Starting /dee2/code/volunteer_pipeline.sh SRR13165349 current disk space = 1542260027392 free memory = 1599760804 SRR13165349 SRAfilesize cf2ebf9a6a4eb71e664fcf2503cc6c20 SRR13165349.sra SRR13165349.sra file validated SRR13165349 is paired end SRR13165349 is conventional basespace SRR13165349 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165349_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5545 37.0 37.0 37.0 37.0 37.0 2 36.03575 37.0 37.0 37.0 37.0 37.0 3 36.555 37.0 37.0 37.0 37.0 37.0 4 36.437 37.0 37.0 37.0 37.0 37.0 5 36.598 37.0 37.0 37.0 37.0 37.0 6 36.5705 37.0 37.0 37.0 37.0 37.0 7 36.429 37.0 37.0 37.0 37.0 37.0 8 36.568 37.0 37.0 37.0 37.0 37.0 9 36.5005 37.0 37.0 37.0 37.0 37.0 10-14 36.5419 37.0 37.0 37.0 37.0 37.0 15-19 36.4779 37.0 37.0 37.0 37.0 37.0 20-24 36.4887 37.0 37.0 37.0 37.0 37.0 25-29 36.3992 37.0 37.0 37.0 37.0 37.0 30-34 36.4054 37.0 37.0 37.0 37.0 37.0 35-39 36.349199999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.338300000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.272000000000006 37.0 37.0 37.0 37.0 37.0 50-54 36.35459999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.3272 37.0 37.0 37.0 37.0 37.0 60-64 36.340999999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.2489 37.0 37.0 37.0 37.0 37.0 70-74 36.250299999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.222 37.0 37.0 37.0 37.0 37.0 80-84 36.130399999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.1907 37.0 37.0 37.0 37.0 37.0 90-94 36.1559 37.0 37.0 37.0 37.0 37.0 95-99 36.0798 37.0 37.0 37.0 37.0 37.0 100-104 36.123599999999996 37.0 37.0 37.0 37.0 37.0 105-109 36.136199999999995 37.0 37.0 37.0 37.0 37.0 110-114 36.0916 37.0 37.0 37.0 37.0 37.0 115-119 36.044200000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.9959 37.0 37.0 37.0 37.0 37.0 125-129 35.912 37.0 37.0 37.0 37.0 37.0 130-134 35.846500000000006 37.0 37.0 37.0 37.0 37.0 135-139 35.7471 37.0 37.0 37.0 37.0 37.0 140-144 35.5608 37.0 37.0 37.0 37.0 37.0 145-149 35.3376 37.0 37.0 37.0 34.6 37.0 150-151 35.10725 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 1.0 23 2.0 24 7.0 25 4.0 26 5.0 27 7.0 28 13.0 29 31.0 30 32.0 31 37.0 32 49.0 33 87.0 34 156.0 35 323.0 36 2822.0 37 423.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 54.6 10.225 5.55 29.625 2 23.2435154872828 10.82850667338202 31.427851926466886 34.5001259128683 3 20.849999999999998 17.299999999999997 24.9 36.95 4 28.525 20.474999999999998 21.6 29.4 5 27.474999999999998 27.800000000000004 21.2 23.525 6 25.2 30.975 21.425 22.400000000000002 7 21.3 25.85 36.8 16.05 8 20.125 22.900000000000002 29.95 27.025 9 21.7 22.825 30.95 24.525 10-14 23.34 25.55 25.740000000000002 25.369999999999997 15-19 24.404999999999998 24.67 25.52 25.405 20-24 24.505 25.224999999999998 24.89 25.380000000000003 25-29 22.965 24.905 25.615 26.515 30-34 24.015 24.925 25.629999999999995 25.430000000000003 35-39 23.505000000000003 25.195 25.11 26.19 40-44 23.175 24.505 26.25 26.07 45-49 23.415 25.635 25.124999999999996 25.825 50-54 24.0 24.82 25.16 26.02 55-59 23.39 24.47 25.69 26.450000000000003 60-64 24.09 24.825 24.65 26.435 65-69 23.375 25.31 25.619999999999997 25.695 70-74 24.015 24.755 24.959999999999997 26.27 75-79 23.455000000000002 25.215 24.935 26.395000000000003 80-84 23.765 25.28 25.435000000000002 25.52 85-89 24.529999999999998 24.47 25.06 25.94 90-94 25.005 24.94 24.4 25.655 95-99 25.014999999999997 25.330000000000002 23.919999999999998 25.735000000000003 100-104 24.610000000000003 25.22 24.58 25.590000000000003 105-109 24.445 24.975 24.64 25.94 110-114 25.040000000000003 25.285000000000004 23.625 26.05 115-119 24.47 24.9 24.15 26.479999999999997 120-124 24.41 25.795 23.905 25.89 125-129 24.215 25.86 23.375 26.55 130-134 23.965 25.81 23.965 26.26 135-139 23.885 24.985 24.215 26.915 140-144 23.87 25.369999999999997 24.265 26.495 145-149 24.36 25.130000000000003 23.915 26.595000000000002 150-151 23.3125 25.5625 24.5375 26.5875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 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 0.5 12 0.5 13 0.5 14 0.5 15 0.0 16 0.5 17 1.0 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 1.0 24 2.0 25 2.5 26 1.5 27 1.0 28 2.0 29 2.0 30 1.5 31 9.5 32 19.5 33 20.5 34 23.0 35 32.0 36 43.0 37 49.0 38 69.0 39 87.5 40 101.5 41 136.5 42 166.5 43 210.5 44 214.0 45 184.5 46 175.0 47 182.5 48 186.0 49 192.0 50 182.5 51 143.0 52 123.5 53 123.0 54 106.5 55 86.5 56 96.0 57 87.0 58 71.0 59 76.5 60 86.5 61 74.0 62 59.5 63 62.5 64 61.0 65 42.5 66 37.0 67 41.0 68 43.5 69 48.0 70 44.5 71 35.0 72 27.0 73 23.0 74 28.5 75 26.5 76 13.5 77 9.5 78 9.0 79 5.0 80 0.0 81 3.0 82 3.5 83 0.5 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 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 0.7250000000000001 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 71.325 #Duplication Level Percentage of deduplicated Percentage of total 1 72.9758149316509 52.05 2 18.436733263231687 26.3 3 5.538030143708377 11.85 4 1.9978969505783386 5.7 5 0.6659656501927795 2.375 6 0.28040658955485454 1.2 7 0.10515247108307045 0.525 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 warn #Sequence Count Percentage Possible Source GCCAGAACCCATCATTCCAACTAGGTAAACACAACGGTCATTCAAGCAAG 7 0.17500000000000002 No Hit GTACATGTTGCAGCCGTTGCAGCCGCTGCCGCACTTGCAGGATGACCCGC 7 0.17500000000000002 No Hit CCTAGAACCGCAAATTAAGCTAACCAACGAGCCCATGATATCGCACAAGC 7 0.17500000000000002 No Hit ACTCGATTCATGTGTACAAGGCACAAAGCAGAGTACCCCCAGACAGGTTT 6 0.15 No Hit GCTGCGTTTTCCTTACATGAGCCTTTTATGATGCATTTCTCTTCTGTAGT 6 0.15 No Hit GGGCAAAAGCAAACGCATCGTTCCTCTCCATCCCTCACCGGGCTCAAAAC 6 0.15 No Hit AGCAGTGTAGGCCACGATCTTGGCTTCGATTTCATCCTTCTTGCCACCAA 6 0.15 No Hit GGCAGCTTACTCGACGCCGTACTTCTTCTTGAGCACGCCGATGAACTCAT 6 0.15 No Hit GGGGGCGGTCTCCGGCGAGGAGGCGTAGGGGGAGCCCGGGGCTTCCATCG 6 0.15 No Hit GTAAGGAAGAGGAGGCAGTGACAGCAGTTTTTCACAATTCCAAATTTTAA 6 0.15 No Hit CAGGGAACTTCTTGGCGTACTCAGCGAAGACAGGGGCTATGATGCGGCAA 6 0.15 No Hit CTACCCACGTGCGCCCAAATATCAAGTTGTTGACTTTTGTCAAAGGTGGT 5 0.125 No Hit GTGTAGTCAGGGTTCAAATGTACATATGCTCCTCGAGCCCATGTCGGTAC 5 0.125 No Hit CAGTAAAGGGAGCAGCTTCACCATCTGCTTCGTCTCCTCCACCTCCGTCA 5 0.125 No Hit GCTGACGTTCCCCAGAACCATCAGTCTGCACTGATTCCTTATTCGCATCA 5 0.125 No Hit GGAAAGACTTTGGAAGTGATGCAATTGGCAAGGCAGTAGCATCAAGGTAC 5 0.125 No Hit GCCACGCTGATCGTGTCCAAGGAGGAGAGAGTAGCTGGCGGGATTTTAAA 5 0.125 No Hit GCCTGTATCATTTAGCTTGCGCTCTGCAGCTAGCAAAGCAGCCATTGTTT 5 0.125 No Hit GGGGTGCCCGTGGTCGTCTTGAAGATCTTCTTCACGTCCTCCAGGAGCGT 5 0.125 No Hit GTAGGAGCTCTAGGTGCTGATTTCTCGGCCATCACAACACTTATTTTATG 5 0.125 No Hit TGCTCGACGATGGGTCCGACGAGGTCGAGGCGGTTGGCGACGCCCCATGC 5 0.125 No Hit GTCCTCAAGTGCCAATGTTTGTGACAGAAATGATGCACCAACAGTTACCT 5 0.125 No Hit CTCTAAATTACTCCACCAGTTGTGTTTATGAGATTCCCAGTTAAATGCCT 5 0.125 No Hit GTATAAGTAATCAGAGCACTCTGAACCATGGTCCGAGGAATGGGAAGAGC 5 0.125 No Hit CAAGAATATCAAGCATGCGTGTCATCTGGGAGAAAATCAGTACACGGTTC 5 0.125 No Hit TCGACAATGTCATCTTCATTAACAATTACATAATTTTCATCATCAATTCC 5 0.125 No Hit GTGCCATTGCAGCAGAATTCCTTCTTGAGATCCTTGAGGATCTTGTTGTA 5 0.125 No Hit CATCGGTGAAGTGGTGGACCGGATGCAGAGGAAGATGGAGTCGGAGCCGG 5 0.125 No Hit CACATTGGAAGGATTTTCCTTGACCCTTGCCTCCCCAGATACCCAAGATG 5 0.125 No Hit GCCTGAATTAGCTAGCTTATTCTCCCAATTGCCAACCAGCTCGGTGCAAC 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 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.0875 0.0 0.0 0.0 0.0 56-57 0.1125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.2625 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.47500000000000003 0.0 0.0 0.0 0.0 78-79 0.6 0.0 0.0 0.0 0.0 80-81 0.6375 0.0 0.0 0.0 0.0 82-83 0.8125 0.0 0.0 0.0 0.0 84-85 0.9125000000000001 0.0 0.0 0.0 0.0 86-87 1.1625 0.0 0.0 0.0 0.0 88-89 1.425 0.0 0.0 0.0 0.0 90-91 1.75 0.0 0.0 0.0 0.0 92-93 2.0125 0.0 0.0 0.0 0.0 94-95 2.4125 0.0 0.0 0.0 0.0 96-97 2.8375 0.0 0.0 0.0 0.0 98-99 3.225 0.0 0.0 0.0 0.0 100-101 3.7874999999999996 0.0 0.0 0.0 0.0 102-103 4.1625 0.0 0.0 0.0 0.0 104-105 4.862500000000001 0.0 0.0 0.0 0.0 106-107 5.3875 0.0 0.0 0.0 0.0 108-109 5.85 0.0 0.0 0.0 0.0 110-111 6.4625 0.0 0.0 0.0 0.0 112-113 7.0375 0.0 0.0 0.0 0.0 114-115 7.574999999999999 0.0 0.0 0.0 0.0 116-117 8.0375 0.0 0.0 0.0 0.0 118-119 8.662500000000001 0.0 0.0 0.0 0.0 120-121 9.6375 0.0 0.0 0.0 0.0 122-123 10.4875 0.0 0.0 0.0 0.0 124-125 11.1625 0.0 0.0 0.0 0.0 126-127 11.925 0.0 0.0 0.0 0.0 128-129 12.975000000000001 0.0 0.0 0.0 0.0 130-131 13.7375 0.0 0.0 0.0 0.0 132-133 14.5875 0.0 0.0 0.0 0.0 134-135 15.3125 0.0 0.0 0.0 0.0 136-137 16.0375 0.0 0.0 0.0 0.0 138-139 16.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAAC 10 0.006830828 145.0 145 AGCTTAC 10 0.006830828 145.0 4 ATCCACC 10 0.006830828 145.0 8 TTACTCG 10 0.006830828 145.0 7 GCAGCTT 10 0.006830828 145.0 2 CTTACTC 10 0.006830828 145.0 6 GGCAGCT 10 0.006830828 145.0 1 GCTTACT 10 0.006830828 145.0 5 >>END_MODULE SRR13165349 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165349_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.98925 37.0 37.0 37.0 37.0 37.0 2 36.0945 37.0 37.0 37.0 37.0 37.0 3 36.0415 37.0 37.0 37.0 37.0 37.0 4 36.11 37.0 37.0 37.0 37.0 37.0 5 36.3025 37.0 37.0 37.0 37.0 37.0 6 36.2395 37.0 37.0 37.0 37.0 37.0 7 36.189 37.0 37.0 37.0 37.0 37.0 8 36.301 37.0 37.0 37.0 37.0 37.0 9 36.336 37.0 37.0 37.0 37.0 37.0 10-14 36.229699999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.19500000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.160399999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.1055 37.0 37.0 37.0 37.0 37.0 30-34 36.08670000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.024 37.0 37.0 37.0 37.0 37.0 40-44 36.025099999999995 37.0 37.0 37.0 37.0 37.0 45-49 35.961200000000005 37.0 37.0 37.0 37.0 37.0 50-54 35.93730000000001 37.0 37.0 37.0 37.0 37.0 55-59 35.9889 37.0 37.0 37.0 37.0 37.0 60-64 35.9225 37.0 37.0 37.0 37.0 37.0 65-69 35.85625 37.0 37.0 37.0 37.0 37.0 70-74 35.793400000000005 37.0 37.0 37.0 37.0 37.0 75-79 35.889500000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.832100000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.7774 37.0 37.0 37.0 37.0 37.0 90-94 35.67 37.0 37.0 37.0 37.0 37.0 95-99 35.7182 37.0 37.0 37.0 37.0 37.0 100-104 35.647 37.0 37.0 37.0 37.0 37.0 105-109 35.6643 37.0 37.0 37.0 37.0 37.0 110-114 35.6375 37.0 37.0 37.0 37.0 37.0 115-119 35.5394 37.0 37.0 37.0 37.0 37.0 120-124 35.3988 37.0 37.0 37.0 37.0 37.0 125-129 35.4193 37.0 37.0 37.0 37.0 37.0 130-134 35.2986 37.0 37.0 37.0 34.6 37.0 135-139 35.1727 37.0 37.0 37.0 34.6 37.0 140-144 34.9356 37.0 37.0 37.0 27.4 37.0 145-149 34.788799999999995 37.0 37.0 37.0 25.0 37.0 150-151 34.320499999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 6.0 14 6.0 15 6.0 16 2.0 17 4.0 18 1.0 19 1.0 20 1.0 21 5.0 22 5.0 23 2.0 24 7.0 25 7.0 26 12.0 27 13.0 28 14.0 29 18.0 30 28.0 31 53.0 32 81.0 33 90.0 34 199.0 35 588.0 36 2594.0 37 255.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.4049233860839 20.823913589550365 6.556141672946496 24.215021351419242 2 29.45 23.575 27.425 19.55 3 23.625 24.375 28.799999999999997 23.200000000000003 4 28.125 29.125 19.875 22.875 5 29.325000000000003 31.85 18.6 20.225 6 23.724999999999998 35.05 19.025 22.2 7 25.6 19.125 31.35 23.925 8 23.75 22.675 26.1 27.474999999999998 9 25.45 21.65 25.4 27.500000000000004 10-14 26.515 26.87 22.720000000000002 23.895 15-19 26.325 25.430000000000003 24.2 24.044999999999998 20-24 26.663331665832917 25.052526263131565 23.816908454227114 24.467233616808404 25-29 25.962981490745374 25.227613806903452 23.901950975487743 24.907453726863434 30-34 26.00300150075038 24.787393696848426 24.20210105052526 25.007503751875937 35-39 25.18759379689845 25.77288644322161 23.951975987993997 25.087543771885944 40-44 26.36818409204602 24.637318659329665 23.676838419209606 25.317658829414707 45-49 26.45822911455728 25.297648824412207 24.307153576788394 23.936968484242122 50-54 26.61830915457729 24.987493746873437 23.986993496748372 24.4072036018009 55-59 25.797898949474735 24.627313656828413 24.352176088044022 25.222611305652826 60-64 26.61830915457729 24.977488744372188 23.83191595797899 24.572286143071537 65-69 25.931669251163026 25.881646741033464 23.70566755039768 24.481016457405833 70-74 26.418209104552275 24.827413706853427 24.427213606803402 24.327163581790895 75-79 27.078539269634817 25.082541270635318 23.591795897948977 24.24712356178089 80-84 26.45822911455728 24.882441220610303 23.821910955477737 24.83741870935468 85-89 26.97848924462231 25.357678839419712 23.71185592796398 23.951975987993997 90-94 26.7983991995998 25.077538769384695 24.007003501750876 24.117058529264632 95-99 27.283641820910454 25.5727863931966 23.411705852926463 23.731865932966485 100-104 26.80840420210105 25.6328164082041 23.806903451725862 23.751875937968983 105-109 27.49374687343672 25.41770885442721 23.306653326663334 23.781890945472735 110-114 27.428714357178592 24.99749874937469 23.446723361680842 24.127063531765884 115-119 27.878939469734863 25.677838919459727 23.176588294147074 23.26663331665833 120-124 28.134067033516757 25.267633816908454 23.206603301650823 23.391695847923963 125-129 28.199099549774886 25.042521260630313 23.486743371685844 23.271635817908955 130-134 28.299149574787393 25.202601300650322 23.176588294147074 23.321660830415208 135-139 28.8144072036018 25.56778389194597 23.486743371685844 22.131065532766385 140-144 29.114557278639317 24.74737368684342 23.836918459229615 22.301150575287643 145-149 29.79489744872436 25.012506253126567 23.736868434217108 21.455727863931966 150-151 32.103551775887944 24.77488744372186 22.26113056528264 20.860430215107552 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.0 3 0.5 4 0.5 5 0.5 6 1.5 7 1.5 8 0.0 9 0.5 10 1.0 11 0.5 12 0.0 13 0.0 14 1.0 15 1.5 16 0.5 17 0.0 18 1.0 19 3.0 20 2.0 21 0.0 22 0.5 23 0.5 24 0.5 25 2.5 26 3.0 27 1.5 28 3.5 29 5.5 30 6.5 31 9.0 32 13.5 33 19.0 34 19.5 35 27.5 36 37.5 37 44.5 38 73.0 39 99.0 40 133.5 41 151.0 42 130.5 43 130.5 44 155.5 45 169.0 46 183.5 47 183.5 48 167.0 49 172.0 50 160.0 51 145.5 52 140.0 53 121.5 54 109.5 55 101.0 56 101.5 57 117.5 58 95.0 59 68.0 60 76.0 61 79.5 62 63.5 63 52.0 64 57.0 65 64.5 66 65.5 67 59.0 68 52.0 69 48.5 70 44.0 71 42.0 72 37.5 73 35.0 74 31.5 75 13.0 76 9.5 77 14.0 78 7.0 79 1.5 80 1.5 81 1.0 82 1.0 83 1.5 84 1.0 85 0.5 86 0.5 87 1.5 88 1.0 89 0.0 90 0.5 91 1.5 92 1.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.5 98 1.0 99 1.0 100 7.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.475 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 0.05 25-29 0.05 30-34 0.05 35-39 0.05 40-44 0.05 45-49 0.05 50-54 0.05 55-59 0.05 60-64 0.05 65-69 0.045 70-74 0.05 75-79 0.05 80-84 0.05 85-89 0.05 90-94 0.05 95-99 0.05 100-104 0.05 105-109 0.05 110-114 0.05 115-119 0.05 120-124 0.05 125-129 0.05 130-134 0.05 135-139 0.05 140-144 0.05 145-149 0.05 150-151 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.55 #Duplication Level Percentage of deduplicated Percentage of total 1 73.340321453529 52.47500000000001 2 18.16911250873515 26.0 3 5.450733752620545 11.700000000000001 4 2.0614954577218727 5.8999999999999995 5 0.6988120195667366 2.5 6 0.17470300489168414 0.75 7 0.06988120195667365 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.034940600978336823 0.325 >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 13 0.325 No Hit CTATCATTAAGCCAAGTGTGGAGCGAGTGGCTTATGATTTGACTGAATAT 7 0.17500000000000002 No Hit AGAAAGTCCATTATTCTGCTGATGAAGCTCTAATACTAAAGCAAAAAGCA 7 0.17500000000000002 No Hit GTTTTTCGGTGGGGAACACGGGTTCGGGTTCGTGGATGCCGCCTTCGCGC 6 0.15 No Hit AGCGAACTCAACCACTGGTCTTTGTGATCCATACAAGTACCAGATACGCC 6 0.15 No Hit AGCTAACAGATCAATCCCCAAGTCAAAGAAAACCTCTCTCTGATCTTACT 6 0.15 No Hit GTATTTTGGTTGCATTAGAGGCCTTAACTTTGATAACTTGAGAAGGCTAG 6 0.15 No Hit GCCGCATCATAGCCCCTGTCTTCGCTGAGTACGCCAAGAAGTTCCCTGGT 6 0.15 No Hit GGACTAACAAAAACCATAATTGTTCAACGGCACCAAGCGTGACACTTGCA 5 0.125 No Hit CATAATCGTCTTGTAGCATCAGTCAACAATGGTAACTTCCTTGCTCACCT 5 0.125 No Hit GGAGCTGATAGTAACACTAGTGCTGGTGGTGGTGATGCAGCGAGAGCGAG 5 0.125 No Hit GCTTCTTAGAGGGACTATCGCCGTTTAGGCGACGGAAGTTTGAGGCAATA 5 0.125 No Hit CACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTT 5 0.125 No Hit CAGTATCTCTTTCCAGGACTAGAAGTAAAACAGAATGCAGGAGAGGATGC 5 0.125 No Hit GTTTTCAGATATCTGCCAGCTAAAGTTAGATCCCTTCATTTTAGAGATTC 5 0.125 No Hit GGTCCCTACAAGCCTGCTCACTACCGGTACTAGTTTGTCCAGCAAAGACT 5 0.125 No Hit CATTGGATAGATCCTAGCACCAATTCACCCTTTATTTGGTTCTCCTTAAC 5 0.125 No Hit AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 5 0.125 No Hit TGGTTTCGGATGGTGTTGTGCAAGAACAGGCAGCTCGCAATGGTGGGATC 5 0.125 No Hit GCCGAGGTCTACGCTAACGGCCGCGCCGAGGAGATCATGGGCCAGGCCAT 5 0.125 No Hit GTTCGTTCTCTCTCGCTCTCCACTCTCCTCGCGTCGCCTCCCTCTCGTCC 5 0.125 No Hit CACACAGATTGAAGAGCTAAAAATACTGATCAGGATGTTTCCAATCTGGG 5 0.125 No Hit AGCCAGGGCCTAAGGAAGTACGACTTCGACAACACCATGGGAGGCTTCTA 5 0.125 No Hit GCAAGAGCTTTTTGGAGGAATTGGCCAGGTTGGAAGGATCAAGCAAAAAC 5 0.125 No Hit CCCAGGGCTTGCGAACTACGACGGCGAGAAATGGGCGAAGCACCGGAGGA 5 0.125 No Hit GATGGATTCCACGAGCTCCATGAAGTTCCTCAACAAGGCCGCCGTGAAGG 5 0.125 No Hit GTGATAGTTACTGGAAGATGATGAGCAAGTACATAGGGTCAGATGTTACA 5 0.125 No Hit ACTGTGATTGCAAGGAGTTCAGCAATTCGACAAGATGCTGTGAACAAAGC 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 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.0875 0.0 0.0 0.0 0.0 56-57 0.1125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.2625 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.4625 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.6125 0.0 0.0 0.0 0.0 82-83 0.7875 0.0 0.0 0.0 0.0 84-85 0.8875 0.0 0.0 0.0 0.0 86-87 1.125 0.0 0.0 0.0 0.0 88-89 1.375 0.0 0.0 0.0 0.0 90-91 1.7 0.0 0.0 0.0 0.0 92-93 1.9625 0.0 0.0 0.0 0.0 94-95 2.35 0.0 0.0 0.0 0.0 96-97 2.7625 0.0 0.0 0.0 0.0 98-99 3.15 0.0 0.0 0.0 0.0 100-101 3.7125000000000004 0.0 0.0 0.0 0.0 102-103 4.0875 0.0 0.0 0.0 0.0 104-105 4.7875 0.0 0.0 0.0 0.0 106-107 5.300000000000001 0.0 0.0 0.0 0.0 108-109 5.75 0.0 0.0 0.0 0.0 110-111 6.3125 0.0 0.0 0.0 0.0 112-113 6.85 0.0 0.0 0.0 0.0 114-115 7.4125 0.0 0.0 0.0 0.0 116-117 7.8875 0.0 0.0 0.0 0.0 118-119 8.4875 0.0 0.0 0.0 0.0 120-121 9.45 0.0 0.0 0.0 0.0 122-123 10.3125 0.0 0.0 0.0 0.0 124-125 11.0625 0.0 0.0 0.0 0.0 126-127 11.875 0.0 0.0 0.0 0.0 128-129 12.925 0.0 0.0 0.0 0.0 130-131 13.774999999999999 0.0 0.0 0.0 0.0 132-133 14.6375 0.0 0.0 0.0 0.0 134-135 15.4 0.0 0.0 0.0 0.0 136-137 16.1375 0.0 0.0 0.0 0.0 138-139 17.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCAGCGG 10 0.006830828 145.0 145 TTTTCGG 10 0.006830828 145.0 3 TTTTTCG 10 0.006830828 145.0 2 GTTTTTC 10 0.006830828 145.0 1 CGGTGGG 10 0.006830828 145.0 7 TTCGGTG 10 0.006830828 145.0 5 TTTCGGT 10 0.006830828 145.0 4 >>END_MODULE Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401803 spots for SRR13165349.sra Written 1401803 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra Read 1401791 spots for SRR13165349.sra Written 1401791 spots for SRR13165349.sra SRR ids: ['SRR13165349.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qn_33s88 SRR13165349.sra spots: 28035832 blocks: [[1, 1401791], [1401792, 2803582], [2803583, 4205373], [4205374, 5607164], [5607165, 7008955], [7008956, 8410746], [8410747, 9812537], [9812538, 11214328], [11214329, 12616119], [12616120, 14017910], [14017911, 15419701], [15419702, 16821492], [16821493, 18223283], [18223284, 19625074], [19625075, 21026865], [21026866, 22428656], [22428657, 23830447], [23830448, 25232238], [25232239, 26634029], [26634030, 28035832]] SRR13165349 file size 9506101 SRR13165349 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 SRR13165349 SRR13165349_1.fastq SRR13165349_2.fastq Input file: SRR13165349_1.fastq Paired file: SRR13165349_2.fastq trimmed: SRR13165349-trimmed-pair1.fastq, SRR13165349-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 15:45:41 2024 >> started Sat Dec 7 15:46:18 2024 >> done (36.846s) 28035832 read pairs processed; of these: 541 ( 0.00%) short read pairs filtered out after trimming by size control 21449 ( 0.08%) empty read pairs filtered out after trimming by size control 28013842 (99.92%) read pairs available; of these: 5840625 (20.85%) trimmed read pairs available after processing 22173217 (79.15%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 35 0.00% 20 30 0.00% 21 60 0.00% 22 56 0.00% 23 71 0.00% 24 106 0.00% 25 79 0.00% 26 94 0.00% 27 132 0.00% 28 130 0.00% 29 134 0.00% 30 166 0.00% 31 190 0.00% 32 177 0.00% 33 177 0.00% 34 184 0.00% 35 212 0.00% 36 209 0.00% 37 200 0.00% 38 265 0.00% 39 276 0.00% 40 342 0.00% 41 398 0.00% 42 346 0.00% 43 385 0.00% 44 352 0.00% 45 405 0.00% 46 429 0.00% 47 525 0.00% 48 546 0.00% 49 670 0.00% 50 725 0.00% 51 790 0.00% 52 1005 0.00% 53 927 0.00% 54 1000 0.00% 55 1178 0.00% 56 1244 0.00% 57 1369 0.00% 58 1529 0.01% 59 1776 0.01% 60 2120 0.01% 61 2364 0.01% 62 2610 0.01% 63 3087 0.01% 64 3113 0.01% 65 3535 0.01% 66 3759 0.01% 67 4234 0.02% 68 4641 0.02% 69 5160 0.02% 70 5736 0.02% 71 6398 0.02% 72 7399 0.03% 73 8375 0.03% 74 9267 0.03% 75 10316 0.04% 76 11155 0.04% 77 12130 0.04% 78 12900 0.05% 79 14725 0.05% 80 15972 0.06% 81 17141 0.06% 82 19522 0.07% 83 21552 0.08% 84 24292 0.09% 85 26069 0.09% 86 28084 0.10% 87 29273 0.10% 88 31220 0.11% 89 32377 0.12% 90 35587 0.13% 91 37678 0.13% 92 39901 0.14% 93 42513 0.15% 94 46257 0.17% 95 48906 0.17% 96 51895 0.19% 97 53254 0.19% 98 54995 0.20% 99 57422 0.20% 100 59567 0.21% 101 61912 0.22% 102 64486 0.23% 103 66184 0.24% 104 68506 0.24% 105 70457 0.25% 106 73499 0.26% 107 74852 0.27% 108 77245 0.28% 109 78473 0.28% 110 79366 0.28% 111 82157 0.29% 112 83418 0.30% 113 84109 0.30% 114 87871 0.31% 115 90107 0.32% 116 91616 0.33% 117 91974 0.33% 118 93031 0.33% 119 94339 0.34% 120 96342 0.34% 121 96401 0.34% 122 97202 0.35% 123 99298 0.35% 124 100626 0.36% 125 101890 0.36% 126 103852 0.37% 127 104958 0.37% 128 104786 0.37% 129 106656 0.38% 130 106319 0.38% 131 106649 0.38% 132 107761 0.38% 133 108661 0.39% 134 109958 0.39% 135 110311 0.39% 136 111321 0.40% 137 109913 0.39% 138 110583 0.39% 139 112674 0.40% 140 112863 0.40% 141 112450 0.40% 142 115346 0.41% 143 114567 0.41% 144 116107 0.41% 145 117738 0.42% 146 118959 0.42% 147 124490 0.44% 148 120110 0.43% 149 122595 0.44% 150 120181 0.43% 151 22173217 79.15% 28013842 reads passed initial QC criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=2.97 fanout-score-rank=23 prefix-density=0.56 prefix-fanout=2.6 sequence=GCAGGTGCAGCTGGTGC criterion=fanout-score sequence-density=0.07 sequence-density-rank=29 fanout-score=30.57 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=7.8 sequence=TTTCTTCTCCGGCGCCATGCCGAGAACCACCACCTGGGCCTGGGTGCTGCTGGTGGTGCTGGCCTGCTCTGCCAGGTCTGGGTACATCTTCCCGCAAGTGCAGTTTGAGCCACAGTTGCAGCTTGATCCACAGCTGCAAGACATCT criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=3.32 fanout-score-rank=23 prefix-density=0.37 prefix-fanout=2.7 sequence=GCACCAGCTGCACCTGC criterion=fanout-score sequence-density=0.09 sequence-density-rank=24 fanout-score=129.36 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=21.6 sequence=CAAGAAGAAGGTGCAGACCGAGTGCGCCTCCATGCCTTTCGATGACCAATGCGCCGTCTTGGAAAAGGAGGCCGTGAACGTGTCCCTCGAGAACCTCAAGACCTACCCGTTCGTCAAGGAAGGCGTCGCCAACGGAACCCTCAAGCT SRR13165349 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:47:08 Started mapping on | Dec 07 15:47:09 Finished on | Dec 07 15:50:37 Mapping speed, Million of reads per hour | 484.85 Number of input reads | 28013842 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 26165931 Uniquely mapped reads % | 93.40% Average mapped length | 288.56 Number of splices: Total | 26398170 Number of splices: Annotated (sjdb) | 24730226 Number of splices: GT/AG | 26028311 Number of splices: GC/AG | 315147 Number of splices: AT/AC | 11261 Number of splices: Non-canonical | 43451 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.56 Insertion rate per base | 0.01% Insertion average length | 2.45 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 437662 % of reads mapped to multiple loci | 1.56% Number of reads mapped to too many loci | 71459 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.71% % of reads unmapped: other | 1.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1410574 1410574 1410574 N_multimapping 437662 437662 437662 N_noFeature 1047904 25410996 1287615 N_ambiguous 614624 4418 99589 UnstrandedReadsAssigned:24503403 PositiveStrandReadsAssigned:750517 NegativeStrandReadsAssigned:24778727 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR13165349 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: SRR13165349-trimmed-pair1.fastq SRR13165349-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,013,842 reads, 25,207,010 reads pseudoaligned [quant] estimated average fragment length: 238.425 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,227 rounds 52973 SRR13165349.ke.tsv 35125 SRR13165349.se.tsv 88098 total ==> SRR13165349.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 699.199 0 0 PNS24247 1044 806.575 65.7668 4.6441 PNS24249 1928 1690.58 228.416 7.69543 PNS24246 1044 806.575 65.7668 4.6441 PNS24248 1044 806.575 65.7668 4.6441 PNS24244 1471 1233.58 100.283 4.63022 PNS24243 293 113.073 0 0 KQK14069 1603 1365.58 1580.57 65.9232 KQK14071 474 256.745 25.6921 5.69951 ==> SRR13165349.se.tsv <== BRADI_1g14170v3 1705 BRADI_1g53295v3 130 BRADI_1g59795v3 603 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 482 BRADI_1g74790v3 702 BRADI_1g09890v3 0 BRADI_1g77505v3 329 BRADI_1g48960v3 0 SRR13165349 completed mapping pipeline successfully