.0625 0.0 0.0 0.0 0.0 40-41 0.1125 0.0 0.0 0.0 0.0 42-43 0.16249999999999998 0.0 0.0 0.0 0.0 44-45 0.1875 0.0 0.0 0.0 0.0 46-47 0.21250000000000002 0.0 0.0 0.0 0.0 48-49 0.2375 0.0 0.0 0.0 0.0 50-51 0.35 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.4 0.0 0.0 0.0 0.0 56-57 0.4625 0.0 0.0 0.0 0.0 58-59 0.5875 0.0 0.0 0.0 0.0 60-61 0.65 0.0 0.0 0.0 0.0 62-63 0.8375 0.0 0.0 0.0 0.0 64-65 1.0875 0.0 0.0 0.0 0.0 66-67 1.3375 0.0 0.0 0.0 0.0 68-69 1.5 0.0 0.0 0.0 0.0 70-71 1.65 0.0 0.0 0.0 0.0 72-73 1.975 0.0 0.0 0.0 0.0 74-75 2.25 0.0 0.0 0.0 0.0 76-77 2.7 0.0 0.0 0.0 0.0 78-79 3.1875 0.0 0.0 0.0 0.0 80-81 3.5375 0.0 0.0 0.0 0.0 82-83 3.8875 0.0 0.0 0.0 0.0 84-85 4.525 0.0 0.0 0.0 0.0 86-87 5.0 0.0 0.0 0.0 0.0 88-89 5.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450081 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450081_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 35.934 37.0 37.0 37.0 37.0 37.0 2 35.9515 37.0 37.0 37.0 37.0 37.0 3 35.9415 37.0 37.0 37.0 37.0 37.0 4 36.183 37.0 37.0 37.0 37.0 37.0 5 36.13 37.0 37.0 37.0 37.0 37.0 6 36.0665 37.0 37.0 37.0 37.0 37.0 7 36.1625 37.0 37.0 37.0 37.0 37.0 8 36.24 37.0 37.0 37.0 37.0 37.0 9 36.082 37.0 37.0 37.0 37.0 37.0 10-11 36.1325 37.0 37.0 37.0 37.0 37.0 12-13 36.1145 37.0 37.0 37.0 37.0 37.0 14-15 36.101 37.0 37.0 37.0 37.0 37.0 16-17 36.06525 37.0 37.0 37.0 37.0 37.0 18-19 36.08725 37.0 37.0 37.0 37.0 37.0 20-21 36.110749999999996 37.0 37.0 37.0 37.0 37.0 22-23 36.152 37.0 37.0 37.0 37.0 37.0 24-25 36.072 37.0 37.0 37.0 37.0 37.0 26-27 36.0475 37.0 37.0 37.0 37.0 37.0 28-29 36.11275 37.0 37.0 37.0 37.0 37.0 30-31 36.06225 37.0 37.0 37.0 37.0 37.0 32-33 36.02975 37.0 37.0 37.0 37.0 37.0 34-35 36.019 37.0 37.0 37.0 37.0 37.0 36-37 36.122749999999996 37.0 37.0 37.0 37.0 37.0 38-39 36.028999999999996 37.0 37.0 37.0 37.0 37.0 40-41 35.985749999999996 37.0 37.0 37.0 37.0 37.0 42-43 35.99325 37.0 37.0 37.0 37.0 37.0 44-45 35.98075 37.0 37.0 37.0 37.0 37.0 46-47 35.999 37.0 37.0 37.0 37.0 37.0 48-49 35.865750000000006 37.0 37.0 37.0 37.0 37.0 50-51 35.987750000000005 37.0 37.0 37.0 37.0 37.0 52-53 35.96625 37.0 37.0 37.0 37.0 37.0 54-55 35.94425 37.0 37.0 37.0 37.0 37.0 56-57 36.022 37.0 37.0 37.0 37.0 37.0 58-59 35.963499999999996 37.0 37.0 37.0 37.0 37.0 60-61 35.95925 37.0 37.0 37.0 37.0 37.0 62-63 35.99825 37.0 37.0 37.0 37.0 37.0 64-65 35.987750000000005 37.0 37.0 37.0 37.0 37.0 66-67 35.933 37.0 37.0 37.0 37.0 37.0 68-69 35.90175 37.0 37.0 37.0 37.0 37.0 70-71 35.96525 37.0 37.0 37.0 37.0 37.0 72-73 35.9445 37.0 37.0 37.0 37.0 37.0 74-75 35.8685 37.0 37.0 37.0 37.0 37.0 76-77 35.89325 37.0 37.0 37.0 37.0 37.0 78-79 35.86475 37.0 37.0 37.0 37.0 37.0 80-81 35.869749999999996 37.0 37.0 37.0 37.0 37.0 82-83 35.81525 37.0 37.0 37.0 37.0 37.0 84-85 35.885000000000005 37.0 37.0 37.0 37.0 37.0 86-87 35.78275 37.0 37.0 37.0 37.0 37.0 88-89 35.775 37.0 37.0 37.0 37.0 37.0 90-91 35.7715 37.0 37.0 37.0 37.0 37.0 92-93 35.8215 37.0 37.0 37.0 37.0 37.0 94-95 35.86175 37.0 37.0 37.0 37.0 37.0 96-97 35.686 37.0 37.0 37.0 37.0 37.0 98-99 35.644999999999996 37.0 37.0 37.0 37.0 37.0 100-101 35.66175 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 2.0 15 6.0 16 2.0 17 1.0 18 9.0 19 5.0 20 8.0 21 13.0 22 10.0 23 12.0 24 20.0 25 9.0 26 19.0 27 16.0 28 22.0 29 21.0 30 26.0 31 35.0 32 47.0 33 62.0 34 98.0 35 219.0 36 2002.0 37 1335.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.375 17.7 12.675 29.25 2 26.950000000000003 22.35 27.650000000000002 23.05 3 24.75 23.075000000000003 27.675 24.5 4 29.725 27.775 18.175 24.325 5 30.099999999999998 30.5 19.025 20.375 6 24.85 33.050000000000004 20.125 21.975 7 25.7 18.9 31.424999999999997 23.974999999999998 8 25.874999999999996 20.65 23.45 30.025000000000002 9 26.450000000000003 22.55 25.474999999999998 25.525 10-11 28.712500000000002 26.825 20.2125 24.25 12-13 29.7 23.400000000000002 21.3625 25.5375 14-15 27.6125 24.637500000000003 23.2625 24.4875 16-17 29.049999999999997 25.424999999999997 22.112499999999997 23.4125 18-19 27.900000000000002 24.9125 22.6875 24.5 20-21 27.800000000000004 24.6625 22.8625 24.675 22-23 27.5125 25.6 22.375 24.5125 24-25 27.224999999999998 24.8 23.599999999999998 24.375 26-27 27.375 24.6125 23.0875 24.925 28-29 27.500000000000004 25.5375 22.725 24.2375 30-31 27.462500000000002 25.55 22.112499999999997 24.875 32-33 27.187499999999996 26.337500000000002 22.787499999999998 23.6875 34-35 27.6 24.887500000000003 22.787499999999998 24.725 36-37 27.462500000000002 25.0125 22.45 25.074999999999996 38-39 27.287499999999998 25.374999999999996 22.9625 24.375 40-41 27.250000000000004 24.925 23.075000000000003 24.75 42-43 27.3 25.074999999999996 22.15 25.474999999999998 44-45 26.474999999999998 25.724999999999998 23.65 24.15 46-47 26.987499999999997 25.6 22.725 24.6875 48-49 28.3875 24.7375 21.925 24.95 50-51 27.287499999999998 24.9 22.875 24.9375 52-53 27.3 24.8 23.775 24.125 54-55 27.3625 25.687500000000004 22.1875 24.762500000000003 56-57 28.050000000000004 24.7375 23.1375 24.075 58-59 27.1125 25.650000000000002 22.725 24.5125 60-61 28.6625 25.4875 22.325 23.525 62-63 27.750000000000004 25.2 23.1375 23.9125 64-65 27.750000000000004 24.175 23.400000000000002 24.675 66-67 27.450000000000003 24.375 23.6875 24.4875 68-69 27.987499999999997 25.05 22.025 24.9375 70-71 28.712500000000002 24.925 22.7125 23.65 72-73 26.974999999999998 25.4875 23.4125 24.125 74-75 26.650000000000002 25.687500000000004 23.1125 24.55 76-77 27.962500000000002 24.975 22.475 24.587500000000002 78-79 27.725 24.825 23.1625 24.2875 80-81 27.6625 26.25 22.825 23.2625 82-83 26.6125 25.587500000000002 23.400000000000002 24.4 84-85 28.725 24.625 22.3375 24.3125 86-87 27.575 25.45 23.525 23.45 88-89 28.125 25.45 22.4375 23.9875 90-91 27.5625 24.6 24.25 23.5875 92-93 27.525 25.85 22.625 24.0 94-95 29.4125 25.35 21.712500000000002 23.525 96-97 29.2875 25.8625 21.3625 23.4875 98-99 29.025000000000002 26.1625 21.712500000000002 23.1 100-101 28.4125 25.362499999999997 22.8375 23.3875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 1.0 5 1.5 6 1.0 7 1.0 8 1.5 9 1.0 10 0.5 11 1.5 12 1.5 13 3.0 14 4.5 15 2.5 16 2.0 17 2.0 18 2.0 19 2.0 20 1.0 21 1.0 22 3.0 23 2.5 24 1.0 25 3.5 26 3.0 27 1.5 28 3.5 29 5.5 30 4.5 31 4.0 32 4.0 33 7.5 34 12.5 35 16.0 36 21.0 37 33.5 38 46.5 39 60.5 40 80.5 41 109.0 42 123.0 43 121.0 44 135.0 45 154.5 46 160.5 47 172.5 48 179.0 49 169.5 50 162.0 51 166.5 52 177.0 53 167.0 54 146.5 55 144.0 56 142.5 57 113.5 58 96.0 59 88.5 60 76.5 61 70.0 62 74.5 63 71.0 64 59.0 65 62.5 66 57.5 67 49.5 68 60.5 69 56.5 70 37.5 71 39.0 72 37.5 73 25.5 74 21.5 75 21.0 76 22.0 77 18.0 78 11.0 79 7.5 80 7.5 81 7.5 82 4.0 83 2.0 84 2.5 85 1.5 86 0.5 87 0.5 88 0.5 89 0.5 90 1.0 91 1.5 92 1.0 93 1.0 94 1.0 95 1.5 96 1.5 97 1.0 98 1.0 99 1.0 100 5.5 >>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 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.25 #Duplication Level Percentage of deduplicated Percentage of total 1 87.65217391304347 75.6 2 10.057971014492754 17.349999999999998 3 1.6811594202898552 4.35 4 0.3188405797101449 1.0999999999999999 5 0.17391304347826086 0.75 6 0.028985507246376812 0.15 7 0.028985507246376812 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.057971014492753624 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 11 0.27499999999999997 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 10 0.25 No Hit GTTTGTTTGATGGTACGTGCTACTCGGATAACCGTAGTAATTCTAGAGCT 7 0.17500000000000002 No Hit CAACGAGTATATAGCCTTGGCCGACAGGCCCGGGTAATCTTGGGAAATTT 6 0.15 No Hit GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 5 0.125 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 5 0.125 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 5 0.125 No Hit CCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACG 5 0.125 No Hit CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACC 5 0.125 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.0625 0.0 0.0 0.0 0.0 40-41 0.1125 0.0 0.0 0.0 0.0 42-43 0.16249999999999998 0.0 0.0 0.0 0.0 44-45 0.1875 0.0 0.0 0.0 0.0 46-47 0.21250000000000002 0.0 0.0 0.0 0.0 48-49 0.2375 0.0 0.0 0.0 0.0 50-51 0.35 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.4 0.0 0.0 0.0 0.0 56-57 0.4625 0.0 0.0 0.0 0.0 58-59 0.5875 0.0 0.0 0.0 0.0 60-61 0.65 0.0 0.0 0.0 0.0 62-63 0.8375 0.0 0.0 0.0 0.0 64-65 1.0875 0.0 0.0 0.0 0.0 66-67 1.3375 0.0 0.0 0.0 0.0 68-69 1.475 0.0 0.0 0.0 0.0 70-71 1.625 0.0 0.0 0.0 0.0 72-73 1.975 0.0 0.0 0.0 0.0 74-75 2.2375 0.0 0.0 0.0 0.0 76-77 2.7 0.0 0.0 0.0 0.0 78-79 3.1875 0.0 0.0 0.0 0.0 80-81 3.5625 0.0 0.0 0.0 0.0 82-83 3.9125 0.0 0.0 0.0 0.0 84-85 4.5375 0.0 0.0 0.0 0.0 86-87 5.012499999999999 0.0 0.0 0.0 0.0 88-89 5.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534679 spots for ERR3450081.sra Written 2534679 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra Read 2534661 spots for ERR3450081.sra Written 2534661 spots for ERR3450081.sra SRR ids: ['ERR3450081.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4o__27vt ERR3450081.sra spots: 50693238 blocks: [[1, 2534661], [2534662, 5069322], [5069323, 7603983], [7603984, 10138644], [10138645, 12673305], [12673306, 15207966], [15207967, 17742627], [17742628, 20277288], [20277289, 22811949], [22811950, 25346610], [25346611, 27881271], [27881272, 30415932], [30415933, 32950593], [32950594, 35485254], [35485255, 38019915], [38019916, 40554576], [40554577, 43089237], [43089238, 45623898], [45623899, 48158559], [48158560, 50693238]] ERR3450081 file size 12206063 ERR3450081 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 ERR3450081 ERR3450081_1.fastq ERR3450081_2.fastq Input file: ERR3450081_1.fastq Paired file: ERR3450081_2.fastq trimmed: ERR3450081-trimmed-pair1.fastq, ERR3450081-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 14:53:48 2024 >> started Sat Dec 7 14:54:32 2024 >> done (43.096s) 50693238 read pairs processed; of these: 355 ( 0.00%) short read pairs filtered out after trimming by size control 116890 ( 0.23%) empty read pairs filtered out after trimming by size control 50575993 (99.77%) read pairs available; of these: 4620142 ( 9.14%) trimmed read pairs available after processing 45955851 (90.86%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 75 0.00% 19 108 0.00% 20 337 0.00% 21 810 0.00% 22 1063 0.00% 23 544 0.00% 24 547 0.00% 25 724 0.00% 26 1091 0.00% 27 1496 0.00% 28 2063 0.00% 29 2775 0.01% 30 3292 0.01% 31 4005 0.01% 32 4152 0.01% 33 3975 0.01% 34 4005 0.01% 35 3968 0.01% 36 4517 0.01% 37 4936 0.01% 38 5860 0.01% 39 6810 0.01% 40 8177 0.02% 41 9256 0.02% 42 10621 0.02% 43 11290 0.02% 44 10293 0.02% 45 10352 0.02% 46 11095 0.02% 47 12109 0.02% 48 13463 0.03% 49 14818 0.03% 50 16450 0.03% 51 18519 0.04% 52 20354 0.04% 53 21137 0.04% 54 22381 0.04% 55 23733 0.05% 56 24671 0.05% 57 25752 0.05% 58 28165 0.06% 59 30432 0.06% 60 33154 0.07% 61 36089 0.07% 62 39421 0.08% 63 43105 0.09% 64 44647 0.09% 65 46376 0.09% 66 48227 0.10% 67 50928 0.10% 68 52939 0.10% 69 55099 0.11% 70 59645 0.12% 71 63525 0.13% 72 68723 0.14% 73 72365 0.14% 74 75204 0.15% 75 78272 0.15% 76 80935 0.16% 77 83682 0.17% 78 87373 0.17% 79 91911 0.18% 80 94742 0.19% 81 98613 0.19% 82 104505 0.21% 83 108451 0.21% 84 112956 0.22% 85 117294 0.23% 86 121960 0.24% 87 126359 0.25% 88 130455 0.26% 89 135258 0.27% 90 138642 0.27% 91 146449 0.29% 92 153325 0.30% 93 157587 0.31% 94 162742 0.32% 95 167979 0.33% 96 171372 0.34% 97 177045 0.35% 98 180890 0.36% 99 183289 0.36% 100 218388 0.43% 101 45955851 90.86% 50575993 reads passed initial QC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=2.22 fanout-score-rank=21 prefix-density=0.42 prefix-fanout=2.1 sequence=TTCGCTATCGGTC criterion=fanout-score sequence-density=0.09 sequence-density-rank=19 fanout-score=48.18 fanout-score-rank=1 prefix-density=1.10 prefix-fanout=4.0 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACGTTCTCCGGCCGTCCTC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=26 prefix-density=0.23 prefix-fanout=2.0 sequence=AGCCAGAGGAAA criterion=fanout-score sequence-density=0.08 sequence-density-rank=20 fanout-score=174.98 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=22.1 sequence=GCGGCGGCGGCG ERR3450081 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:55:00 Started mapping on | Dec 07 14:55:01 Finished on | Dec 07 14:58:40 Mapping speed, Million of reads per hour | 831.39 Number of input reads | 50575993 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 35917025 Uniquely mapped reads % | 71.02% Average mapped length | 198.18 Number of splices: Total | 22054977 Number of splices: Annotated (sjdb) | 20844981 Number of splices: GT/AG | 21752481 Number of splices: GC/AG | 262270 Number of splices: AT/AC | 11964 Number of splices: Non-canonical | 28262 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3839413 % of reads mapped to multiple loci | 7.59% Number of reads mapped to too many loci | 1769143 % of reads mapped to too many loci | 3.50% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.47% % of reads unmapped: other | 14.42% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10819555 10819555 10819555 N_multimapping 3839413 3839413 3839413 N_noFeature 1630360 34457915 2473403 N_ambiguous 779776 6232 175531 UnstrandedReadsAssigned:33506889 PositiveStrandReadsAssigned:1452878 NegativeStrandReadsAssigned:33268091 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450081 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: ERR3450081-trimmed-pair1.fastq ERR3450081-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 50,575,993 reads, 36,072,722 reads pseudoaligned [quant] estimated average fragment length: 187.645 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,206 rounds 52973 ERR3450081.ke.tsv 35125 ERR3450081.se.tsv 88098 total ==> ERR3450081.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 749.535 0 0 PNS24247 1044 857.355 106.768 5.04118 PNS24249 1928 1741.35 599.515 13.9368 PNS24246 1044 857.355 106.768 5.04118 PNS24248 1044 857.355 106.768 5.04118 PNS24244 1471 1284.35 101.18 3.18905 PNS24243 293 127.823 3 0.950085 KQK14069 1603 1416.35 13896 397.162 KQK14071 474 291.378 652.455 90.6451 ==> ERR3450081.se.tsv <== BRADI_1g14170v3 15142 BRADI_1g53295v3 60 BRADI_1g59795v3 522 BRADI_1g07683v3 0 BRADI_1g00485v3 37 BRADI_1g20270v3 2628 BRADI_1g74790v3 410 BRADI_1g09890v3 21 BRADI_1g77505v3 564 BRADI_1g48960v3 0 ERR3450081 completed mapping pipeline successfully