Starting /dee2/code/volunteer_pipeline.sh SRR12951324 current disk space = 1543116537856 free memory = 1606455312 SRR12951324 SRAfilesize eaaf21c87f9bfb66abff44360f07f97f SRR12951324.sra SRR12951324.sra file validated SRR12951324 is paired end SRR12951324 is conventional basespace SRR12951324 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951324_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.557 37.0 37.0 37.0 37.0 37.0 2 36.13575 37.0 37.0 37.0 37.0 37.0 3 36.4835 37.0 37.0 37.0 37.0 37.0 4 36.614 37.0 37.0 37.0 37.0 37.0 5 36.6075 37.0 37.0 37.0 37.0 37.0 6 36.522 37.0 37.0 37.0 37.0 37.0 7 36.4745 37.0 37.0 37.0 37.0 37.0 8 36.611 37.0 37.0 37.0 37.0 37.0 9 36.5635 37.0 37.0 37.0 37.0 37.0 10-14 36.5947 37.0 37.0 37.0 37.0 37.0 15-19 36.54600000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.554899999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.5135 37.0 37.0 37.0 37.0 37.0 30-34 36.4912 37.0 37.0 37.0 37.0 37.0 35-39 36.463499999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.4708 37.0 37.0 37.0 37.0 37.0 45-49 36.421 37.0 37.0 37.0 37.0 37.0 50-54 36.4 37.0 37.0 37.0 37.0 37.0 55-59 36.316 37.0 37.0 37.0 37.0 37.0 60-64 36.363699999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.212500000000006 37.0 37.0 37.0 37.0 37.0 70-74 36.2555 37.0 37.0 37.0 37.0 37.0 75-79 36.2495 37.0 37.0 37.0 37.0 37.0 80-84 36.303700000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.265299999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.2804 37.0 37.0 37.0 37.0 37.0 95-99 36.186 37.0 37.0 37.0 37.0 37.0 100-104 36.2237 37.0 37.0 37.0 37.0 37.0 105-109 36.1956 37.0 37.0 37.0 37.0 37.0 110-114 36.0946 37.0 37.0 37.0 37.0 37.0 115-119 36.1532 37.0 37.0 37.0 37.0 37.0 120-124 36.017999999999994 37.0 37.0 37.0 37.0 37.0 125-129 35.9686 37.0 37.0 37.0 37.0 37.0 130-134 35.9973 37.0 37.0 37.0 37.0 37.0 135-139 36.008900000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.88270000000001 37.0 37.0 37.0 37.0 37.0 145-149 35.7462 37.0 37.0 37.0 37.0 37.0 150-151 35.759 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 2.0 23 2.0 24 1.0 25 0.0 26 4.0 27 11.0 28 10.0 29 23.0 30 32.0 31 30.0 32 42.0 33 86.0 34 128.0 35 262.0 36 2853.0 37 513.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.849999999999994 10.4 4.275 34.475 2 22.55714644561668 9.947249434815374 33.45892991710625 34.03667420246169 3 18.35 15.6 26.5 39.550000000000004 4 25.775 21.75 22.3 30.175 5 27.075 27.200000000000003 22.55 23.175 6 25.55 28.675 21.6 24.175 7 20.1 24.7 36.025 19.175 8 20.3 25.0 29.625 25.074999999999996 9 21.15 20.724999999999998 32.6 25.525 10-14 23.005 26.44 24.4 26.155 15-19 23.849999999999998 24.325 25.255 26.57 20-24 22.939999999999998 24.51 25.495 27.055 25-29 23.41 25.235000000000003 24.995 26.36 30-34 24.104999999999997 24.465 24.709999999999997 26.72 35-39 24.285 24.775 24.435000000000002 26.505000000000003 40-44 24.654999999999998 24.765 24.675 25.905 45-49 24.27 24.605 24.665 26.46 50-54 23.31 24.44 24.775 27.474999999999998 55-59 22.994999999999997 25.115 24.5 27.389999999999997 60-64 23.785 24.245 24.51 27.46 65-69 24.05 24.404999999999998 24.695 26.85 70-74 24.435000000000002 24.57 24.240000000000002 26.755000000000003 75-79 24.95 24.55 23.815 26.685 80-84 24.32 25.22 24.04 26.419999999999998 85-89 24.955 24.11 24.75 26.185000000000002 90-94 25.185000000000002 23.94 24.63 26.245 95-99 24.404999999999998 24.44 24.795 26.36 100-104 24.560000000000002 23.669999999999998 24.4 27.37 105-109 25.085 24.675 23.645 26.595000000000002 110-114 25.085 24.560000000000002 24.02 26.334999999999997 115-119 25.135 24.645 23.165 27.055 120-124 25.845000000000002 24.875 22.564999999999998 26.715 125-129 25.580000000000002 25.174999999999997 23.16 26.085 130-134 25.540000000000003 23.799999999999997 23.82 26.840000000000003 135-139 25.169999999999998 24.34 23.13 27.36 140-144 24.02 24.245 23.885 27.85 145-149 25.580000000000002 24.240000000000002 23.785 26.395000000000003 150-151 24.775 24.4875 23.400000000000002 27.3375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 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 0.5 16 0.5 17 0.0 18 0.5 19 0.5 20 0.5 21 1.0 22 0.5 23 0.0 24 0.5 25 0.5 26 0.0 27 1.0 28 4.0 29 6.0 30 6.5 31 9.0 32 14.0 33 21.0 34 32.0 35 38.0 36 40.5 37 61.5 38 82.0 39 86.0 40 100.0 41 120.0 42 123.0 43 133.5 44 157.0 45 152.0 46 155.5 47 176.0 48 178.0 49 181.5 50 174.0 51 172.5 52 157.5 53 138.0 54 137.0 55 114.0 56 101.0 57 108.0 58 99.5 59 78.0 60 66.0 61 61.5 62 62.5 63 67.0 64 63.5 65 60.0 66 57.0 67 51.0 68 48.0 69 41.5 70 49.0 71 41.5 72 31.0 73 32.0 74 20.0 75 13.0 76 16.5 77 19.0 78 13.0 79 7.0 80 4.0 81 5.5 82 4.0 83 1.5 84 1.0 85 0.5 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 0.475 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 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.2 #Duplication Level Percentage of deduplicated Percentage of total 1 79.11269430051814 61.075 2 15.284974093264248 23.599999999999998 3 4.080310880829016 9.45 4 0.9067357512953367 2.8000000000000003 5 0.2590673575129534 1.0 6 0.16191709844559585 0.75 7 0.06476683937823835 0.35000000000000003 8 0.032383419689119175 0.2 9 0.032383419689119175 0.22499999999999998 >10 0.06476683937823835 0.5499999999999999 >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 GTCGTCTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAG 11 0.27499999999999997 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGAGTTATCTCGTAT 11 0.27499999999999997 TruSeq Adapter, Index 6 (97% over 36bp) CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 9 0.22499999999999998 No Hit CTCTTGTTCATCTCAGCAGCCTCCTTCTCGAACCTCTCGATCACACGCTT 8 0.2 No Hit CCCTTGTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCC 7 0.17500000000000002 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 7 0.17500000000000002 No Hit CTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAGGCGGC 6 0.15 No Hit GGCTTGCGACCGCAGGTGCCGTCGTCGGCGATCCCATCGGCGCACCGGTA 6 0.15 No Hit CTCGCCTGTATTTAGCCTTGGACGGAGTCTACCGCCCGATTTGGGCTGCA 6 0.15 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGAGTTATCGCGTAT 6 0.15 TruSeq Adapter, Index 6 (97% over 36bp) GTCGGATGGGGAGCCCGCAGGCCGTTGCAGCGCAGTGCCCCGAGGGACAC 5 0.125 No Hit CCTAAATATGCCATATTTATCTTCAAGTGGAGGCCTGATTCATTTTCCAA 5 0.125 No Hit GTACTACAGTAAAGGAAGCAACAACCCAGCATTTTACTTTCGAAGACAGA 5 0.125 No Hit GAGATAAATTCTTCTGAAGTGGGATATTTTTCTAATACATGCTTTACACT 5 0.125 No Hit GTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGACGGAGTCTACCGC 5 0.125 No Hit ATTTTTTGCCTCTTCAAGAGCTTTAAGTGTTGTCTGGTAGAACTCTTGCA 5 0.125 No Hit CTTGAGTTTACTCTTGTCCACCCCACACATTACATCAGGAAACACCTTAT 5 0.125 No Hit GGCAGAAATCACATTGCGTCAGCATCCGCGAGGACCATCGCAATGCTTTG 5 0.125 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 0.0 0.0 0.0 0.0 0.0 64-65 0.0125 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.1125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.4375 0.0 0.0 0.0 0.0 84-85 0.5125 0.0 0.0 0.0 0.0 86-87 0.6125 0.0 0.0 0.0 0.0 88-89 0.75 0.0 0.0 0.0 0.0 90-91 0.8375 0.0 0.0 0.0 0.0 92-93 0.9875 0.0 0.0 0.0 0.0 94-95 1.0625 0.0 0.0 0.0 0.0 96-97 1.175 0.0 0.0 0.0 0.0 98-99 1.5750000000000002 0.0 0.0 0.0 0.0 100-101 2.025 0.0 0.0 0.0 0.0 102-103 2.2750000000000004 0.0 0.0 0.0 0.0 104-105 2.5999999999999996 0.0 0.0 0.0 0.0 106-107 3.0125 0.0 0.0 0.0 0.0 108-109 3.3625 0.0 0.0 0.0 0.0 110-111 3.7625 0.0 0.0 0.0 0.0 112-113 4.1625 0.0 0.0 0.0 0.0 114-115 4.75 0.0 0.0 0.0 0.0 116-117 5.4125 0.0 0.0 0.0 0.0 118-119 6.1875 0.0 0.0 0.0 0.0 120-121 7.0375 0.0 0.0 0.0 0.0 122-123 7.5 0.0 0.0 0.0 0.0 124-125 8.125 0.0 0.0 0.0 0.0 126-127 8.6125 0.0 0.0 0.0 0.0 128-129 9.525 0.0 0.0 0.0 0.0 130-131 10.3125 0.0 0.0 0.0 0.0 132-133 10.8 0.0 0.0 0.0 0.0 134-135 11.2625 0.0 0.0 0.0 0.0 136-137 11.875 0.0 0.0 0.0 0.0 138-139 12.725 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12951324 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951324_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.183 37.0 37.0 37.0 37.0 37.0 2 36.0175 37.0 37.0 37.0 37.0 37.0 3 36.047 37.0 37.0 37.0 37.0 37.0 4 36.182 37.0 37.0 37.0 37.0 37.0 5 36.12 37.0 37.0 37.0 37.0 37.0 6 36.221 37.0 37.0 37.0 37.0 37.0 7 36.1765 37.0 37.0 37.0 37.0 37.0 8 36.187 37.0 37.0 37.0 37.0 37.0 9 36.1025 37.0 37.0 37.0 37.0 37.0 10-14 36.0517 37.0 37.0 37.0 37.0 37.0 15-19 36.0393 37.0 37.0 37.0 37.0 37.0 20-24 35.9695 37.0 37.0 37.0 37.0 37.0 25-29 35.912099999999995 37.0 37.0 37.0 37.0 37.0 30-34 35.8673 37.0 37.0 37.0 37.0 37.0 35-39 35.806799999999996 37.0 37.0 37.0 37.0 37.0 40-44 35.8722 37.0 37.0 37.0 37.0 37.0 45-49 35.8831 37.0 37.0 37.0 37.0 37.0 50-54 35.801700000000004 37.0 37.0 37.0 37.0 37.0 55-59 35.801 37.0 37.0 37.0 37.0 37.0 60-64 35.794200000000004 37.0 37.0 37.0 37.0 37.0 65-69 35.7504 37.0 37.0 37.0 37.0 37.0 70-74 35.7068 37.0 37.0 37.0 37.0 37.0 75-79 35.6497 37.0 37.0 37.0 37.0 37.0 80-84 35.6197 37.0 37.0 37.0 37.0 37.0 85-89 35.611599999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.6798 37.0 37.0 37.0 37.0 37.0 95-99 35.61 37.0 37.0 37.0 37.0 37.0 100-104 35.6213 37.0 37.0 37.0 37.0 37.0 105-109 35.557 37.0 37.0 37.0 37.0 37.0 110-114 35.5622 37.0 37.0 37.0 37.0 37.0 115-119 35.6316 37.0 37.0 37.0 37.0 37.0 120-124 35.437400000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.4628 37.0 37.0 37.0 37.0 37.0 130-134 35.39640000000001 37.0 37.0 37.0 34.6 37.0 135-139 35.314499999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.2011 37.0 37.0 37.0 34.6 37.0 145-149 34.992000000000004 37.0 37.0 37.0 25.0 37.0 150-151 34.675 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 3.0 13 8.0 14 8.0 15 11.0 16 4.0 17 3.0 18 2.0 19 1.0 20 10.0 21 2.0 22 11.0 23 7.0 24 8.0 25 10.0 26 10.0 27 19.0 28 21.0 29 27.0 30 23.0 31 44.0 32 50.0 33 80.0 34 155.0 35 539.0 36 2638.0 37 305.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.225 20.225 7.1499999999999995 26.400000000000002 2 30.425 21.5 25.775 22.3 3 25.1 23.45 28.95 22.5 4 28.000000000000004 29.575000000000003 20.599999999999998 21.825 5 28.999999999999996 32.725 17.925 20.349999999999998 6 25.95 33.275 19.775000000000002 21.0 7 26.8 19.225 31.075000000000003 22.900000000000002 8 26.55 22.2 22.85 28.4 9 25.25 21.825 26.224999999999998 26.700000000000003 10-14 27.155 25.66 22.105 25.080000000000002 15-19 26.965 24.66 23.625 24.75 20-24 27.305 25.045 23.794999999999998 23.855 25-29 27.279999999999998 24.925 22.965 24.83 30-34 26.700000000000003 24.8 24.215 24.285 35-39 26.729999999999997 24.77 23.575 24.925 40-44 27.12 24.985 22.919999999999998 24.975 45-49 26.555 24.279999999999998 23.635 25.53 50-54 27.48 24.990000000000002 23.455000000000002 24.075 55-59 27.815 25.095 23.505000000000003 23.585 60-64 27.389999999999997 24.535 23.565 24.51 65-69 27.425 23.695 24.22 24.66 70-74 27.839999999999996 24.21 23.5 24.45 75-79 27.33 24.59 22.965 25.115 80-84 27.655 24.715 23.395 24.235 85-89 27.529999999999998 24.34 23.025000000000002 25.105 90-94 27.46 25.014999999999997 23.535 23.990000000000002 95-99 28.144999999999996 24.755 22.985 24.115000000000002 100-104 27.755000000000003 24.0 23.974999999999998 24.27 105-109 27.93 25.419999999999998 22.845 23.805 110-114 28.970000000000002 24.535 23.07 23.425 115-119 28.415000000000003 24.665 23.11 23.810000000000002 120-124 28.65 24.14 23.200000000000003 24.01 125-129 28.925 24.46 22.745 23.87 130-134 29.625 24.235 22.770000000000003 23.369999999999997 135-139 29.235 25.135 23.244999999999997 22.384999999999998 140-144 30.43 25.380000000000003 22.165000000000003 22.025 145-149 31.155 24.535 22.475 21.834999999999997 150-151 31.587500000000002 23.575 22.3375 22.5 >>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 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 1.0 14 1.0 15 0.0 16 0.5 17 1.0 18 0.5 19 0.0 20 0.5 21 1.0 22 0.5 23 1.0 24 2.0 25 2.0 26 1.5 27 1.5 28 1.5 29 2.0 30 7.5 31 13.0 32 13.0 33 11.5 34 17.5 35 29.5 36 42.5 37 51.5 38 66.0 39 81.5 40 100.5 41 130.5 42 132.5 43 132.5 44 150.0 45 159.0 46 167.0 47 165.5 48 165.5 49 161.5 50 149.0 51 135.5 52 140.5 53 159.5 54 135.5 55 99.0 56 86.5 57 89.5 58 91.0 59 99.5 60 100.0 61 83.0 62 63.5 63 56.0 64 74.0 65 77.5 66 65.5 67 69.5 68 72.0 69 57.5 70 43.0 71 35.5 72 32.5 73 25.0 74 17.0 75 16.0 76 15.5 77 11.5 78 12.5 79 10.5 80 4.5 81 4.5 82 4.5 83 3.0 84 1.5 85 2.0 86 3.0 87 3.0 88 1.5 89 0.0 90 0.0 91 0.0 92 0.5 93 1.0 94 1.5 95 3.0 96 4.5 97 3.0 98 1.5 99 2.0 100 8.0 >>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 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.175 #Duplication Level Percentage of deduplicated Percentage of total 1 80.1726894787336 62.675000000000004 2 14.550687559961625 22.75 3 3.7416053725615606 8.774999999999999 4 0.9593859929645028 3.0 5 0.3197953309881676 1.25 6 0.1598976654940838 0.75 7 0.03197953309881676 0.17500000000000002 8 0.0 0.0 9 0.03197953309881676 0.22499999999999998 >10 0.03197953309881676 0.4 >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 16 0.4 No Hit CAGGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAG 9 0.22499999999999998 No Hit GTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGT 7 0.17500000000000002 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 6 0.15 No Hit GTGAAATACCACTACTTTTAACGTTATTTTACTTATTCCGTGGGTCGGAA 6 0.15 No Hit ATTCCCCTCTCCCCGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAG 6 0.15 No Hit GTCAGGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGA 6 0.15 No Hit AGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGC 6 0.15 No Hit GCACCTGTAGTGTATAACAACATGAGTTCAACTGTTCCAGCAAATGGGGC 5 0.125 No Hit AACTAGATTGTCAAATAATTCTTGATAAGAAGATGTGTTTGATTCGGGAG 5 0.125 No Hit GGTACACCCAAATGGACTGGTACCAACATATTCCATTCCAAGAGCCAAAC 5 0.125 No Hit GCTGACTTTTGAAGACAAGGATGGAGACTGGATGCTCGTTGGCGACGTTC 5 0.125 No Hit GCCCTGCTCGCGCCGCCGCCTCCCTCGCAGCAGCAGCAAGCAATCACCGT 5 0.125 No Hit TATAAACAACATAATGGATTTTGTTTCTGGATCTGCTAGCCAGAACTTTT 5 0.125 No Hit GCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGCGAATGG 5 0.125 No Hit AGACAGGTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAA 5 0.125 No Hit CCCGGCCCCAAACCCGTCGGCTGTCGGCGGATTGCTCGAGCTGCTCACGC 5 0.125 No Hit CTTTGTTCGGAAAGTCTAATAGAAGCAATCAAGCAAAGATGAAGAGTAGC 5 0.125 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 0.0 0.0 0.0 0.0 0.0 64-65 0.0125 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.1125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.35 0.0 0.0 0.0 0.0 82-83 0.4625 0.0 0.0 0.0 0.0 84-85 0.5375000000000001 0.0 0.0 0.0 0.0 86-87 0.6375 0.0 0.0 0.0 0.0 88-89 0.775 0.0 0.0 0.0 0.0 90-91 0.825 0.0 0.0 0.0 0.0 92-93 0.9624999999999999 0.0 0.0 0.0 0.0 94-95 1.0625 0.0 0.0 0.0 0.0 96-97 1.175 0.0 0.0 0.0 0.0 98-99 1.5750000000000002 0.0 0.0 0.0 0.0 100-101 2.025 0.0 0.0 0.0 0.0 102-103 2.2750000000000004 0.0 0.0 0.0 0.0 104-105 2.5999999999999996 0.0 0.0 0.0 0.0 106-107 3.0125 0.0 0.0 0.0 0.0 108-109 3.3625 0.0 0.0 0.0 0.0 110-111 3.7625 0.0 0.0 0.0 0.0 112-113 4.1625 0.0 0.0 0.0 0.0 114-115 4.725 0.0 0.0 0.0 0.0 116-117 5.3875 0.0 0.0 0.0 0.0 118-119 6.1625 0.0 0.0 0.0 0.0 120-121 7.0125 0.0 0.0 0.0 0.0 122-123 7.475 0.0 0.0 0.0 0.0 124-125 8.1 0.0 0.0 0.0 0.0 126-127 8.5875 0.0 0.0 0.0 0.0 128-129 9.5 0.0 0.0 0.0 0.0 130-131 10.2625 0.0 0.0 0.0 0.0 132-133 10.7625 0.0 0.0 0.0 0.0 134-135 11.2375 0.0 0.0 0.0 0.0 136-137 11.85 0.0 0.0 0.0 0.0 138-139 12.725 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 140 8.016417E-6 15.535715 145 >>END_MODULE Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822386 spots for SRR12951324.sra Written 1822386 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra Read 1822370 spots for SRR12951324.sra Written 1822370 spots for SRR12951324.sra SRR ids: ['SRR12951324.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bs0lec0o SRR12951324.sra spots: 36447416 blocks: [[1, 1822370], [1822371, 3644740], [3644741, 5467110], [5467111, 7289480], [7289481, 9111850], [9111851, 10934220], [10934221, 12756590], [12756591, 14578960], [14578961, 16401330], [16401331, 18223700], [18223701, 20046070], [20046071, 21868440], [21868441, 23690810], [23690811, 25513180], [25513181, 27335550], [27335551, 29157920], [29157921, 30980290], [30980291, 32802660], [32802661, 34625030], [34625031, 36447416]] SRR12951324 file size 12364726 SRR12951324 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 SRR12951324 SRR12951324_1.fastq SRR12951324_2.fastq Input file: SRR12951324_1.fastq Paired file: SRR12951324_2.fastq trimmed: SRR12951324-trimmed-pair1.fastq, SRR12951324-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 11:55:26 2024 >> started Sat Dec 7 11:56:20 2024 >> done (53.511s) 36447416 read pairs processed; of these: 134 ( 0.00%) short read pairs filtered out after trimming by size control 136228 ( 0.37%) empty read pairs filtered out after trimming by size control 36311054 (99.63%) read pairs available; of these: 5631726 (15.51%) trimmed read pairs available after processing 30679328 (84.49%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 13 0.00% 20 30 0.00% 21 29 0.00% 22 17 0.00% 23 33 0.00% 24 38 0.00% 25 35 0.00% 26 48 0.00% 27 55 0.00% 28 57 0.00% 29 56 0.00% 30 66 0.00% 31 70 0.00% 32 80 0.00% 33 75 0.00% 34 81 0.00% 35 82 0.00% 36 87 0.00% 37 139 0.00% 38 113 0.00% 39 97 0.00% 40 149 0.00% 41 129 0.00% 42 143 0.00% 43 151 0.00% 44 159 0.00% 45 171 0.00% 46 206 0.00% 47 195 0.00% 48 238 0.00% 49 267 0.00% 50 321 0.00% 51 405 0.00% 52 417 0.00% 53 483 0.00% 54 496 0.00% 55 537 0.00% 56 692 0.00% 57 759 0.00% 58 898 0.00% 59 1016 0.00% 60 1220 0.00% 61 1407 0.00% 62 1588 0.00% 63 1760 0.00% 64 1821 0.01% 65 1846 0.01% 66 2316 0.01% 67 2400 0.01% 68 2881 0.01% 69 3064 0.01% 70 3810 0.01% 71 4417 0.01% 72 5203 0.01% 73 5812 0.02% 74 6347 0.02% 75 7070 0.02% 76 7660 0.02% 77 8320 0.02% 78 9069 0.02% 79 10125 0.03% 80 11308 0.03% 81 13349 0.04% 82 14827 0.04% 83 15973 0.04% 84 17935 0.05% 85 19468 0.05% 86 21566 0.06% 87 22262 0.06% 88 23644 0.07% 89 24615 0.07% 90 26586 0.07% 91 29026 0.08% 92 30989 0.09% 93 34274 0.09% 94 36105 0.10% 95 39246 0.11% 96 41235 0.11% 97 42739 0.12% 98 43905 0.12% 99 46169 0.13% 100 48561 0.13% 101 49860 0.14% 102 52202 0.14% 103 55437 0.15% 104 57245 0.16% 105 58942 0.16% 106 60966 0.17% 107 62610 0.17% 108 63722 0.18% 109 65729 0.18% 110 68331 0.19% 111 70314 0.19% 112 72942 0.20% 113 74656 0.21% 114 77999 0.21% 115 80724 0.22% 116 84581 0.23% 117 85111 0.23% 118 86082 0.24% 119 86865 0.24% 120 89864 0.25% 121 90368 0.25% 122 93186 0.26% 123 97548 0.27% 124 100972 0.28% 125 101224 0.28% 126 105546 0.29% 127 106069 0.29% 128 106039 0.29% 129 109251 0.30% 130 108532 0.30% 131 109530 0.30% 132 111961 0.31% 133 113867 0.31% 134 115992 0.32% 135 118390 0.33% 136 118853 0.33% 137 122626 0.34% 138 123249 0.34% 139 123716 0.34% 140 124257 0.34% 141 128284 0.35% 142 129560 0.36% 143 129291 0.36% 144 134627 0.37% 145 133740 0.37% 146 132357 0.36% 147 135088 0.37% 148 132874 0.37% 149 134429 0.37% 150 135060 0.37% 151 30679328 84.49% 36311054 reads passed initial QC criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=2.22 fanout-score-rank=27 prefix-density=0.44 prefix-fanout=2.2 sequence=CCGTCAATTCCTTT criterion=fanout-score sequence-density=0.08 sequence-density-rank=27 fanout-score=136.05 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=19.3 sequence=CGCCGCCGCCGCGTAGCTTCTGGTGGACGGGGCCAGCAGCTGGGCCAGCGCGCGGGCAGCAGCCGAGGAACCGGAGAGAGCGAGAGCCATCGATTGATCTGTGTGTTTTGATCGGATGGCTGGTGGCGCTCCGGCTCTCTGCTGCTGCTCCAACGTGGGTTGCTGG criterion=sequence-density sequence-density=0.70 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=27 prefix-density=0.70 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.12 sequence-density-rank=23 fanout-score=168.13 fanout-score-rank=1 prefix-density=0.90 prefix-fanout=22.1 sequence=CGCCGCCGCCGACGTCGCGAGAAGTCCATTGAACCTTATCATTTAGAGGAAGGAGAAG SRR12951324 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:57:07 Started mapping on | Dec 07 11:57:07 Finished on | Dec 07 12:05:04 Mapping speed, Million of reads per hour | 274.05 Number of input reads | 36311054 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 28706072 Uniquely mapped reads % | 79.06% Average mapped length | 292.67 Number of splices: Total | 26964652 Number of splices: Annotated (sjdb) | 24886592 Number of splices: GT/AG | 26558108 Number of splices: GC/AG | 335809 Number of splices: AT/AC | 16734 Number of splices: Non-canonical | 54001 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.22 Insertion rate per base | 0.01% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 313284 % of reads mapped to multiple loci | 0.86% Number of reads mapped to too many loci | 546387 % of reads mapped to too many loci | 1.50% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.09% % of reads unmapped: other | 10.48% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7291698 7291698 7291698 N_multimapping 313284 313284 313284 N_noFeature 1361282 27875174 1653167 N_ambiguous 646499 3922 107736 UnstrandedReadsAssigned:26698291 PositiveStrandReadsAssigned:826976 NegativeStrandReadsAssigned:26945169 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951324 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: SRR12951324-trimmed-pair1.fastq SRR12951324-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 36,311,054 reads, 27,512,701 reads pseudoaligned [quant] estimated average fragment length: 256.709 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,192 rounds 52973 SRR12951324.ke.tsv 35125 SRR12951324.se.tsv 88098 total ==> SRR12951324.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 680.851 0 0 PNS24247 1044 788.291 156.723 10.2595 PNS24249 1928 1672.29 422.235 13.0294 PNS24246 1044 788.291 156.723 10.2595 PNS24248 1044 788.291 156.723 10.2595 PNS24244 1471 1215.29 173.595 7.37121 PNS24243 293 106.446 3 1.45436 KQK14069 1603 1347.29 67898 2600.62 KQK14071 474 245.154 318.493 67.0413 ==> SRR12951324.se.tsv <== BRADI_1g14170v3 68106 BRADI_1g53295v3 253 BRADI_1g59795v3 982 BRADI_1g07683v3 0 BRADI_1g00485v3 19 BRADI_1g20270v3 603 BRADI_1g74790v3 2537 BRADI_1g09890v3 0 BRADI_1g77505v3 327 BRADI_1g48960v3 0 SRR12951324 completed mapping pipeline successfully