Starting /dee2/code/volunteer_pipeline.sh SRR12671693 current disk space = 3049131483136 free memory = 1576969540 SRR12671693 SRAfilesize 973590e23bbac2b32abcb0e8d9ef7508 SRR12671693.sra SRR12671693.sra file validated SRR12671693 is paired end SRR12671693 is conventional basespace SRR12671693 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671693_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 25 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.52 NaN NaN NaN NaN NaN 2 36.52 NaN NaN NaN NaN NaN 3 37.0 NaN NaN NaN NaN NaN 4 37.0 NaN NaN NaN NaN NaN 5 36.52 NaN NaN NaN NaN NaN 6 37.0 NaN NaN NaN NaN NaN 7 37.0 NaN NaN NaN NaN NaN 8 36.52 NaN NaN NaN NaN NaN 9 36.04 NaN NaN NaN NaN NaN 10-14 36.104 NaN NaN NaN NaN NaN 15-19 36.424 NaN NaN NaN NaN NaN 20-24 36.424 NaN NaN NaN NaN NaN 25-29 36.104 NaN NaN NaN NaN NaN 30-34 36.696000000000005 NaN NaN NaN NaN NaN 35-39 36.215999999999994 NaN NaN NaN NaN NaN 40-44 36.184000000000005 NaN NaN NaN NaN NaN 45-49 35.0 NaN NaN NaN NaN NaN 50-54 36.184000000000005 NaN NaN NaN NaN NaN 55-59 35.416 NaN NaN NaN NaN NaN 60-64 34.648 NaN NaN NaN NaN NaN 65-69 34.264 NaN NaN NaN NaN NaN 70-74 34.151999999999994 NaN NaN NaN NaN NaN 75-79 35.784000000000006 NaN NaN NaN NaN NaN 80-84 35.784 NaN NaN NaN NaN NaN 85-89 35.592 NaN NaN NaN NaN NaN 90-94 35.239999999999995 NaN NaN NaN NaN NaN 95-99 35.879999999999995 NaN NaN NaN NaN NaN 100-104 35.928000000000004 NaN NaN NaN NaN NaN 105-109 34.888 NaN NaN NaN NaN NaN 110-114 35.512 NaN NaN NaN NaN NaN 115-119 35.879999999999995 NaN NaN NaN NaN NaN 120-124 34.80799999999999 NaN NaN NaN NaN NaN 125-129 34.872 NaN NaN NaN NaN NaN 130-134 33.608 NaN NaN NaN NaN NaN 135-139 34.007999999999996 NaN NaN NaN NaN NaN 140-144 34.6 NaN NaN NaN NaN NaN 145-149 34.568 NaN NaN NaN NaN NaN 150-151 34.68 NaN NaN NaN NaN NaN >>END_MODULE >>Per sequence quality scores pass #Quality Count 30 2.0 31 1.0 32 0.0 33 1.0 34 4.0 35 2.0 36 13.0 37 2.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.0 0.0 16.0 48.0 2 12.0 28.000000000000004 44.0 16.0 3 8.0 16.0 36.0 40.0 4 24.0 40.0 12.0 24.0 5 28.000000000000004 32.0 24.0 16.0 6 24.0 24.0 28.000000000000004 24.0 7 16.0 20.0 40.0 24.0 8 24.0 36.0 24.0 16.0 9 24.0 24.0 24.0 28.000000000000004 10-14 17.599999999999998 32.800000000000004 25.6 24.0 15-19 24.0 21.6 31.2 23.200000000000003 20-24 25.6 21.6 27.200000000000003 25.6 25-29 20.8 25.6 30.4 23.200000000000003 30-34 21.6 24.0 25.6 28.799999999999997 35-39 26.400000000000002 32.0 20.0 21.6 40-44 24.0 17.599999999999998 35.199999999999996 23.200000000000003 45-49 24.8 31.2 24.0 20.0 50-54 24.0 21.6 27.200000000000003 27.200000000000003 55-59 12.8 23.200000000000003 38.4 25.6 60-64 24.0 24.0 27.200000000000003 24.8 65-69 24.8 28.799999999999997 27.200000000000003 19.2 70-74 32.800000000000004 21.6 24.0 21.6 75-79 27.200000000000003 36.8 16.8 19.2 80-84 30.4 32.0 18.4 19.2 85-89 26.400000000000002 24.0 25.6 24.0 90-94 28.799999999999997 19.2 27.200000000000003 24.8 95-99 28.799999999999997 30.4 16.0 24.8 100-104 36.8 25.6 16.0 21.6 105-109 30.4 18.4 28.000000000000004 23.200000000000003 110-114 32.0 20.8 28.000000000000004 19.2 115-119 33.6 23.200000000000003 23.200000000000003 20.0 120-124 27.200000000000003 21.6 28.799999999999997 22.400000000000002 125-129 26.400000000000002 24.8 25.6 23.200000000000003 130-134 28.799999999999997 24.0 22.400000000000002 24.8 135-139 36.0 28.799999999999997 21.6 13.600000000000001 140-144 40.8 20.0 15.2 24.0 145-149 40.8 21.6 17.599999999999998 20.0 150-151 36.0 18.0 20.0 26.0 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.5 37 0.5 38 0.0 39 1.0 40 2.0 41 2.0 42 1.0 43 0.0 44 0.5 45 2.0 46 1.5 47 2.0 48 2.5 49 1.0 50 1.0 51 0.5 52 0.5 53 0.5 54 0.5 55 1.0 56 1.0 57 0.5 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.5 66 1.5 67 1.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 25.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.0 #Duplication Level Percentage of deduplicated Percentage of total 1 91.30434782608695 84.0 2 8.695652173913043 16.0 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 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 fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACTCATATCTCGTAT 2 8.0 TruSeq Adapter, Index 23 (97% over 39bp) CTCTATCAATGGAATCTTGATTGGCTTCACCAAGAGAAGCCTCGCTCAGG 2 8.0 No Hit TGAAAAGGAAAGGCACACGCTCGCCACCAGGCAGCTGAACGGTCACAGCA 1 4.0 No Hit CTTGAGTTACCTGTCTTTCCTTTGATCGGCGGGAGGAAGATGGTGGGAGG 1 4.0 No Hit CTCAAATTCTTCTCTCCCATGTTTCTTCTCAGCAAAATATTTGTGAAGCT 1 4.0 No Hit CTGATCCTTACCTTGAAATAGAGCCTGTGCAGGATTGTGCTTACTATCTG 1 4.0 No Hit GGCACCGGTGTGCAGATTCCACCATTTGCAACTCTTGAGTATATTGTTGA 1 4.0 No Hit GAAAAGGAGAGTTGGGGTGGTGGCACCGGGGTTTTGGGAGGTGGGTTTGA 1 4.0 No Hit GTCGCCTCAAACTTGGTATGTGGAGTAATTGACCCTGGCTTCGACAAAAC 1 4.0 No Hit TTTGGCTGCACCAGTGCTTGTTGGGACTATGTTCAATGCTGCAGCCCTGG 1 4.0 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACTCATATCGCGTAT 1 4.0 TruSeq Adapter, Index 23 (97% over 39bp) GATGTCTACAACTCGTCTACCCTGGGTTTTTAACCCCTATTCTTGAACTC 1 4.0 No Hit CTTTTTCGTAAAGGGAAGGAAAGCTGATGAACTGCGGAGGCCTGAGAAAT 1 4.0 No Hit CACCCTTGTCAGTAGCTTAATTGGAGGTGAGGTTGCGAGTGGGCGGCTTC 1 4.0 No Hit CCAAGCTCAATGATTGTCTCATCAGTATAAGGTTTCAACCATTCGACAGG 1 4.0 No Hit CTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTAC 1 4.0 No Hit CACCATTATAATTTCTTTGCCTTGAACCATGTCCAGAATAGTGAAAAAGC 1 4.0 No Hit TTCATAATCAAGTAGTACCTTCTCATAAAACCCTCGAAATGTCCACGAAA 1 4.0 No Hit GTCCTTCTCCACCAACAAATTACACATAACATGCTACACCACAGCTCACA 1 4.0 No Hit TCTAGACCCACCATCAGGATCCTCATTTCTTTCCTTGCAAAGAGTAGCTT 1 4.0 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAATCAACGCATGCTGATGACA 1 4.0 No Hit GCAAAAAAGTTTCCAACGGTGACATCTGGACCAGTATAATCCTTTGGAAC 1 4.0 No Hit CCCAGATCTTAACTTTTCTGCAAAATGCATTTCTTTGGGGTTTTATTGCC 1 4.0 No Hit >>END_MODULE >>Adapter Content fail #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 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 2.0 0.0 0.0 0.0 0.0 64-65 4.0 0.0 0.0 0.0 0.0 66-67 4.0 0.0 0.0 0.0 0.0 68-69 6.0 0.0 0.0 0.0 0.0 70-71 8.0 0.0 0.0 0.0 0.0 72-73 8.0 0.0 0.0 0.0 0.0 74-75 8.0 0.0 0.0 0.0 0.0 76-77 8.0 0.0 0.0 0.0 0.0 78-79 8.0 0.0 0.0 0.0 0.0 80-81 8.0 0.0 0.0 0.0 0.0 82-83 8.0 0.0 0.0 0.0 0.0 84-85 8.0 0.0 0.0 0.0 0.0 86-87 8.0 0.0 0.0 0.0 0.0 88-89 10.0 0.0 0.0 0.0 0.0 90-91 12.0 0.0 0.0 0.0 0.0 92-93 12.0 0.0 0.0 0.0 0.0 94-95 16.0 0.0 0.0 0.0 0.0 96-97 20.0 0.0 0.0 0.0 0.0 98-99 20.0 0.0 0.0 0.0 0.0 100-101 20.0 0.0 0.0 0.0 0.0 102-103 20.0 0.0 0.0 0.0 0.0 104-105 20.0 0.0 0.0 0.0 0.0 106-107 20.0 0.0 0.0 0.0 0.0 108-109 20.0 0.0 0.0 0.0 0.0 110-111 20.0 0.0 0.0 0.0 0.0 112-113 20.0 0.0 0.0 0.0 0.0 114-115 20.0 0.0 0.0 0.0 0.0 116-117 22.0 0.0 0.0 0.0 0.0 118-119 24.0 0.0 0.0 0.0 0.0 120-121 24.0 0.0 0.0 0.0 0.0 122-123 24.0 0.0 0.0 0.0 0.0 124-125 26.0 0.0 0.0 0.0 0.0 126-127 28.0 0.0 0.0 0.0 0.0 128-129 30.0 0.0 0.0 0.0 0.0 130-131 36.0 0.0 0.0 0.0 0.0 132-133 36.0 0.0 0.0 0.0 0.0 134-135 36.0 0.0 0.0 0.0 0.0 136-137 38.0 0.0 0.0 0.0 0.0 138-139 42.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671693 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671693_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 25 Sequences flagged as poor quality 0 Sequence length 151 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.48 NaN NaN NaN NaN NaN 2 34.52 NaN NaN NaN NaN NaN 3 36.04 NaN NaN NaN NaN NaN 4 36.52 NaN NaN NaN NaN NaN 5 35.96 NaN NaN NaN NaN NaN 6 35.0 NaN NaN NaN NaN NaN 7 33.4 NaN NaN NaN NaN NaN 8 32.84 NaN NaN NaN NaN NaN 9 33.4 NaN NaN NaN NaN NaN 10-14 33.512 NaN NaN NaN NaN NaN 15-19 32.488 NaN NaN NaN NaN NaN 20-24 33.64 NaN NaN NaN NaN NaN 25-29 33.096000000000004 NaN NaN NaN NaN NaN 30-34 32.984 NaN NaN NaN NaN NaN 35-39 32.072 NaN NaN NaN NaN NaN 40-44 32.2 NaN NaN NaN NaN NaN 45-49 31.576 NaN NaN NaN NaN NaN 50-54 32.504 NaN NaN NaN NaN NaN 55-59 32.216 NaN NaN NaN NaN NaN 60-64 32.967999999999996 NaN NaN NaN NaN NaN 65-69 32.728 NaN NaN NaN NaN NaN 70-74 31.944 NaN NaN NaN NaN NaN 75-79 32.696000000000005 NaN NaN NaN NaN NaN 80-84 32.504000000000005 NaN NaN NaN NaN NaN 85-89 33.00000000000001 NaN NaN NaN NaN NaN 90-94 33.064 NaN NaN NaN NaN NaN 95-99 33.944 NaN NaN NaN NaN NaN 100-104 34.760000000000005 NaN NaN NaN NaN NaN 105-109 33.224000000000004 NaN NaN NaN NaN NaN 110-114 34.36 NaN NaN NaN NaN NaN 115-119 34.968 NaN NaN NaN NaN NaN 120-124 34.199999999999996 NaN NaN NaN NaN NaN 125-129 34.232 NaN NaN NaN NaN NaN 130-134 33.432 NaN NaN NaN NaN NaN 135-139 31.992 NaN NaN NaN NaN NaN 140-144 30.296000000000003 NaN NaN NaN NaN NaN 145-149 31.159999999999997 NaN NaN NaN NaN NaN 150-151 34.959999999999994 NaN NaN NaN NaN NaN >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 0.0 23 0.0 24 2.0 25 0.0 26 0.0 27 1.0 28 1.0 29 0.0 30 0.0 31 1.0 32 2.0 33 0.0 34 1.0 35 2.0 36 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 60.0 12.0 0.0 28.000000000000004 2 24.0 28.000000000000004 36.0 12.0 3 24.0 28.000000000000004 36.0 12.0 4 32.0 28.000000000000004 16.0 24.0 5 32.0 24.0 32.0 12.0 6 28.000000000000004 40.0 28.000000000000004 4.0 7 36.0 24.0 28.000000000000004 12.0 8 24.0 20.0 24.0 32.0 9 24.0 16.0 24.0 36.0 10-14 27.200000000000003 18.4 32.0 22.400000000000002 15-19 28.799999999999997 24.0 28.799999999999997 18.4 20-24 32.800000000000004 28.000000000000004 16.0 23.200000000000003 25-29 24.0 36.0 23.200000000000003 16.8 30-34 24.8 26.400000000000002 32.0 16.8 35-39 20.8 29.599999999999998 28.000000000000004 21.6 40-44 18.4 24.0 30.4 27.200000000000003 45-49 38.4 20.0 20.8 20.8 50-54 28.799999999999997 19.2 27.200000000000003 24.8 55-59 34.4 21.6 26.400000000000002 17.599999999999998 60-64 36.8 18.4 23.200000000000003 21.6 65-69 27.200000000000003 21.6 28.000000000000004 23.200000000000003 70-74 35.199999999999996 26.400000000000002 15.2 23.200000000000003 75-79 33.6 21.6 32.0 12.8 80-84 22.400000000000002 21.6 30.4 25.6 85-89 27.200000000000003 24.8 28.000000000000004 20.0 90-94 36.0 18.4 25.6 20.0 95-99 31.2 28.799999999999997 21.6 18.4 100-104 35.199999999999996 20.8 22.400000000000002 21.6 105-109 44.0 18.4 20.8 16.8 110-114 40.8 25.6 17.599999999999998 16.0 115-119 43.2 28.799999999999997 19.2 8.799999999999999 120-124 45.6 24.8 13.600000000000001 16.0 125-129 36.8 21.6 22.400000000000002 19.2 130-134 40.0 24.8 16.0 19.2 135-139 52.0 20.8 21.6 5.6000000000000005 140-144 50.4 20.8 14.399999999999999 14.399999999999999 145-149 52.800000000000004 17.599999999999998 19.2 10.4 150-151 54.0 20.0 16.0 10.0 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.5 32 0.5 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.5 40 2.0 41 1.5 42 0.5 43 1.5 44 2.0 45 1.5 46 1.0 47 2.0 48 2.0 49 0.5 50 1.0 51 1.0 52 0.5 53 0.5 54 0.5 55 0.5 56 0.0 57 1.0 58 1.0 59 0.0 60 0.0 61 0.0 62 0.5 63 0.5 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.5 92 0.5 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 25.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.0 #Duplication Level Percentage of deduplicated Percentage of total 1 95.83333333333334 92.0 2 4.166666666666666 8.0 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 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 fail #Sequence Count Percentage Possible Source CAACTTCCCGGCATGTACAACAAGGAGGAGAATCCACGTGTCCCCATCAT 2 8.0 No Hit GTTTAAACCTCCTAAGTTCTACGGAGATCTCCTAAACTGTCTTAAGCTGT 1 4.0 No Hit GACAGGGTTTCTCCTTGGAAAATAGAACGTGCTTTGGCTCCTTCTCTGGA 1 4.0 No Hit GAAAGATTATGAATGCATACACTCTTGCTTATCAGCAAGTCACTTGATGA 1 4.0 No Hit GGGGGGGGGGGCGGGGTGGGGGGGGAAAAAGTGAAAACAAAAATGTGGGG 1 4.0 No Hit GATGGAACCATCAAGTTTGAGGAGAAAGATGGTATTGACTATGCTGCTGT 1 4.0 No Hit GGGGGGGGGGGCGGGGGGGGGGGGGCGGGGGGGGGGCCAGGGGGGGGGGG 1 4.0 No Hit GTTGATAAAATATATGAACTTATGGATAATGTTGATAATTATATACCAAT 1 4.0 No Hit AGGAAAACCTGCCGACCAAAGCATTATGTTGGTAAAGTTTTTGGGAACTT 1 4.0 No Hit GTTATATTGTGTTTGGCTGCAAAATCAATCATCTCTTGTGTCTCCTTCAT 1 4.0 No Hit GGGGGGGGGGGGGGGGGTGGGGGGGGGTGTGTGGGCGCACTGGTGGGGGG 1 4.0 No Hit CGTCGTGGCTGGACCCTGCCGCACCACGAGGCGCTGTCTGCGAGTCGGGT 1 4.0 No Hit GGCGCGGCTCTGTTTCGATAGCTCAATTATTAAGCGGATCTGTCCCTTCC 1 4.0 No Hit AAACTGACCCCTACAGAATTCCCAACAAACAAAACATGAGGATGGCATTA 1 4.0 No Hit CTTTATCTCTCCCAAACTTCCTCTCCTTCTTCTCACCTTCAAACCCACCT 1 4.0 No Hit CCAAGGTGGGTTTTTTTTTCCCTGGTATCTATAAAAATTCTCTAGAGTTC 1 4.0 No Hit CTTGTAGTGCTGCTACACCAACACAAACACTACTACTACTACTAGTTCGA 1 4.0 No Hit GTGGAAGATATACTATGTGCGGTATTTTTTTCTATCATAATTCAGGGGGG 1 4.0 No Hit GCAATATCTAGACTCGTGAAGCTACTCTTTGCAAGGAAAGAAATGAGGAT 1 4.0 No Hit AAATTATACATTATGACTTGTGGGCTCGAGAATATGCTGCTAACCTGCAA 1 4.0 No Hit CTCCCAGAAGCCTTTGCCATCAGCTGCCAAGACTGTTAGCTCTAGAAAGA 1 4.0 No Hit GCTCCCTTTGTGAAGGTCATGGATGAGGAATTCGGCATTGTCAAGGGAAC 1 4.0 No Hit GTGATTTGTCTGCTTAATTGCGATAACGAACGAGACCTTAACCTGCTAAA 1 4.0 No Hit GTTTATAAAGGAGTTCCAAAGGATTATACTGGTCCAGATGTCACCGTTGG 1 4.0 No Hit >>END_MODULE >>Adapter Content fail #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 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 2.0 0.0 0.0 0.0 0.0 64-65 4.0 0.0 0.0 0.0 0.0 66-67 4.0 0.0 0.0 0.0 0.0 68-69 6.0 0.0 0.0 0.0 0.0 70-71 8.0 0.0 0.0 0.0 0.0 72-73 8.0 0.0 0.0 0.0 0.0 74-75 8.0 0.0 0.0 0.0 0.0 76-77 8.0 0.0 0.0 0.0 0.0 78-79 8.0 0.0 0.0 0.0 0.0 80-81 8.0 0.0 0.0 0.0 0.0 82-83 8.0 0.0 0.0 0.0 0.0 84-85 8.0 0.0 0.0 0.0 0.0 86-87 8.0 0.0 0.0 0.0 0.0 88-89 10.0 0.0 0.0 0.0 0.0 90-91 12.0 0.0 0.0 0.0 0.0 92-93 12.0 0.0 0.0 0.0 0.0 94-95 16.0 0.0 0.0 0.0 0.0 96-97 20.0 0.0 0.0 0.0 0.0 98-99 20.0 0.0 0.0 0.0 0.0 100-101 20.0 0.0 0.0 0.0 0.0 102-103 20.0 0.0 0.0 0.0 0.0 104-105 20.0 0.0 0.0 0.0 0.0 106-107 20.0 0.0 0.0 0.0 0.0 108-109 20.0 0.0 0.0 0.0 0.0 110-111 20.0 0.0 0.0 0.0 0.0 112-113 20.0 0.0 0.0 0.0 0.0 114-115 20.0 0.0 0.0 0.0 0.0 116-117 22.0 0.0 0.0 0.0 0.0 118-119 24.0 0.0 0.0 0.0 0.0 120-121 24.0 0.0 0.0 0.0 0.0 122-123 24.0 0.0 0.0 0.0 0.0 124-125 26.0 0.0 0.0 0.0 0.0 126-127 28.0 0.0 0.0 0.0 0.0 128-129 30.0 0.0 0.0 0.0 0.0 130-131 36.0 0.0 0.0 0.0 0.0 132-133 36.0 0.0 0.0 0.0 0.0 134-135 36.0 0.0 0.0 0.0 0.0 136-137 38.0 0.0 0.0 0.0 0.0 138-139 42.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 6 spots for SRR12671693.sra Written 6 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra Read 1 spots for SRR12671693.sra Written 1 spots for SRR12671693.sra SRR ids: ['SRR12671693.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_m4_t06mc SRR12671693.sra spots: 25 blocks: [[1, 1], [2, 2], [3, 3], [4, 4], [5, 5], [6, 6], [7, 7], [8, 8], [9, 9], [10, 10], [11, 11], [12, 12], [13, 13], [14, 14], [15, 15], [16, 16], [17, 17], [18, 18], [19, 19], [20, 25]] SRR12671693 file size 9 SRR12671693 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 SRR12671693 SRR12671693_1.fastq SRR12671693_2.fastq Input file: SRR12671693_1.fastq Paired file: SRR12671693_2.fastq trimmed: SRR12671693-trimmed-pair1.fastq, SRR12671693-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 Wed Feb 12 04:11:38 2025 >> started Wed Feb 12 04:11:38 2025 >> done (0.001s) 25 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 3 (12.00%) empty read pairs filtered out after trimming by size control 22 (88.00%) read pairs available; of these: 11 (50.00%) trimmed read pairs available after processing 11 (50.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 62 1 4.55% 63 0 0.00% 64 0 0.00% 65 0 0.00% 66 0 0.00% 67 0 0.00% 68 1 4.55% 69 0 0.00% 70 0 0.00% 71 0 0.00% 72 0 0.00% 73 0 0.00% 74 0 0.00% 75 0 0.00% 76 0 0.00% 77 0 0.00% 78 0 0.00% 79 0 0.00% 80 0 0.00% 81 0 0.00% 82 0 0.00% 83 0 0.00% 84 0 0.00% 85 0 0.00% 86 0 0.00% 87 0 0.00% 88 1 4.55% 89 0 0.00% 90 0 0.00% 91 0 0.00% 92 0 0.00% 93 0 0.00% 94 2 9.09% 95 0 0.00% 96 0 0.00% 97 0 0.00% 98 0 0.00% 99 0 0.00% 100 0 0.00% 101 0 0.00% 102 0 0.00% 103 0 0.00% 104 0 0.00% 105 0 0.00% 106 0 0.00% 107 0 0.00% 108 0 0.00% 109 0 0.00% 110 0 0.00% 111 0 0.00% 112 0 0.00% 113 0 0.00% 114 0 0.00% 115 0 0.00% 116 1 4.55% 117 0 0.00% 118 0 0.00% 119 0 0.00% 120 0 0.00% 121 0 0.00% 122 0 0.00% 123 0 0.00% 124 1 4.55% 125 0 0.00% 126 0 0.00% 127 0 0.00% 128 1 4.55% 129 1 4.55% 130 0 0.00% 131 0 0.00% 132 0 0.00% 133 0 0.00% 134 0 0.00% 135 0 0.00% 136 1 4.55% 137 0 0.00% 138 1 4.55% 139 0 0.00% 140 0 0.00% 141 0 0.00% 142 0 0.00% 143 0 0.00% 144 0 0.00% 145 0 0.00% 146 0 0.00% 147 0 0.00% 148 0 0.00% 149 0 0.00% 150 0 0.00% 151 11 50.00% 22 reads passed initial QC SRR12671693 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 04:11:46 Started mapping on | Feb 12 04:11:46 Finished on | Feb 12 04:11:47 Mapping speed, Million of reads per hour | 0.08 Number of input reads | 22 Average input read length | 258 UNIQUE READS: Uniquely mapped reads number | 19 Uniquely mapped reads % | 86.36% Average mapped length | 253.32 Number of splices: Total | 22 Number of splices: Annotated (sjdb) | 20 Number of splices: GT/AG | 22 Number of splices: GC/AG | 0 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 0 Mismatch rate per base, % | 0.19% Deletion rate per base | 0.12% Deletion average length | 6.00 Insertion rate per base | 0.00% Insertion average length | 0.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 0 % of reads mapped to multiple loci | 0.00% Number of reads mapped to too many loci | 1 % of reads mapped to too many loci | 4.55% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.55% % of reads unmapped: other | 4.55% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3 3 3 N_multimapping 0 0 0 N_noFeature 0 18 1 N_ambiguous 0 0 0 UnstrandedReadsAssigned:19 PositiveStrandReadsAssigned:1 NegativeStrandReadsAssigned:18 Dataset is classified negative stranded MeadianReadLen=136 20thPercentileLength=88 echo kmer=83 SRR12671693 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR12671693-trimmed-pair1.fastq SRR12671693-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22 reads, 19 reads pseudoaligned [quant] estimated average fragment length: 132.625 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 97 rounds 52401 SRR12671693.ke.tsv 34699 SRR12671693.se.tsv 87100 total ==> SRR12671693.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1886.38 0 0 Potri.005G024800.1.v4.1 1035 903.375 0 0 Potri.004G059700.1.v4.1 961 829.375 0 0 Potri.007G009000.2.v4.1 1416 1284.38 0 0 Potri.003G141000.2.v4.1 2943 2811.38 0 0 Potri.016G087400.1.v4.1 270 163.286 0 0 Potri.015G069301.1.v4.1 564 432.375 0 0 Potri.010G195200.1.v4.1 1773 1641.38 0 0 Potri.012G127500.1.v4.1 977 845.375 0 0 ==> SRR12671693.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 0 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12671693 completed mapping pipeline successfully