Starting /dee2/code/volunteer_pipeline.sh SRR24040057 current disk space = 1548896948224 free memory = 1389707496 SRR24040057 SRAfilesize 568990eedcc679b885bd4c96ae5a9d4b SRR24040057.sra SRR24040057.sra file validated SRR24040057 is paired end SRR24040057 is conventional basespace SRR24040057 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040057_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 35.91425 37.0 37.0 37.0 37.0 37.0 2 36.4555 37.0 37.0 37.0 37.0 37.0 3 36.24 37.0 37.0 37.0 37.0 37.0 4 36.581 37.0 37.0 37.0 37.0 37.0 5 36.6175 37.0 37.0 37.0 37.0 37.0 6 35.2065 37.0 37.0 37.0 37.0 37.0 7 36.507 37.0 37.0 37.0 37.0 37.0 8 36.629 37.0 37.0 37.0 37.0 37.0 9 33.366 37.0 37.0 37.0 25.0 37.0 10-14 36.553900000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.4868 37.0 37.0 37.0 37.0 37.0 20-24 36.458600000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.4225 37.0 37.0 37.0 37.0 37.0 30-34 36.0938 37.0 37.0 37.0 34.6 37.0 35-39 36.45 37.0 37.0 37.0 37.0 37.0 40-44 36.3856 37.0 37.0 37.0 37.0 37.0 45-49 36.3163 37.0 37.0 37.0 37.0 37.0 50-54 36.382600000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.170399999999994 37.0 37.0 37.0 37.0 37.0 60-64 36.249900000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.321 37.0 37.0 37.0 37.0 37.0 70-74 36.355900000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.4088 37.0 37.0 37.0 37.0 37.0 80-84 36.0843 37.0 37.0 37.0 37.0 37.0 85-89 36.247800000000005 37.0 37.0 37.0 37.0 37.0 90-94 36.3507 37.0 37.0 37.0 37.0 37.0 95-99 36.3042 37.0 37.0 37.0 37.0 37.0 100-104 36.21320000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.22729999999999 37.0 37.0 37.0 37.0 37.0 110-114 36.137800000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.9208 37.0 37.0 37.0 37.0 37.0 120-124 35.804500000000004 37.0 37.0 37.0 37.0 37.0 125-129 36.003499999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.660700000000006 37.0 37.0 37.0 34.6 37.0 135-139 35.7418 37.0 37.0 37.0 37.0 37.0 140-144 35.4206 37.0 37.0 37.0 37.0 37.0 145-149 35.3237 37.0 37.0 37.0 34.6 37.0 150 32.236 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 2.0 24 2.0 25 4.0 26 8.0 27 9.0 28 14.0 29 29.0 30 27.0 31 36.0 32 49.0 33 79.0 34 143.0 35 479.0 36 2787.0 37 332.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.654896068119214 11.470072627097421 5.284247433007764 37.590783871775606 2 26.200000000000003 12.3 30.75 30.75 3 23.474999999999998 15.024999999999999 22.525000000000002 38.975 4 28.875 21.475 20.0 29.65 5 28.475 25.724999999999998 21.349999999999998 24.45 6 24.975 28.4 23.724999999999998 22.900000000000002 7 20.825 19.675 37.25 22.25 8 21.525 19.15 29.65 29.675 9 21.05 19.75 30.975 28.225 10-14 26.14 23.355 22.96 27.544999999999998 15-19 26.279999999999998 22.21 23.65 27.860000000000003 20-24 25.979999999999997 22.86 23.9 27.26 25-29 26.1 22.695 23.375 27.83 30-34 25.474999999999998 21.790000000000003 24.195 28.54 35-39 25.8 22.335 23.990000000000002 27.875 40-44 25.71 21.98 24.39 27.92 45-49 26.009999999999998 21.365000000000002 24.505 28.12 50-54 25.474999999999998 21.875 24.445 28.205000000000002 55-59 25.074999999999996 21.759999999999998 25.245 27.92 60-64 25.650000000000002 22.035 24.585 27.73 65-69 25.34 21.705 24.560000000000002 28.395 70-74 26.035000000000004 22.54 23.200000000000003 28.225 75-79 26.185000000000002 22.295 23.599999999999998 27.92 80-84 25.919999999999998 21.46 23.880000000000003 28.74 85-89 26.21 22.16 23.73 27.900000000000002 90-94 26.590000000000003 21.63 23.54 28.24 95-99 26.05 21.935 23.84 28.175 100-104 26.165 22.57 22.745 28.52 105-109 25.740000000000002 22.965 23.400000000000002 27.894999999999996 110-114 26.55 22.945 22.25 28.255000000000003 115-119 26.290000000000003 23.765 22.189999999999998 27.755000000000003 120-124 26.945000000000004 22.71 22.650000000000002 27.694999999999997 125-129 26.6 23.035 21.98 28.384999999999998 130-134 27.445000000000004 22.24 22.465 27.85 135-139 27.05 23.080000000000002 22.575 27.295 140-144 28.08 22.45 22.03 27.439999999999998 145-149 29.225 22.07 21.505 27.200000000000003 150 28.575 24.125 21.45 25.85 >>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 4.0 33 6.5 34 6.5 35 8.5 36 15.0 37 25.5 38 30.5 39 35.0 40 45.5 41 56.0 42 61.5 43 83.0 44 108.0 45 123.0 46 151.5 47 180.5 48 188.5 49 185.5 50 188.5 51 169.0 52 155.5 53 159.0 54 152.0 55 145.0 56 148.5 57 156.0 58 139.5 59 107.5 60 101.5 61 101.0 62 93.0 63 95.0 64 92.0 65 80.5 66 73.5 67 80.5 68 84.5 69 76.5 70 71.0 71 60.5 72 45.0 73 39.0 74 23.0 75 16.0 76 15.0 77 7.0 78 5.5 79 3.0 80 1.0 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 0.17500000000000002 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 83.95 #Duplication Level Percentage of deduplicated Percentage of total 1 87.73079213817748 73.65 2 8.24895771292436 13.850000000000001 3 2.5908278737343657 6.525 4 0.7742703990470519 2.6 5 0.3275759380583681 1.375 6 0.14889815366289458 0.75 7 0.05955926146515784 0.35000000000000003 8 0.05955926146515784 0.4 9 0.0 0.0 >10 0.05955926146515784 0.5 >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 GGGAAATTCTGACCGTTGAGGCGTGCGATACTGCCAGCACGTGGGTTGTA 10 0.25 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGC 10 0.25 TruSeq Adapter, Index 11 (100% over 50bp) GTATGATTAACAGCTGCCCTCGACGAAGAAGTCCATTGAACACATTGCGG 8 0.2 No Hit GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 8 0.2 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 7 0.17500000000000002 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 7 0.17500000000000002 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 6 0.15 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 6 0.15 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 6 0.15 No Hit GTGAGGTCTTTATTTCACCCTAATAGTTATCATACTAACTCATTCACTCC 6 0.15 No Hit AGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGC 6 0.15 No Hit GTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTC 5 0.125 No Hit CTTCACTCTCCGCCTTCTTTAAAACGACATAGTTTTGTGGTATGATTAAC 5 0.125 No Hit GTCGAAGATGAATCCACGTCTCCGATCGGGTAACTCTGGCAGCTGCTTTG 5 0.125 No Hit CCCGGATCGGCCCGGTCAGACCGGGCCTTGGAGCCAAAAGGAGGGGACTT 5 0.125 No Hit GCTGCTTTGGGGGAAATTCGGAGTCAACACACCAATCTCTTCTCCCCTGT 5 0.125 No Hit GCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCC 5 0.125 No Hit CCCGCTTCCGACCCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTAT 5 0.125 No Hit TGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTCA 5 0.125 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 5 0.125 No Hit GTCCCGACAGGCGTGCTCCAACTCGAACCCTTCACAGAAGATCAGGGTCG 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 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 0.0125 0.0 0.0 0.0 0.0 40-41 0.037500000000000006 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.0625 0.0 0.0 0.0 0.0 46-47 0.1125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.21250000000000002 0.0 0.0 0.0 0.0 52-53 0.25 0.0 0.0 0.0 0.0 54-55 0.2875 0.0 0.0 0.0 0.0 56-57 0.35 0.0 0.0 0.0 0.0 58-59 0.5375 0.0 0.0 0.0 0.0 60-61 0.75 0.0 0.0 0.0 0.0 62-63 0.9624999999999999 0.0 0.0 0.0 0.0 64-65 1.2 0.0 0.0 0.0 0.0 66-67 1.3625 0.0 0.0 0.0 0.0 68-69 1.525 0.0 0.0 0.0 0.0 70-71 1.9375 0.0 0.0 0.0 0.0 72-73 2.2 0.0 0.0 0.0 0.0 74-75 2.5625 0.0 0.0 0.0 0.0 76-77 3.0125 0.0 0.0 0.0 0.0 78-79 3.4625000000000004 0.0 0.0 0.0 0.0 80-81 3.7875 0.0 0.0 0.0 0.0 82-83 4.1375 0.0 0.0 0.0 0.0 84-85 4.75 0.0 0.0 0.0 0.0 86-87 5.4875 0.0 0.0 0.0 0.0 88-89 6.1625 0.0 0.0 0.0 0.0 90-91 6.7 0.0 0.0 0.0 0.0 92-93 7.324999999999999 0.0 0.0 0.0 0.0 94-95 8.0375 0.0 0.0 0.0 0.0 96-97 8.9375 0.0 0.0 0.0 0.0 98-99 9.7 0.0 0.0 0.0 0.0 100-101 10.412500000000001 0.0 0.0 0.0 0.0 102-103 11.45 0.0 0.0 0.0 0.0 104-105 12.4 0.0 0.0 0.0 0.0 106-107 13.35 0.0 0.0 0.0 0.0 108-109 14.3125 0.0 0.0 0.0 0.0 110-111 15.225 0.0 0.0 0.0 0.0 112-113 16.2125 0.0 0.0 0.0 0.0 114-115 17.225 0.0 0.0 0.0 0.0 116-117 18.1 0.0 0.0 0.0 0.0 118-119 19.0125 0.0 0.0 0.0 0.0 120-121 20.0625 0.0 0.0 0.0 0.0 122-123 21.325000000000003 0.0 0.0 0.0 0.0 124-125 22.275 0.0 0.0 0.0 0.0 126-127 23.25 0.0 0.0 0.0 0.0 128-129 24.4625 0.0 0.0 0.0 0.0 130-131 25.3375 0.0 0.0 0.0 0.0 132-133 26.425 0.0 0.0 0.0 0.0 134-135 27.4125 0.0 0.0 0.0 0.0 136-137 28.625 0.0 0.0 0.0 0.0 138 29.4 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTACCTG 10 0.006973645 144.0 4 CTTTACC 10 0.006973645 144.0 2 TTTTTTT 10 0.006973645 144.0 2 TTTTTTA 10 0.006973645 144.0 3 CCTGATA 10 0.006973645 144.0 7 TTTTTAT 10 0.006973645 144.0 4 GTTTTTT 10 0.006973645 144.0 1 CTGATAG 10 0.006973645 144.0 8 TTTTATT 10 0.006973645 144.0 5 AGGGAAT 10 0.006973645 144.0 1 ACCTGAT 10 0.006973645 144.0 6 GAATCAT 10 0.006973645 144.0 4 TACCTGA 10 0.006973645 144.0 5 TTTACCT 10 0.006973645 144.0 3 GCTTTAC 10 0.006973645 144.0 1 ATTTATG 10 0.006973645 144.0 9 >>END_MODULE SRR24040057 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR24040057_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 36.431 37.0 37.0 37.0 37.0 37.0 2 35.979 37.0 37.0 37.0 37.0 37.0 3 32.7285 37.0 37.0 37.0 11.0 37.0 4 35.781 37.0 37.0 37.0 37.0 37.0 5 36.299 37.0 37.0 37.0 37.0 37.0 6 36.2585 37.0 37.0 37.0 37.0 37.0 7 36.169 37.0 37.0 37.0 37.0 37.0 8 35.771 37.0 37.0 37.0 37.0 37.0 9 34.248 37.0 37.0 37.0 25.0 37.0 10-14 35.5162 37.0 37.0 37.0 34.6 37.0 15-19 35.2806 37.0 37.0 37.0 34.6 37.0 20-24 35.584199999999996 37.0 37.0 37.0 34.6 37.0 25-29 35.719100000000005 37.0 37.0 37.0 37.0 37.0 30-34 34.4223 37.0 34.6 37.0 26.6 37.0 35-39 35.9426 37.0 37.0 37.0 37.0 37.0 40-44 35.807199999999995 37.0 37.0 37.0 37.0 37.0 45-49 35.9778 37.0 37.0 37.0 37.0 37.0 50-54 35.964600000000004 37.0 37.0 37.0 37.0 37.0 55-59 35.996599999999994 37.0 37.0 37.0 37.0 37.0 60-64 35.885400000000004 37.0 37.0 37.0 37.0 37.0 65-69 35.6426 37.0 37.0 37.0 34.6 37.0 70-74 35.49480000000001 37.0 37.0 37.0 34.6 37.0 75-79 35.053399999999996 37.0 37.0 37.0 31.8 37.0 80-84 35.552 37.0 37.0 37.0 34.6 37.0 85-89 35.1851 37.0 37.0 37.0 32.2 37.0 90-94 34.5246 37.0 37.0 37.0 27.0 37.0 95-99 35.41610000000001 37.0 37.0 37.0 37.0 37.0 100-104 34.9454 37.0 37.0 37.0 32.2 37.0 105-109 35.1887 37.0 37.0 37.0 37.0 37.0 110-114 34.4688 37.0 37.0 37.0 22.2 37.0 115-119 34.7304 37.0 37.0 37.0 25.0 37.0 120-124 34.1221 37.0 37.0 37.0 25.0 37.0 125-129 34.0835 37.0 37.0 37.0 25.0 37.0 130-134 33.81529999999999 37.0 37.0 37.0 22.2 37.0 135-139 33.7432 37.0 37.0 37.0 19.4 37.0 140-144 33.5879 37.0 37.0 37.0 16.6 37.0 145-149 33.2029 37.0 37.0 37.0 11.0 37.0 150 33.2485 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 8.0 14 11.0 15 3.0 16 8.0 17 7.0 18 7.0 19 6.0 20 11.0 21 12.0 22 11.0 23 11.0 24 16.0 25 10.0 26 13.0 27 12.0 28 14.0 29 21.0 30 46.0 31 103.0 32 155.0 33 211.0 34 361.0 35 751.0 36 2039.0 37 151.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.575 19.575 7.475 32.375 2 32.35 22.75 24.725 20.175 3 24.675 25.35 24.65 25.324999999999996 4 29.15 31.125000000000004 16.7 23.025000000000002 5 31.45 31.25 16.025 21.275 6 26.625 32.925 17.424999999999997 23.025000000000002 7 25.15 18.575 30.275000000000002 26.0 8 25.025 22.325 23.025000000000002 29.625 9 25.35 22.475 25.575 26.6 10-14 28.410000000000004 24.959999999999997 20.025000000000002 26.605 15-19 28.205000000000002 24.015 21.52 26.26 20-24 28.499999999999996 24.55 21.315 25.635 25-29 28.15 24.455 21.275 26.119999999999997 30-34 27.060000000000002 25.545 21.21 26.185000000000002 35-39 27.810000000000002 25.319999999999997 20.205000000000002 26.665 40-44 28.04 24.57 21.055 26.334999999999997 45-49 28.02 24.990000000000002 20.965 26.025 50-54 27.32 25.259999999999998 21.365000000000002 26.055 55-59 28.360000000000003 23.835 21.959999999999997 25.845000000000002 60-64 28.64 23.925 21.395 26.040000000000003 65-69 28.970000000000002 24.0 21.115000000000002 25.915 70-74 28.515 24.14 20.805 26.540000000000003 75-79 28.77 23.995 21.255 25.979999999999997 80-84 29.294999999999998 24.345 20.69 25.669999999999998 85-89 29.609999999999996 24.57 20.45 25.369999999999997 90-94 29.74 25.03 20.695 24.535 95-99 30.464999999999996 24.205 20.560000000000002 24.77 100-104 30.585 25.36 20.24 23.815 105-109 31.44 24.185000000000002 21.060000000000002 23.315 110-114 32.28 25.25 19.455 23.015 115-119 33.085 24.310000000000002 20.03 22.575 120-124 33.915 24.98 19.685 21.42 125-129 34.82 24.5 19.765 20.915 130-134 35.96 23.799999999999997 19.17 21.07 135-139 38.269999999999996 23.405 18.43 19.895 140-144 39.900000000000006 23.080000000000002 17.635 19.384999999999998 145-149 40.495 23.23 17.29 18.985 150 43.0 22.475 16.55 17.974999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.5 8 1.0 9 1.0 10 1.5 11 2.5 12 3.0 13 3.0 14 2.0 15 0.5 16 0.0 17 0.0 18 0.5 19 2.5 20 2.5 21 1.5 22 1.5 23 1.0 24 1.5 25 1.5 26 1.0 27 1.0 28 1.0 29 2.0 30 3.0 31 3.0 32 3.5 33 3.5 34 4.0 35 7.0 36 11.5 37 17.5 38 22.5 39 32.0 40 51.5 41 60.5 42 65.5 43 88.5 44 108.0 45 121.0 46 132.0 47 147.0 48 162.0 49 160.5 50 159.5 51 175.5 52 177.5 53 174.5 54 170.5 55 160.5 56 143.0 57 124.0 58 119.0 59 116.5 60 111.5 61 111.5 62 105.0 63 82.5 64 83.0 65 87.5 66 92.5 67 98.5 68 86.5 69 68.5 70 64.5 71 59.0 72 43.5 73 39.5 74 26.0 75 14.5 76 15.0 77 10.0 78 6.5 79 2.5 80 0.0 81 0.0 82 0.0 83 0.5 84 1.0 85 1.0 86 1.0 87 0.5 88 0.0 89 1.0 90 1.5 91 1.0 92 2.0 93 3.0 94 2.0 95 2.5 96 2.5 97 1.5 98 2.5 99 4.0 100 4.5 >>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 88.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 90.51405850610622 79.675 2 7.043453564328315 12.4 3 1.7324623686452711 4.575 4 0.3976143141153081 1.4000000000000001 5 0.1420051121840386 0.625 6 0.028401022436807723 0.15 7 0.0 0.0 8 0.08520306731042318 0.6 9 0.0 0.0 >10 0.05680204487361545 0.575 >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 GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 13 0.325 No Hit GGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCA 10 0.25 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit GTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGT 8 0.2 No Hit AAGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCG 6 0.15 No Hit CACGGCCCTCGTGCCGGCGACGCATCATTCAAATTTCTGCCCTATCAACT 5 0.125 No Hit GTCGACGGGTTCTGAAACCTGGGATGCGCAAGGAAGCTGACGAGCGGGAG 5 0.125 No Hit GTGAAATACCACTACTTTTAACGTTATTTTACTTATTCCGTGGGTCGGAA 5 0.125 No Hit CATAAACATAAACATCAAAGCAAACTAGTAGCCAGCCACCATGAAGACCT 5 0.125 No Hit AGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGC 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 0.0125 0.0 0.0 0.0 0.0 40-41 0.037500000000000006 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.0625 0.0 0.0 0.0 0.0 46-47 0.1125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.21250000000000002 0.0 0.0 0.0 0.0 52-53 0.25 0.0 0.0 0.0 0.0 54-55 0.2875 0.0 0.0 0.0 0.0 56-57 0.35 0.0 0.0 0.0 0.0 58-59 0.55 0.0 0.0 0.0 0.0 60-61 0.7749999999999999 0.0 0.0 0.0 0.0 62-63 0.975 0.0 0.0 0.0 0.0 64-65 1.1875 0.0 0.0 0.0 0.0 66-67 1.3625 0.0 0.0 0.0 0.0 68-69 1.5375 0.0 0.0 0.0 0.0 70-71 1.925 0.0 0.0 0.0 0.0 72-73 2.175 0.0 0.0 0.0 0.0 74-75 2.5 0.0 0.0 0.0 0.0 76-77 2.9375 0.0 0.0 0.0 0.0 78-79 3.3875 0.0 0.0 0.0 0.0 80-81 3.7125 0.0 0.0 0.0 0.0 82-83 4.0875 0.0 0.0 0.0 0.0 84-85 4.675000000000001 0.0 0.0 0.0 0.0 86-87 5.4 0.0 0.0 0.0 0.0 88-89 6.0375 0.0 0.0 0.0 0.0 90-91 6.55 0.0 0.0 0.0 0.0 92-93 7.175000000000001 0.0 0.0 0.0 0.0 94-95 7.875 0.0 0.0 0.0 0.0 96-97 8.774999999999999 0.0 0.0 0.0 0.0 98-99 9.5375 0.0 0.0 0.0 0.0 100-101 10.2375 0.0 0.0 0.0 0.0 102-103 11.2625 0.0 0.0 0.0 0.0 104-105 12.212499999999999 0.0 0.0 0.0 0.0 106-107 13.162500000000001 0.0 0.0 0.0 0.0 108-109 14.125 0.0 0.0 0.0 0.0 110-111 15.0125 0.0 0.0 0.0 0.0 112-113 15.975 0.0 0.0 0.0 0.0 114-115 16.950000000000003 0.0 0.0 0.0 0.0 116-117 17.825000000000003 0.0 0.0 0.0 0.0 118-119 18.775 0.0 0.0 0.0 0.0 120-121 19.825000000000003 0.0 0.0 0.0 0.0 122-123 21.075 0.0 0.0 0.0 0.0 124-125 22.0 0.0 0.0 0.0 0.0 126-127 22.975 0.0 0.0 0.0 0.0 128-129 24.200000000000003 0.0 0.0 0.0 0.0 130-131 25.075 0.0 0.0 0.0 0.0 132-133 26.175 0.0 0.0 0.0 0.0 134-135 27.1625 0.0 0.0 0.0 0.0 136-137 28.375 0.0 0.0 0.0 0.0 138 29.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTCACAA 10 0.006973645 144.0 1 AATTAGT 10 0.006973645 144.0 5 TAGTTCA 10 0.006973645 144.0 8 GAGTCTG 10 0.006973645 144.0 3 TCTGACA 10 0.006973645 144.0 6 GGGAAAT 10 0.006973645 144.0 1 AGTCTGA 10 0.006973645 144.0 4 TTAGTTC 10 0.006973645 144.0 7 AGTTCAT 10 0.006973645 144.0 9 GGAAATT 10 0.006973645 144.0 2 GGAGTCT 10 0.006973645 144.0 2 GGGGGGG 325 0.0 13.292308 140-144 >>END_MODULE Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112223 spots for SRR24040057.sra Written 4112223 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra Read 4112207 spots for SRR24040057.sra Written 4112207 spots for SRR24040057.sra SRR ids: ['SRR24040057.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2f7fj_v7 SRR24040057.sra spots: 82244156 blocks: [[1, 4112207], [4112208, 8224414], [8224415, 12336621], [12336622, 16448828], [16448829, 20561035], [20561036, 24673242], [24673243, 28785449], [28785450, 32897656], [32897657, 37009863], [37009864, 41122070], [41122071, 45234277], [45234278, 49346484], [49346485, 53458691], [53458692, 57570898], [57570899, 61683105], [61683106, 65795312], [65795313, 69907519], [69907520, 74019726], [74019727, 78131933], [78131934, 82244156]] SRR24040057 file size 27767828 SRR24040057 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 SRR24040057 SRR24040057_1.fastq SRR24040057_2.fastq Input file: SRR24040057_1.fastq Paired file: SRR24040057_2.fastq trimmed: SRR24040057-trimmed-pair1.fastq, SRR24040057-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 22:16:32 2024 >> started Fri Dec 6 22:23:28 2024 >> done (415.772s) 82244156 read pairs processed; of these: 22753 ( 0.03%) short read pairs filtered out after trimming by size control 255174 ( 0.31%) empty read pairs filtered out after trimming by size control 81966229 (99.66%) read pairs available; of these: 28994485 (35.37%) trimmed read pairs available after processing 52971744 (64.63%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 828 0.00% 19 811 0.00% 20 647 0.00% 21 692 0.00% 22 869 0.00% 23 561 0.00% 24 683 0.00% 25 845 0.00% 26 994 0.00% 27 885 0.00% 28 1168 0.00% 29 1407 0.00% 30 2474 0.00% 31 1695 0.00% 32 2154 0.00% 33 2209 0.00% 34 2470 0.00% 35 2907 0.00% 36 3426 0.00% 37 3877 0.00% 38 4844 0.01% 39 6160 0.01% 40 7000 0.01% 41 8200 0.01% 42 8586 0.01% 43 9333 0.01% 44 10229 0.01% 45 11227 0.01% 46 13201 0.02% 47 16206 0.02% 48 19553 0.02% 49 22912 0.03% 50 26720 0.03% 51 30410 0.04% 52 32869 0.04% 53 34842 0.04% 54 36423 0.04% 55 38249 0.05% 56 42009 0.05% 57 46836 0.06% 58 56061 0.07% 59 61371 0.07% 60 68943 0.08% 61 75879 0.09% 62 83455 0.10% 63 85868 0.10% 64 87989 0.11% 65 89875 0.11% 66 92759 0.11% 67 100636 0.12% 68 108951 0.13% 69 114846 0.14% 70 120071 0.15% 71 129637 0.16% 72 140009 0.17% 73 154232 0.19% 74 154685 0.19% 75 158235 0.19% 76 163175 0.20% 77 169540 0.21% 78 175903 0.21% 79 189608 0.23% 80 202487 0.25% 81 211272 0.26% 82 221676 0.27% 83 226093 0.28% 84 237528 0.29% 85 252963 0.31% 86 265013 0.32% 87 266569 0.33% 88 266394 0.33% 89 266739 0.33% 90 277267 0.34% 91 279373 0.34% 92 297693 0.36% 93 310169 0.38% 94 310360 0.38% 95 330138 0.40% 96 336102 0.41% 97 335002 0.41% 98 346398 0.42% 99 342879 0.42% 100 352380 0.43% 101 348576 0.43% 102 351251 0.43% 103 363870 0.44% 104 363190 0.44% 105 356969 0.44% 106 366189 0.45% 107 372894 0.45% 108 360604 0.44% 109 373410 0.46% 110 366422 0.45% 111 383339 0.47% 112 389034 0.47% 113 378999 0.46% 114 388988 0.47% 115 396116 0.48% 116 403963 0.49% 117 392769 0.48% 118 387738 0.47% 119 404321 0.49% 120 415997 0.51% 121 408488 0.50% 122 418397 0.51% 123 431203 0.53% 124 436884 0.53% 125 430823 0.53% 126 431832 0.53% 127 428799 0.52% 128 420266 0.51% 129 433353 0.53% 130 415292 0.51% 131 423135 0.52% 132 417230 0.51% 133 426985 0.52% 134 428828 0.52% 135 427065 0.52% 136 432753 0.53% 137 441245 0.54% 138 429020 0.52% 139 430423 0.53% 140 423327 0.52% 141 427434 0.52% 142 444691 0.54% 143 437036 0.53% 144 450543 0.55% 145 431511 0.53% 146 436803 0.53% 147 436865 0.53% 148 426987 0.52% 149 428994 0.52% 150 52971744 64.63% 81966229 reads passed initial QC criterion=sequence-density sequence-density=1.45 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=32 prefix-density=1.46 prefix-fanout=2.0 sequence=TTTGGCTTTGGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=37 fanout-score=64.52 fanout-score-rank=1 prefix-density=0.48 prefix-fanout=2.8 sequence=CAGCACGGCCACGCGGCGGTCGCCGACGGGGGAGTCCCTGAGGAGCTCGTGGGTGAAGCGCTCCAGGACCCTGAAGCGCCCGTGGCGCGTGGTTGTCCTGTACTTGAAGCTCTCTTCGCCGTAGTGGTACGGCCGGCCGGACGACGAGTATCGTCCTTGTTCTTGTTCTCCTTCTCCTTGCCGTCCGGCAGATTGGCCGCCCCTTTCTTCCCTCTCCGTATCCCAGTCGGACGCGGAGGAGACGGAGAGGCAGAGGGAGAGGATTGCTAGTGCCAGCACTAGCAACAATCGCGATCTTGCTGTGAGCTTCATGGTGCTTGATCGAGTTGGTTGGTTGATTG criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=5.56 fanout-score-rank=11 prefix-density=1.74 prefix-fanout=2.5 sequence=CCAAAGCCAAAAGTTGGGAGATGTGCACCAGAGAGTCCACCAGTTTACACAAGGAGATGTTGTTGCACTGCCAGCCGGTGTCGCGCATTGGTTCTACAATGGTGGTGATGCGCCAGTTGTAGCAGTCTATGTTTTTGACGTAAACAATAATGCTAACCAGCTTGAACCTAGGCAAAAGGAGTTTTTGTTGGCTGGTAACTACAACGGAGTGCTACAATCTGGACGGAACATACTCAATGGTTTAAATGCCCAGTTGCTTAGCCAGGCCTTTGGTATCAATGAACAAACATCACGAATAATTCAGAATCAGAATGACGGAAGAGGTGAAATAGTTCGTGTGGAATATGGACTTCAATTTCTGACGCCCGTCGTCACCCAACAACAGCAGAAACAACCCTTCCTACCAATCGAACCTCAGGAAGGACAATCGAGTCGCAACGGTTTGGAGGAGAACTTCTGTTCACTCGAGCCAAGGCAAAACATCGAGGATCCCAACCGTGCCGACACATAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=253.73 fanout-score-rank=1 prefix-density=1.26 prefix-fanout=6.4 sequence=AGCAGCAGCAAGAACAGGGGCAGCAAGGTCAGATCCCTTCGCGCCGGTTCGGGGCCCAGTCACAGGAGTGCGGACAACAGGGTATCTTCTCGCCCCAGCTGCTAGCTCAGATACTACCGGCGATGTGCAATGTGTACCTCCCACCGTACTGCCGCGCCACCGCCGCTGATCAGCCATTCGGACCCGGTGGCTACTGATAAGACAAAGGGCTCTTGTAGTAGATAGATAGGGATCACCGCT SRR24040057 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 22:24:40 Started mapping on | Dec 06 22:24:41 Finished on | Dec 06 22:56:08 Mapping speed, Million of reads per hour | 156.37 Number of input reads | 81966229 Average input read length | 273 UNIQUE READS: Uniquely mapped reads number | 41960640 Uniquely mapped reads % | 51.19% Average mapped length | 273.53 Number of splices: Total | 29097970 Number of splices: Annotated (sjdb) | 27006266 Number of splices: GT/AG | 28259332 Number of splices: GC/AG | 402929 Number of splices: AT/AC | 12832 Number of splices: Non-canonical | 422877 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 2.41 Insertion rate per base | 0.01% Insertion average length | 2.49 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 10348630 % of reads mapped to multiple loci | 12.63% Number of reads mapped to too many loci | 4555052 % of reads mapped to too many loci | 5.56% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.52% % of reads unmapped: other | 27.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 29656959 29656959 29656959 N_multimapping 10348630 10348630 10348630 N_noFeature 1319276 40922874 1643285 N_ambiguous 998292 2478 457982 UnstrandedReadsAssigned:39643072 PositiveStrandReadsAssigned:1035288 NegativeStrandReadsAssigned:39859373 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=119 echo kmer=115 SRR24040057 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: SRR24040057-trimmed-pair1.fastq SRR24040057-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 81,966,229 reads, 49,046,906 reads pseudoaligned [quant] estimated average fragment length: 183.277 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,188 rounds 52973 SRR24040057.ke.tsv 35125 SRR24040057.se.tsv 88098 total ==> SRR24040057.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 753.916 245.47 7.74665 PNS24247 1044 861.723 17.4427 0.481599 PNS24249 1928 1745.72 312.407 4.25779 PNS24246 1044 861.723 17.4427 0.481599 PNS24248 1044 861.723 17.4427 0.481599 PNS24244 1471 1288.72 69.7948 1.28855 PNS24243 293 130.603 0 0 KQK14069 1603 1420.72 11204 187.63 KQK14071 474 294.726 33.1839 2.67885 ==> SRR24040057.se.tsv <== BRADI_1g14170v3 11042 BRADI_1g53295v3 24 BRADI_1g59795v3 63 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 873 BRADI_1g74790v3 78 BRADI_1g09890v3 14 BRADI_1g77505v3 439 BRADI_1g48960v3 8 SRR24040057 completed mapping pipeline successfully