Starting /dee2/code/volunteer_pipeline.sh SRR24040055 current disk space = 1548900077568 free memory = 1600016204 SRR24040055 SRAfilesize 5e957785781827fe0ffe8cd4d41bc235 SRR24040055.sra SRR24040055.sra file validated SRR24040055 is paired end SRR24040055 is conventional basespace SRR24040055 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040055_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 54 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.07825 37.0 37.0 37.0 37.0 37.0 2 36.3345 37.0 37.0 37.0 37.0 37.0 3 36.073 37.0 37.0 37.0 37.0 37.0 4 36.5645 37.0 37.0 37.0 37.0 37.0 5 36.585 37.0 37.0 37.0 37.0 37.0 6 35.4835 37.0 37.0 37.0 37.0 37.0 7 36.5235 37.0 37.0 37.0 37.0 37.0 8 36.6215 37.0 37.0 37.0 37.0 37.0 9 34.2655 37.0 37.0 37.0 25.0 37.0 10-14 36.5115 37.0 37.0 37.0 37.0 37.0 15-19 36.411699999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.4833 37.0 37.0 37.0 37.0 37.0 25-29 36.349000000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.24849999999999 37.0 37.0 37.0 37.0 37.0 35-39 36.4296 37.0 37.0 37.0 37.0 37.0 40-44 36.3575 37.0 37.0 37.0 37.0 37.0 45-49 36.244099999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.2576 37.0 37.0 37.0 37.0 37.0 55-59 36.069900000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.0418 37.0 37.0 37.0 37.0 37.0 65-69 36.199 37.0 37.0 37.0 37.0 37.0 70-74 36.2204 37.0 37.0 37.0 37.0 37.0 75-79 36.3359 37.0 37.0 37.0 37.0 37.0 80-84 36.0045 37.0 37.0 37.0 37.0 37.0 85-89 36.2389 37.0 37.0 37.0 37.0 37.0 90-94 36.2596 37.0 37.0 37.0 37.0 37.0 95-99 36.1727 37.0 37.0 37.0 37.0 37.0 100-104 36.16199999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.135000000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.9595 37.0 37.0 37.0 37.0 37.0 115-119 35.7188 37.0 37.0 37.0 37.0 37.0 120-124 35.5719 37.0 37.0 37.0 34.6 37.0 125-129 35.6896 37.0 37.0 37.0 37.0 37.0 130-134 35.275400000000005 37.0 37.0 37.0 34.6 37.0 135-139 35.1066 37.0 37.0 37.0 37.0 37.0 140-144 34.7312 37.0 37.0 37.0 25.0 37.0 145-149 34.3887 37.0 37.0 37.0 25.0 37.0 150 32.2905 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 0.0 23 1.0 24 2.0 25 8.0 26 7.0 27 11.0 28 10.0 29 23.0 30 45.0 31 62.0 32 155.0 33 113.0 34 171.0 35 338.0 36 2654.0 37 399.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.18463847885915 10.85814360770578 5.629221916437328 37.32799599699775 2 26.025 12.975 29.9 31.1 3 23.65 16.025 24.275 36.05 4 28.175 22.175 20.225 29.425 5 27.825 26.25 21.725 24.2 6 24.925 27.474999999999998 25.025 22.575 7 19.475 20.4 38.175 21.95 8 22.225 19.85 28.625 29.299999999999997 9 21.65 20.025000000000002 31.175000000000004 27.150000000000002 10-14 25.81 23.865 24.05 26.275 15-19 25.86 21.88 24.4 27.860000000000003 20-24 25.919999999999998 22.689999999999998 24.195 27.195000000000004 25-29 25.44 22.745 23.75 28.065 30-34 25.28 21.8 24.25 28.67 35-39 25.21 21.48 24.665 28.645 40-44 25.91 22.21 23.810000000000002 28.07 45-49 25.575 22.025 24.3 28.1 50-54 25.124999999999996 21.92 24.215 28.74 55-59 25.985000000000003 21.63 24.365000000000002 28.02 60-64 25.515 21.490000000000002 24.64 28.355000000000004 65-69 25.314999999999998 21.82 24.63 28.235 70-74 26.150000000000002 22.445 23.330000000000002 28.075 75-79 26.715 22.220000000000002 23.35 27.715 80-84 26.5 22.125 23.505000000000003 27.87 85-89 27.075 22.1 23.5 27.325 90-94 26.615 21.75 23.799999999999997 27.834999999999997 95-99 25.85 22.08 23.66 28.410000000000004 100-104 27.095000000000002 22.71 22.53 27.665 105-109 26.935 22.56 23.23 27.275 110-114 26.88 22.395 22.650000000000002 28.075 115-119 27.43 22.46 22.725 27.384999999999998 120-124 27.675 22.185 23.015 27.125 125-129 28.310000000000002 22.115000000000002 22.770000000000003 26.805 130-134 28.115000000000002 22.105 22.99 26.790000000000003 135-139 28.994999999999997 22.720000000000002 21.81 26.474999999999998 140-144 29.4 21.475 22.439999999999998 26.685 145-149 29.880000000000003 21.92 21.97 26.229999999999997 150 30.0 23.375 20.75 25.874999999999996 >>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 0.0 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 1.0 29 1.0 30 1.0 31 3.5 32 5.5 33 7.5 34 10.5 35 15.0 36 21.5 37 28.0 38 30.0 39 41.5 40 61.5 41 76.0 42 94.5 43 111.0 44 121.5 45 130.5 46 144.0 47 157.0 48 152.5 49 165.5 50 174.5 51 147.0 52 136.0 53 161.0 54 156.5 55 132.5 56 134.5 57 128.0 58 115.5 59 101.0 60 104.5 61 108.5 62 98.0 63 92.0 64 89.0 65 94.0 66 89.5 67 74.5 68 65.0 69 67.5 70 70.5 71 73.5 72 63.5 73 41.5 74 31.5 75 26.5 76 21.0 77 14.0 78 6.0 79 1.0 80 0.5 81 0.5 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 0.075 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.55000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 89.60138648180242 77.55 2 7.336799537839399 12.7 3 1.9352975158867705 5.025 4 0.6065857885615251 2.1 5 0.28885037550548814 1.25 6 0.11554015020219525 0.6 7 0.05777007510109763 0.35000000000000003 8 0.028885037550548814 0.2 9 0.028885037550548814 0.22499999999999998 >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 CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 9 0.22499999999999998 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 8 0.2 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCTCGGTT 7 0.17500000000000002 TruSeq Adapter, Index 21 (97% over 40bp) GTATGATTAACAGCTGCCCTCGACGAAGAAGTCCATTGAACACATTGCGG 7 0.17500000000000002 No Hit CTCCGATCGGGTAACTCTGGCAGCTGCTTTGGGGGAAATTCGGAGTCAAC 6 0.15 No Hit GGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCG 6 0.15 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 6 0.15 No Hit GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 6 0.15 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 5 0.125 No Hit GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 5 0.125 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 5 0.125 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCGCGGGT 5 0.125 TruSeq Adapter, Index 21 (97% over 40bp) CCTCAACACAAGTACACACAGTTCCCGTCACGCACCCAGGCCCGCCGCTC 5 0.125 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 5 0.125 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 5 0.125 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 5 0.125 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 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 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.0625 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.0875 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.1875 0.0 0.0 0.0 0.0 50-51 0.2 0.0 0.0 0.0 0.0 52-53 0.275 0.0 0.0 0.0 0.0 54-55 0.35 0.0 0.0 0.0 0.0 56-57 0.375 0.0 0.0 0.0 0.0 58-59 0.4375 0.0 0.0 0.0 0.0 60-61 0.5125 0.0 0.0 0.0 0.0 62-63 0.6625 0.0 0.0 0.0 0.0 64-65 0.7875 0.0 0.0 0.0 0.0 66-67 1.0 0.0 0.0 0.0 0.0 68-69 1.1625 0.0 0.0 0.0 0.0 70-71 1.3624999999999998 0.0 0.0 0.0 0.0 72-73 1.5 0.0 0.0 0.0 0.0 74-75 1.75 0.0 0.0 0.0 0.0 76-77 1.925 0.0 0.0 0.0 0.0 78-79 2.1375 0.0 0.0 0.0 0.0 80-81 2.4875 0.0 0.0 0.0 0.0 82-83 2.8625 0.0 0.0 0.0 0.0 84-85 3.25 0.0 0.0 0.0 0.0 86-87 3.7875 0.0 0.0 0.0 0.0 88-89 4.125 0.0 0.0 0.0 0.0 90-91 4.6375 0.0 0.0 0.0 0.0 92-93 5.1 0.0 0.0 0.0 0.0 94-95 5.6625 0.0 0.0 0.0 0.0 96-97 6.300000000000001 0.0 0.0 0.0 0.0 98-99 6.9125 0.0 0.0 0.0 0.0 100-101 7.5625 0.0 0.0 0.0 0.0 102-103 8.462499999999999 0.0 0.0 0.0 0.0 104-105 9.3875 0.0 0.0 0.0 0.0 106-107 10.225 0.0 0.0 0.0 0.0 108-109 11.1125 0.0 0.0 0.0 0.0 110-111 11.8 0.0 0.0 0.0 0.0 112-113 12.5375 0.0 0.0 0.0 0.0 114-115 13.125 0.0 0.0 0.0 0.0 116-117 13.8 0.0 0.0 0.0 0.0 118-119 14.675 0.0 0.0 0.0 0.0 120-121 15.3875 0.0 0.0 0.0 0.0 122-123 16.450000000000003 0.0 0.0 0.0 0.0 124-125 17.575 0.0 0.0 0.0 0.0 126-127 18.2875 0.0 0.0 0.0 0.0 128-129 19.200000000000003 0.0 0.0 0.0 0.0 130-131 20.2375 0.0 0.0 0.0 0.0 132-133 21.225 0.0 0.0 0.0 0.0 134-135 22.1 0.0 0.0 0.0 0.0 136-137 23.012500000000003 0.0 0.0 0.0 0.0 138 23.75 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR24040055 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040055_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.182 37.0 37.0 37.0 37.0 37.0 2 35.801 37.0 37.0 37.0 37.0 37.0 3 33.517 37.0 37.0 37.0 25.0 37.0 4 35.4145 37.0 37.0 37.0 37.0 37.0 5 35.8965 37.0 37.0 37.0 37.0 37.0 6 35.9475 37.0 37.0 37.0 37.0 37.0 7 35.9155 37.0 37.0 37.0 37.0 37.0 8 35.434 37.0 37.0 37.0 37.0 37.0 9 34.595 37.0 37.0 37.0 25.0 37.0 10-14 35.287699999999994 37.0 37.0 37.0 32.2 37.0 15-19 35.1402 37.0 37.0 37.0 32.2 37.0 20-24 35.42059999999999 37.0 37.0 37.0 34.6 37.0 25-29 35.488800000000005 37.0 37.0 37.0 34.6 37.0 30-34 34.5323 37.0 37.0 37.0 27.0 37.0 35-39 35.5173 37.0 37.0 37.0 37.0 37.0 40-44 35.5034 37.0 37.0 37.0 37.0 37.0 45-49 35.5427 37.0 37.0 37.0 37.0 37.0 50-54 35.5717 37.0 37.0 37.0 37.0 37.0 55-59 35.550599999999996 37.0 37.0 37.0 37.0 37.0 60-64 35.464800000000004 37.0 37.0 37.0 37.0 37.0 65-69 35.4171 37.0 37.0 37.0 34.6 37.0 70-74 35.2721 37.0 37.0 37.0 32.2 37.0 75-79 35.043600000000005 37.0 37.0 37.0 31.8 37.0 80-84 35.2564 37.0 37.0 37.0 34.6 37.0 85-89 35.046499999999995 37.0 37.0 37.0 32.2 37.0 90-94 34.6351 37.0 37.0 37.0 27.0 37.0 95-99 35.324 37.0 37.0 37.0 37.0 37.0 100-104 34.889700000000005 37.0 37.0 37.0 29.8 37.0 105-109 35.1193 37.0 37.0 37.0 34.6 37.0 110-114 34.475300000000004 37.0 37.0 37.0 25.0 37.0 115-119 34.6796 37.0 37.0 37.0 25.0 37.0 120-124 34.3848 37.0 37.0 37.0 25.0 37.0 125-129 34.2726 37.0 37.0 37.0 25.0 37.0 130-134 33.9506 37.0 37.0 37.0 22.2 37.0 135-139 33.907300000000006 37.0 37.0 37.0 25.0 37.0 140-144 33.716499999999996 37.0 37.0 37.0 22.2 37.0 145-149 33.3738 37.0 37.0 37.0 13.8 37.0 150 33.29 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 10.0 14 11.0 15 19.0 16 10.0 17 5.0 18 6.0 19 9.0 20 17.0 21 18.0 22 18.0 23 20.0 24 11.0 25 18.0 26 21.0 27 19.0 28 24.0 29 30.0 30 39.0 31 74.0 32 129.0 33 143.0 34 337.0 35 657.0 36 2194.0 37 159.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.449999999999996 18.9 7.35 31.3 2 33.975 22.375 23.599999999999998 20.05 3 26.0 24.525 22.125 27.35 4 29.275000000000002 30.825000000000003 16.950000000000003 22.95 5 30.275000000000002 30.349999999999998 17.775 21.6 6 27.700000000000003 32.65 17.125 22.525000000000002 7 25.25 19.025 29.95 25.775 8 26.85 21.05 21.45 30.65 9 26.5 22.825 23.025000000000002 27.650000000000002 10-14 28.63 24.935 19.845 26.590000000000003 15-19 29.125 24.535 20.1 26.240000000000002 20-24 29.265 24.610000000000003 20.580000000000002 25.545 25-29 28.544999999999998 24.25 20.830000000000002 26.375 30-34 27.400000000000002 25.885 20.78 25.935000000000002 35-39 27.915 25.645 20.205000000000002 26.235000000000003 40-44 28.754999999999995 24.64 20.674999999999997 25.929999999999996 45-49 28.4 24.965 20.845 25.790000000000003 50-54 28.050000000000004 24.38 21.279999999999998 26.290000000000003 55-59 28.765 24.525 21.48 25.230000000000004 60-64 28.87 24.84 21.025 25.264999999999997 65-69 28.285 24.465 21.015 26.235000000000003 70-74 28.660000000000004 24.435000000000002 20.995 25.91 75-79 29.330000000000002 24.455 20.72 25.495 80-84 28.915000000000003 24.610000000000003 21.085 25.39 85-89 29.125 24.945 20.36 25.569999999999997 90-94 29.785 24.88 20.36 24.975 95-99 29.895 24.955 20.285 24.865000000000002 100-104 30.555 25.355 20.349999999999998 23.74 105-109 31.125000000000004 24.66 20.69 23.525 110-114 31.255 25.35 19.56 23.835 115-119 32.645 24.445 19.79 23.119999999999997 120-124 32.695 24.240000000000002 20.07 22.994999999999997 125-129 33.925 25.19 18.865000000000002 22.02 130-134 34.92 24.635 18.96 21.485000000000003 135-139 36.115 23.435 19.205 21.245 140-144 37.375 23.330000000000002 18.825 20.47 145-149 38.545 23.265 18.2 19.99 150 38.800000000000004 23.5 18.7 19.0 >>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 1.0 7 1.5 8 2.0 9 1.5 10 0.5 11 0.5 12 0.5 13 0.5 14 0.5 15 1.5 16 2.0 17 1.5 18 0.5 19 0.5 20 1.0 21 1.5 22 2.0 23 2.0 24 2.5 25 3.5 26 3.5 27 3.5 28 3.0 29 4.5 30 4.0 31 2.5 32 5.0 33 5.0 34 7.5 35 10.5 36 12.5 37 16.5 38 25.0 39 48.0 40 61.5 41 58.5 42 78.0 43 101.5 44 112.5 45 123.5 46 126.5 47 154.0 48 169.5 49 152.5 50 161.0 51 165.0 52 150.5 53 159.5 54 164.0 55 138.5 56 118.0 57 110.0 58 111.0 59 108.5 60 97.5 61 98.0 62 94.5 63 95.0 64 103.0 65 99.5 66 86.5 67 78.5 68 79.0 69 68.5 70 65.0 71 64.5 72 53.0 73 38.5 74 35.0 75 35.0 76 23.5 77 12.5 78 7.0 79 4.5 80 2.0 81 3.5 82 4.0 83 1.5 84 2.5 85 3.5 86 2.5 87 1.0 88 0.0 89 1.0 90 2.0 91 1.0 92 2.0 93 3.0 94 1.5 95 2.5 96 3.0 97 3.0 98 3.5 99 2.5 100 7.5 >>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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.725 #Duplication Level Percentage of deduplicated Percentage of total 1 92.22624686542213 82.75 2 5.934800780161605 10.65 3 1.1145165784341042 3.0 4 0.30649205906937865 1.0999999999999999 5 0.22290331568682087 1.0 6 0.08358874338255781 0.44999999999999996 7 0.02786291446085261 0.17500000000000002 8 0.05572582892170522 0.4 9 0.0 0.0 >10 0.02786291446085261 0.475 >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 19 0.475 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAA 8 0.2 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 7 0.17500000000000002 No Hit GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 6 0.15 No Hit ACTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCT 6 0.15 No Hit GTTCAATGGACTTCTTCGTCGAGGGCAGCTGTTAATCATACCACAAAACT 6 0.15 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 5 0.125 No Hit GTCGTTTTAAAGAAGGCGGAGAGTGAAGGATACCAGTATATCGCTTTCAA 5 0.125 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 5 0.125 No Hit CCCAGCTTGAGAATCGGGCGGCCGTGCCGTCCGAATTGTAGTCTGGAGAG 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit CATTAATGCCCATAGCGTGGTGTACGTGATCCAAGGACAAGCTTCGGTTC 5 0.125 No Hit CGATGATTCATGATAACTCGACGGATCGCACGGCCCTCGTGCCGGCGACG 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 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.0625 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.0875 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1375 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.225 0.0 0.0 0.0 0.0 54-55 0.30000000000000004 0.0 0.0 0.0 0.0 56-57 0.325 0.0 0.0 0.0 0.0 58-59 0.3875 0.0 0.0 0.0 0.0 60-61 0.44999999999999996 0.0 0.0 0.0 0.0 62-63 0.5875 0.0 0.0 0.0 0.0 64-65 0.7125 0.0 0.0 0.0 0.0 66-67 0.925 0.0 0.0 0.0 0.0 68-69 1.0625 0.0 0.0 0.0 0.0 70-71 1.2375 0.0 0.0 0.0 0.0 72-73 1.35 0.0 0.0 0.0 0.0 74-75 1.6 0.0 0.0 0.0 0.0 76-77 1.775 0.0 0.0 0.0 0.0 78-79 1.9875 0.0 0.0 0.0 0.0 80-81 2.35 0.0 0.0 0.0 0.0 82-83 2.7125000000000004 0.0 0.0 0.0 0.0 84-85 3.1 0.0 0.0 0.0 0.0 86-87 3.6125 0.0 0.0 0.0 0.0 88-89 3.9625 0.0 0.0 0.0 0.0 90-91 4.4875 0.0 0.0 0.0 0.0 92-93 4.975 0.0 0.0 0.0 0.0 94-95 5.5 0.0 0.0 0.0 0.0 96-97 6.1375 0.0 0.0 0.0 0.0 98-99 6.737500000000001 0.0 0.0 0.0 0.0 100-101 7.35 0.0 0.0 0.0 0.0 102-103 8.275 0.0 0.0 0.0 0.0 104-105 9.2375 0.0 0.0 0.0 0.0 106-107 10.0625 0.0 0.0 0.0 0.0 108-109 10.925 0.0 0.0 0.0 0.0 110-111 11.575 0.0 0.0 0.0 0.0 112-113 12.25 0.0 0.0 0.0 0.0 114-115 12.825 0.0 0.0 0.0 0.0 116-117 13.5125 0.0 0.0 0.0 0.0 118-119 14.399999999999999 0.0 0.0 0.0 0.0 120-121 15.1125 0.0 0.0 0.0 0.0 122-123 16.200000000000003 0.0 0.0 0.0 0.0 124-125 17.3875 0.0 0.0 0.0 0.0 126-127 18.0875 0.0 0.0 0.0 0.0 128-129 18.975 0.0 0.0 0.0 0.0 130-131 20.025 0.0 0.0 0.0 0.0 132-133 21.075 0.0 0.0 0.0 0.0 134-135 21.9 0.0 0.0 0.0 0.0 136-137 22.7625 0.0 0.0 0.0 0.0 138 23.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 295 0.0 11.715254 140-144 >>END_MODULE Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300644 spots for SRR24040055.sra Written 2300644 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra Read 2300638 spots for SRR24040055.sra Written 2300638 spots for SRR24040055.sra SRR ids: ['SRR24040055.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_44d32j_k SRR24040055.sra spots: 46012766 blocks: [[1, 2300638], [2300639, 4601276], [4601277, 6901914], [6901915, 9202552], [9202553, 11503190], [11503191, 13803828], [13803829, 16104466], [16104467, 18405104], [18405105, 20705742], [20705743, 23006380], [23006381, 25307018], [25307019, 27607656], [27607657, 29908294], [29908295, 32208932], [32208933, 34509570], [34509571, 36810208], [36810209, 39110846], [39110847, 41411484], [41411485, 43712122], [43712123, 46012766]] SRR24040055 file size 15525581 SRR24040055 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 SRR24040055 SRR24040055_1.fastq SRR24040055_2.fastq Input file: SRR24040055_1.fastq Paired file: SRR24040055_2.fastq trimmed: SRR24040055-trimmed-pair1.fastq, SRR24040055-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 Fri Dec 6 22:04:50 2024 >> started Fri Dec 6 22:06:06 2024 >> done (76.562s) 46012766 read pairs processed; of these: 3879 ( 0.01%) short read pairs filtered out after trimming by size control 237229 ( 0.52%) empty read pairs filtered out after trimming by size control 45771658 (99.48%) read pairs available; of these: 13949233 (30.48%) trimmed read pairs available after processing 31822425 (69.52%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 196 0.00% 19 214 0.00% 20 151 0.00% 21 202 0.00% 22 219 0.00% 23 180 0.00% 24 216 0.00% 25 259 0.00% 26 311 0.00% 27 326 0.00% 28 416 0.00% 29 509 0.00% 30 705 0.00% 31 712 0.00% 32 777 0.00% 33 874 0.00% 34 878 0.00% 35 1024 0.00% 36 1182 0.00% 37 1436 0.00% 38 1754 0.00% 39 1984 0.00% 40 2346 0.01% 41 2616 0.01% 42 2843 0.01% 43 2950 0.01% 44 3142 0.01% 45 3680 0.01% 46 4064 0.01% 47 5005 0.01% 48 5900 0.01% 49 6679 0.01% 50 7707 0.02% 51 8852 0.02% 52 9516 0.02% 53 10122 0.02% 54 10865 0.02% 55 11100 0.02% 56 11916 0.03% 57 13596 0.03% 58 16094 0.04% 59 18043 0.04% 60 20093 0.04% 61 22743 0.05% 62 25341 0.06% 63 26133 0.06% 64 26584 0.06% 65 28099 0.06% 66 29580 0.06% 67 31457 0.07% 68 34439 0.08% 69 37471 0.08% 70 39446 0.09% 71 43877 0.10% 72 48520 0.11% 73 52604 0.11% 74 53475 0.12% 75 56456 0.12% 76 58248 0.13% 77 60935 0.13% 78 64635 0.14% 79 69704 0.15% 80 75755 0.17% 81 79024 0.17% 82 84575 0.18% 83 89511 0.20% 84 93057 0.20% 85 98549 0.22% 86 104837 0.23% 87 107308 0.23% 88 108233 0.24% 89 108556 0.24% 90 115525 0.25% 91 118504 0.26% 92 126779 0.28% 93 134228 0.29% 94 136427 0.30% 95 145931 0.32% 96 147218 0.32% 97 147881 0.32% 98 152159 0.33% 99 151731 0.33% 100 158988 0.35% 101 160269 0.35% 102 165967 0.36% 103 171416 0.37% 104 172806 0.38% 105 173072 0.38% 106 175604 0.38% 107 180194 0.39% 108 177716 0.39% 109 181784 0.40% 110 181600 0.40% 111 187764 0.41% 112 194220 0.42% 113 193150 0.42% 114 199745 0.44% 115 204225 0.45% 116 206140 0.45% 117 201239 0.44% 118 201279 0.44% 119 207538 0.45% 120 214156 0.47% 121 211373 0.46% 122 218570 0.48% 123 226418 0.49% 124 229413 0.50% 125 229196 0.50% 126 227907 0.50% 127 225967 0.49% 128 221764 0.48% 129 226861 0.50% 130 220806 0.48% 131 224218 0.49% 132 225249 0.49% 133 231967 0.51% 134 234753 0.51% 135 233792 0.51% 136 235413 0.51% 137 238098 0.52% 138 230340 0.50% 139 232286 0.51% 140 229655 0.50% 141 231519 0.51% 142 239865 0.52% 143 238677 0.52% 144 245769 0.54% 145 238914 0.52% 146 242604 0.53% 147 241959 0.53% 148 235944 0.52% 149 243875 0.53% 150 31822425 69.52% 45771658 reads passed initial QC criterion=sequence-density sequence-density=1.04 sequence-density-rank=1 fanout-score=2.18 fanout-score-rank=24 prefix-density=0.99 prefix-fanout=2.2 sequence=GCGGCTGCTGGCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=78.76 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=3.7 sequence=TTTATTTATATTTTATTGAGAACACAAACATCAAGTGCTGCACACTTGCGATTTATTTATTTTACTCTACAGTTCTCATATATATTAGTTCATTCGCTCTGATGCCTTGCGACTTGAAGCCGATTCCTCAAAACTCTGGTAGCTCAATGGAGGGAATTTAGTAGTGAAGGCGCCAAACTCTTCTCCCC criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=24 prefix-density=0.81 prefix-fanout=2.1 sequence=GACGTGCAGTCCCGATGCC criterion=fanout-score sequence-density=0.06 sequence-density-rank=27 fanout-score=196.67 fanout-score-rank=1 prefix-density=1.79 prefix-fanout=6.9 sequence=AGCAGCAGCAAGAACAGGGGCAGCAAGGTCAGATCCCTTCGCGCCGGTTCGGGGCCCAGTCACAGGAGTGCGGACAACAGGGTATCTTCTCGCCCCAGCTGCTAGCTCAGATACTACCGGCGATGTGCAATGTGTACCTCCCACCGTACTGCCGCGCCACCGCCGCTGATCAGCCATTCGGACCCGGTGGCTACTGATAAGACAAAGGGCTCTTGTAGTAGATAGATAGGGATCACCGCT SRR24040055 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:09:46 Started mapping on | Dec 06 22:09:46 Finished on | Dec 06 22:16:36 Mapping speed, Million of reads per hour | 401.90 Number of input reads | 45771658 Average input read length | 279 UNIQUE READS: Uniquely mapped reads number | 28781663 Uniquely mapped reads % | 62.88% Average mapped length | 277.88 Number of splices: Total | 18745252 Number of splices: Annotated (sjdb) | 17289395 Number of splices: GT/AG | 18158656 Number of splices: GC/AG | 290149 Number of splices: AT/AC | 10912 Number of splices: Non-canonical | 285535 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.01% Deletion average length | 2.24 Insertion rate per base | 0.01% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3841837 % of reads mapped to multiple loci | 8.39% Number of reads mapped to too many loci | 1827259 % of reads mapped to too many loci | 3.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.11% % of reads unmapped: other | 19.63% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 13148158 13148158 13148158 N_multimapping 3841837 3841837 3841837 N_noFeature 834517 28094166 1092608 N_ambiguous 623088 1988 292053 UnstrandedReadsAssigned:27324058 PositiveStrandReadsAssigned:685509 NegativeStrandReadsAssigned:27397002 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=128 echo kmer=123 SRR24040055 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: SRR24040055-trimmed-pair1.fastq SRR24040055-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 45,771,658 reads, 31,121,162 reads pseudoaligned [quant] estimated average fragment length: 189.279 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,135 rounds 52973 SRR24040055.ke.tsv 35125 SRR24040055.se.tsv 88098 total ==> SRR24040055.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 747.886 128.641 6.08887 PNS24247 1044 855.721 16.377 0.677479 PNS24249 1928 1739.72 176.624 3.59388 PNS24246 1044 855.721 16.377 0.677479 PNS24248 1044 855.721 16.377 0.677479 PNS24244 1471 1282.72 98.6047 2.72119 PNS24243 293 123.852 0 0 KQK14069 1603 1414.72 5532.22 138.428 KQK14071 474 287.926 32.2753 3.96811 ==> SRR24040055.se.tsv <== BRADI_1g14170v3 5477 BRADI_1g53295v3 57 BRADI_1g59795v3 109 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 422 BRADI_1g74790v3 50 BRADI_1g09890v3 3 BRADI_1g77505v3 470 BRADI_1g48960v3 10 SRR24040055 completed mapping pipeline successfully