Starting /dee2/code/volunteer_pipeline.sh SRR28623304 current disk space = 3049231839232 free memory = 1479464956 SRR28623304 SRAfilesize 36ad25fc48a23a60bf63a09a5c389b7f SRR28623304.sra SRR28623304.sra file validated SRR28623304 is paired end SRR28623304 is conventional basespace SRR28623304 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623304_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.523 37.0 37.0 37.0 37.0 37.0 2 36.6055 37.0 37.0 37.0 37.0 37.0 3 36.582 37.0 37.0 37.0 37.0 37.0 4 36.71 37.0 37.0 37.0 37.0 37.0 5 36.678 37.0 37.0 37.0 37.0 37.0 6 36.6745 37.0 37.0 37.0 37.0 37.0 7 36.6935 37.0 37.0 37.0 37.0 37.0 8 36.578 37.0 37.0 37.0 37.0 37.0 9 36.613 37.0 37.0 37.0 37.0 37.0 10-14 36.5851 37.0 37.0 37.0 37.0 37.0 15-19 36.5655 37.0 37.0 37.0 37.0 37.0 20-24 36.5106 37.0 37.0 37.0 37.0 37.0 25-29 36.46560000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.4354 37.0 37.0 37.0 37.0 37.0 35-39 36.379999999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.2864 37.0 37.0 37.0 37.0 37.0 45-49 36.2673 37.0 37.0 37.0 37.0 37.0 50-54 36.242399999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.10549999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.0747 37.0 37.0 37.0 37.0 37.0 65-69 36.0895 37.0 37.0 37.0 37.0 37.0 70-74 35.95440000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.950599999999994 37.0 37.0 37.0 37.0 37.0 80-84 35.8596 37.0 37.0 37.0 37.0 37.0 85-89 35.8572 37.0 37.0 37.0 37.0 37.0 90-94 35.824400000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.636 37.0 37.0 37.0 37.0 37.0 100-104 35.7282 37.0 37.0 37.0 37.0 37.0 105-109 35.7574 37.0 37.0 37.0 37.0 37.0 110-114 35.678700000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.700799999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.4422 37.0 37.0 37.0 37.0 37.0 125-129 35.3138 37.0 37.0 37.0 34.6 37.0 130-134 35.42 37.0 37.0 37.0 37.0 37.0 135-139 35.0221 37.0 37.0 37.0 27.4 37.0 140-144 34.634 37.0 37.0 37.0 25.0 37.0 145-149 34.3232 37.0 37.0 37.0 25.0 37.0 150-151 33.644 37.0 37.0 37.0 18.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 3.0 23 7.0 24 4.0 25 7.0 26 7.0 27 19.0 28 24.0 29 43.0 30 39.0 31 50.0 32 78.0 33 132.0 34 209.0 35 475.0 36 2583.0 37 320.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 24.32296890672016 9.202607823470412 11.659979939819458 54.81444332998997 2 13.450000000000001 8.9 41.85 35.8 3 12.825000000000001 11.725 29.625 45.824999999999996 4 21.65 16.35 27.1 34.9 5 23.674999999999997 24.875 28.799999999999997 22.650000000000002 6 22.675 27.35 25.5 24.474999999999998 7 18.025 27.224999999999998 36.55 18.2 8 19.275000000000002 25.5 32.025 23.200000000000003 9 17.325 22.55 34.975 25.15 10-14 20.455000000000002 28.26 27.41 23.875 15-19 20.200000000000003 26.61 28.345 24.845 20-24 21.085 26.275 27.51 25.130000000000003 25-29 20.72 26.085 26.8 26.395000000000003 30-34 20.990000000000002 25.590000000000003 26.634999999999998 26.784999999999997 35-39 20.474999999999998 26.590000000000003 26.76 26.174999999999997 40-44 21.505 26.5 26.779999999999998 25.215 45-49 21.215 26.44 27.11 25.235000000000003 50-54 20.919999999999998 27.200000000000003 26.815 25.064999999999998 55-59 20.7 26.815 27.325 25.16 60-64 21.695 25.69 26.96 25.655 65-69 19.845 26.77 27.97 25.415 70-74 21.455 26.545 26.43 25.569999999999997 75-79 21.01 27.095000000000002 25.46 26.435 80-84 21.36 27.54 25.330000000000002 25.77 85-89 21.39 27.500000000000004 24.66 26.450000000000003 90-94 20.945 27.139999999999997 26.155 25.759999999999998 95-99 20.21 27.474999999999998 26.36 25.955000000000002 100-104 21.375 28.68 24.959999999999997 24.985 105-109 21.385 28.050000000000004 24.535 26.029999999999998 110-114 22.11 27.705000000000002 24.665 25.52 115-119 21.675 27.76 24.905 25.66 120-124 21.6 28.58 24.12 25.7 125-129 22.025 28.360000000000003 23.865 25.75 130-134 21.19 28.23 24.745 25.835 135-139 22.1 28.299999999999997 23.595 26.005 140-144 21.86 28.9 22.97 26.27 145-149 22.585 27.565 23.405 26.445 150-151 22.787499999999998 27.8375 23.8375 25.5375 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 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 1.0 15 2.0 16 1.5 17 1.0 18 2.0 19 3.0 20 2.5 21 2.5 22 4.5 23 3.0 24 0.5 25 3.0 26 6.5 27 13.5 28 19.0 29 18.5 30 20.0 31 25.0 32 26.5 33 34.0 34 46.5 35 56.0 36 73.0 37 83.5 38 95.5 39 126.0 40 134.5 41 161.5 42 208.0 43 196.5 44 178.5 45 185.5 46 172.0 47 165.5 48 165.5 49 159.5 50 139.5 51 115.0 52 122.0 53 127.0 54 134.0 55 164.5 56 179.5 57 141.0 58 111.0 59 104.5 60 70.0 61 39.5 62 43.5 63 30.5 64 11.5 65 15.0 66 17.0 67 12.5 68 7.5 69 5.0 70 1.5 71 1.0 72 1.5 73 2.5 74 2.0 75 0.5 76 1.0 77 1.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.3 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 70.525 #Duplication Level Percentage of deduplicated Percentage of total 1 79.75895072669266 56.25 2 13.222261609358382 18.65 3 3.013115916341723 6.375 4 1.4533853243530663 4.1000000000000005 5 0.673520028358738 2.375 6 0.38993264799716415 1.6500000000000001 7 0.38993264799716415 1.925 8 0.24813895781637718 1.4000000000000001 9 0.24813895781637718 1.575 >10 0.6026231832683445 5.7 >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 CCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGA 22 0.5499999999999999 No Hit CCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTA 22 0.5499999999999999 No Hit GTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCT 18 0.44999999999999996 No Hit CCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGT 18 0.44999999999999996 No Hit CCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTA 14 0.35000000000000003 No Hit GTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCATCGCCTT 14 0.35000000000000003 No Hit CCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAGCTCT 12 0.3 No Hit CTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTC 12 0.3 No Hit CCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTT 12 0.3 No Hit CCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCT 11 0.27499999999999997 No Hit CCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAAT 11 0.27499999999999997 No Hit CACCCTTCCCTCACGGTACTACTTCGCTATCGGTCACCCAGGAGTATTTA 11 0.27499999999999997 No Hit CCTTCCCTCACGGTACTACTTCGCTATCGGTCACCCAGGAGTATTTAGCC 11 0.27499999999999997 No Hit CTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGCACGT 10 0.25 No Hit CTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATC 10 0.25 No Hit CCCTTCCCTCACGGTACTACTTCGCTATCGGTCACCCAGGAGTATTTAGC 10 0.25 No Hit CTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATC 10 0.25 No Hit CTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGG 9 0.22499999999999998 No Hit CTCCGATTCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCAC 9 0.22499999999999998 No Hit CTCCGCACTTGGCTACCCAGCGTTTACCGTGGGCACAATAACTGGTACAC 9 0.22499999999999998 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 9 0.22499999999999998 No Hit CTGCAGGTCGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGA 9 0.22499999999999998 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 9 0.22499999999999998 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGC 9 0.22499999999999998 No Hit CCCCTACCGATGCATTTTTACATCCCACAGCTTCGGCAGATCGCTTAGCC 8 0.2 No Hit CCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAA 8 0.2 No Hit CTCCTTTTGCTCCTCAGCCTACGGGGTATTAGCAGCCGTTTCCAGCTGTT 8 0.2 No Hit CCCAGGCGGGATACTTAACGCGTTAGCTACAGCACTGCACGGGTCGATAC 8 0.2 No Hit CTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTT 8 0.2 No Hit GTCTCTTGCCTGCCCATGGATTCGGCAGCAGTTTGAAAGGTTAACCTATT 8 0.2 No Hit GTCCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGA 8 0.2 No Hit CCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCC 7 0.17500000000000002 No Hit CTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAGT 7 0.17500000000000002 No Hit CCCTCTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCAA 7 0.17500000000000002 No Hit CACCTGACAATGTCTTCCGCCCGGATCGGCCGCCGAAGCGGCCTTGGGTC 7 0.17500000000000002 No Hit CTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTA 7 0.17500000000000002 No Hit CCCGTTTTCACGGTTTAGGCTGCTCCCATTTCGCTCGCCGCTACTACGGG 7 0.17500000000000002 No Hit CTCCCCTACCGATGCATTTTTACATCCCACAGCTTCGGCAGATCGCTTAG 7 0.17500000000000002 No Hit CCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGG 7 0.17500000000000002 No Hit ATTCCGGATAACGCTTGCATCCTCTGTATTACCGCGGCTGCTGGCACAGA 7 0.17500000000000002 No Hit CCCTAGAGTAACTTTTATCCGTTGAGCGACGGCCCTTCCACTCGGCACCG 7 0.17500000000000002 No Hit CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 7 0.17500000000000002 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 6 0.15 No Hit ATCGACTACGCCTTTCGGCCTGATCTTAGGCCCTGACTCACCCTCCGTGG 6 0.15 No Hit ATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAAT 6 0.15 No Hit CCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAAT 6 0.15 No Hit CTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGAC 6 0.15 No Hit GTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGT 6 0.15 No Hit CTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCA 6 0.15 No Hit GCTTTCTTTTCCTCTGGTTACTAAGATGTTTCAGTTCGCCAGGTTGTCTC 6 0.15 No Hit CCTCTGGTTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCTTGCCTGCCC 6 0.15 No Hit CCTGGGAGTATGGCATGGGTTACTTCAGCGCCGTAGCGCCTGGTACTCGA 6 0.15 No Hit GGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCAC 6 0.15 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 5 0.125 No Hit CACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTC 5 0.125 No Hit CCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCT 5 0.125 No Hit CCCACAACCCCGTTTTCACGGTTTAGGCTGCTCCCATTTCGCTCGCCGCT 5 0.125 No Hit CTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCC 5 0.125 No Hit CCCAGGAGTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGAT 5 0.125 No Hit GTCGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGA 5 0.125 No Hit CCCTACCGATGCATTTTTACATCCCACAGCTTCGGCAGATCGCTTAGCCC 5 0.125 No Hit GTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCA 5 0.125 No Hit CCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTG 5 0.125 No Hit CCCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTA 5 0.125 No Hit CTTGGAACATACTACAGCCCCAGGTGGCGAAGAGCCGACATCGAGGTGCC 5 0.125 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 5 0.125 No Hit CCCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGG 5 0.125 No Hit GGGAGTATGGCATGGGTTACTTCAGCGCCGTAGCGCCTGGTACTCGAACA 5 0.125 No Hit CCCGAGGTTACGGATCCATTTTGCCGACTTCCCTTGCCTACATTGTTCCA 5 0.125 No Hit CTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGCGGGATACTTAACGC 5 0.125 No Hit CCTTCCAGAAGTCGGGGTTTGTTGCACGTATTAGCTCTAGAATTACTACG 5 0.125 No Hit CTCAGTGTCAGTGTCGGCCCAGCAGAGTGCTTTCACCGTTGGTGTTCTTT 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 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.037500000000000006 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.4125 0.0 0.0 0.0 0.0 78-79 0.5125 0.0 0.0 0.0 0.0 80-81 0.775 0.0 0.0 0.0 0.0 82-83 1.0125 0.0 0.0 0.0 0.0 84-85 1.2875 0.0 0.0 0.0 0.0 86-87 1.7625 0.0 0.0 0.0 0.0 88-89 2.3 0.0 0.0 0.0 0.0 90-91 2.6 0.0 0.0 0.0 0.0 92-93 3.325 0.0 0.0 0.0 0.0 94-95 4.112500000000001 0.0 0.0 0.0 0.0 96-97 4.7625 0.0 0.0 0.0 0.0 98-99 5.6875 0.0 0.0 0.0 0.0 100-101 6.5 0.0 0.0 0.0 0.0 102-103 7.3625 0.0 0.0 0.0 0.0 104-105 8.4 0.0 0.0 0.0 0.0 106-107 9.75 0.0 0.0 0.0 0.0 108-109 11.425 0.0 0.0 0.0 0.0 110-111 12.725 0.0 0.0 0.0 0.0 112-113 13.975000000000001 0.0 0.0 0.0 0.0 114-115 15.399999999999999 0.0 0.0 0.0 0.0 116-117 17.200000000000003 0.0 0.0 0.0 0.0 118-119 18.825000000000003 0.0 0.0 0.0 0.0 120-121 20.725 0.0 0.0 0.0 0.0 122-123 22.55 0.0 0.0 0.0 0.0 124-125 24.2125 0.0 0.0 0.0 0.0 126-127 25.8375 0.0 0.0 0.0 0.0 128-129 27.512500000000003 0.0 0.0 0.0 0.0 130-131 29.799999999999997 0.0 0.0 0.0 0.0 132-133 32.1125 0.0 0.0 0.0 0.0 134-135 34.275 0.0 0.0 0.0 0.0 136-137 36.825 0.0 0.0 0.0 0.0 138-139 39.1875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCGTTT 10 0.006830828 145.0 1 TTTCAAA 20 0.00593511 29.0 15-19 CGTACCA 80 0.0020131238 12.6875 140-144 CAGTCAC 90 0.0048656333 11.277777 130-134 GTACCAT 90 0.0048656333 11.277777 140-144 ACTTCGT 90 0.0048656333 11.277777 135-139 CACTTCG 90 0.0048656333 11.277777 135-139 >>END_MODULE SRR28623304 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623304_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.418 37.0 37.0 37.0 37.0 37.0 2 36.5455 37.0 37.0 37.0 37.0 37.0 3 36.5635 37.0 37.0 37.0 37.0 37.0 4 36.6165 37.0 37.0 37.0 37.0 37.0 5 36.566 37.0 37.0 37.0 37.0 37.0 6 36.554 37.0 37.0 37.0 37.0 37.0 7 36.582 37.0 37.0 37.0 37.0 37.0 8 36.592 37.0 37.0 37.0 37.0 37.0 9 36.5095 37.0 37.0 37.0 37.0 37.0 10-14 36.5032 37.0 37.0 37.0 37.0 37.0 15-19 36.5316 37.0 37.0 37.0 37.0 37.0 20-24 36.4752 37.0 37.0 37.0 37.0 37.0 25-29 36.493 37.0 37.0 37.0 37.0 37.0 30-34 36.3994 37.0 37.0 37.0 37.0 37.0 35-39 36.4112 37.0 37.0 37.0 37.0 37.0 40-44 36.408100000000005 37.0 37.0 37.0 37.0 37.0 45-49 36.3559 37.0 37.0 37.0 37.0 37.0 50-54 36.3798 37.0 37.0 37.0 37.0 37.0 55-59 36.326 37.0 37.0 37.0 37.0 37.0 60-64 36.3183 37.0 37.0 37.0 37.0 37.0 65-69 36.305899999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.2544 37.0 37.0 37.0 37.0 37.0 75-79 36.3352 37.0 37.0 37.0 37.0 37.0 80-84 36.2406 37.0 37.0 37.0 37.0 37.0 85-89 36.206 37.0 37.0 37.0 37.0 37.0 90-94 36.13590000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.120000000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.0603 37.0 37.0 37.0 37.0 37.0 105-109 36.0752 37.0 37.0 37.0 37.0 37.0 110-114 36.0769 37.0 37.0 37.0 37.0 37.0 115-119 36.0425 37.0 37.0 37.0 37.0 37.0 120-124 36.1052 37.0 37.0 37.0 37.0 37.0 125-129 35.6408 37.0 37.0 37.0 37.0 37.0 130-134 35.8583 37.0 37.0 37.0 37.0 37.0 135-139 35.6451 37.0 37.0 37.0 37.0 37.0 140-144 35.6994 37.0 37.0 37.0 37.0 37.0 145-149 35.5704 37.0 37.0 37.0 37.0 37.0 150-151 35.343 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 3.0 15 1.0 16 0.0 17 1.0 18 0.0 19 0.0 20 0.0 21 4.0 22 2.0 23 5.0 24 3.0 25 3.0 26 4.0 27 10.0 28 7.0 29 17.0 30 14.0 31 30.0 32 37.0 33 63.0 34 122.0 35 382.0 36 2831.0 37 458.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.525 19.05 13.275 30.15 2 27.525 27.35 28.425 16.7 3 23.150000000000002 26.525 28.925 21.4 4 26.6 30.375000000000004 23.525 19.5 5 29.525000000000002 30.9 20.724999999999998 18.85 6 24.95 35.425000000000004 21.475 18.15 7 25.124999999999996 20.375 36.0 18.5 8 25.1 25.775 26.424999999999997 22.7 9 27.1 21.925 27.1 23.875 10-14 26.685 27.16 24.63 21.525 15-19 25.995 26.634999999999998 25.89 21.48 20-24 26.99 26.3 26.31 20.4 25-29 26.135 27.195000000000004 25.840000000000003 20.830000000000002 30-34 26.755000000000003 26.61 25.480000000000004 21.154999999999998 35-39 25.655 27.505000000000003 25.515 21.325 40-44 26.63 26.105 26.365 20.9 45-49 26.52 26.25 26.619999999999997 20.61 50-54 26.455000000000002 26.195 27.139999999999997 20.21 55-59 25.435000000000002 26.565 27.465 20.535 60-64 26.025 25.695 27.315 20.965 65-69 26.1 27.055 26.295 20.549999999999997 70-74 25.75 26.88 26.584999999999997 20.785 75-79 26.055 27.13 26.009999999999998 20.805 80-84 26.33 27.04 25.779999999999998 20.849999999999998 85-89 26.13 27.275 25.61 20.985 90-94 26.119999999999997 26.784999999999997 26.810000000000002 20.285 95-99 26.58 27.175 25.41 20.835 100-104 27.284999999999997 26.895000000000003 26.31 19.509999999999998 105-109 28.025 27.455000000000002 25.665 18.855 110-114 27.045 28.42 25.21 19.325 115-119 29.28 27.584999999999997 24.66 18.475 120-124 29.235 28.060000000000002 24.935 17.77 125-129 29.375 27.560000000000002 24.79 18.275 130-134 30.220000000000002 28.1 24.610000000000003 17.07 135-139 30.28 27.495000000000005 25.345000000000002 16.88 140-144 31.0 28.015 24.38 16.605 145-149 31.480000000000004 26.775 24.815 16.93 150-151 32.074999999999996 26.950000000000003 25.2375 15.737499999999999 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 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 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 1.0 22 1.0 23 0.5 24 0.5 25 1.5 26 5.5 27 7.5 28 9.5 29 11.5 30 17.5 31 21.5 32 27.5 33 38.0 34 51.5 35 85.0 36 91.0 37 90.5 38 105.5 39 125.0 40 146.5 41 156.5 42 165.5 43 177.5 44 192.5 45 187.0 46 168.0 47 178.5 48 177.5 49 148.5 50 121.5 51 101.0 52 120.5 53 160.0 54 169.5 55 161.5 56 160.0 57 136.5 58 97.5 59 71.5 60 62.5 61 45.5 62 28.5 63 25.0 64 18.5 65 15.0 66 16.0 67 11.0 68 11.0 69 20.0 70 16.0 71 8.0 72 7.0 73 5.0 74 1.5 75 2.5 76 3.0 77 0.5 78 0.5 79 2.0 80 1.5 81 0.0 82 1.0 83 1.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.5 89 0.5 90 0.0 91 0.0 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.625 #Duplication Level Percentage of deduplicated Percentage of total 1 80.38647342995169 62.4 2 14.138486312399356 21.95 3 3.7037037037037033 8.625 4 1.030595813204509 3.2 5 0.4830917874396135 1.875 6 0.06441223832528181 0.3 7 0.032206119162640906 0.17500000000000002 8 0.06441223832528181 0.4 9 0.0 0.0 >10 0.0966183574879227 1.075 >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 GGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCC 15 0.375 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 14 0.35000000000000003 No Hit GTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATAC 14 0.35000000000000003 No Hit CATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTT 8 0.2 No Hit CTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGT 8 0.2 No Hit CGTTATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTT 7 0.17500000000000002 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTCTATAGCC 6 0.15 No Hit GTATGAACTAATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTT 6 0.15 No Hit GCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTG 5 0.125 No Hit CGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACA 5 0.125 No Hit GGCTTACGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGTAAG 5 0.125 No Hit GTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTC 5 0.125 No Hit TGAAAATAAGCGTAGATCCGGAGATTCCCGAATAGGTTAACCTTTCAAAC 5 0.125 No Hit GAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGA 5 0.125 No Hit TTTCAAACTGCTGCCGAATCCATGGGCAGGCAAGAGACAACCTGGCGAAC 5 0.125 No Hit CACGAGGCGCTGTCTGCGAGTCGGGTTGTTTGGGAATGCAGCCCCAATCG 5 0.125 No Hit GCTAGTTGGTGAGGCAATAGCTTACCAAGGCGATGATCAGTAGCTGGTCC 5 0.125 No Hit GAGCAAAAGGAGGAATCCGCCCGAGGAGGGGCTCGCGTCTGATTAGCTAG 5 0.125 No Hit GGATTAGATACCCCAGTAGTCCTAGCCGTAAACGATGGATACTGGGCGCT 5 0.125 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 5 0.125 No Hit GTGAGAGCCCCGTCGTGGCTGGACCCTGCCGCACCACGAGGCGCTGTCTG 5 0.125 No Hit GGGTGAGAGCCCCGTCGTGGCTGGACCCTGCCGCACCACGAGGCGCTGTC 5 0.125 No Hit GTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATG 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 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.037500000000000006 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.4125 0.0 0.0 0.0 0.0 78-79 0.5375 0.0 0.0 0.0 0.0 80-81 0.8 0.0 0.0 0.0 0.0 82-83 1.0375 0.0 0.0 0.0 0.0 84-85 1.3375 0.0 0.0 0.0 0.0 86-87 1.8125 0.0 0.0 0.0 0.0 88-89 2.325 0.0 0.0 0.0 0.0 90-91 2.6125 0.0 0.0 0.0 0.0 92-93 3.325 0.0 0.0 0.0 0.0 94-95 4.112500000000001 0.0 0.0 0.0 0.0 96-97 4.7625 0.0 0.0 0.0 0.0 98-99 5.7 0.0 0.0 0.0 0.0 100-101 6.512499999999999 0.0 0.0 0.0 0.0 102-103 7.3875 0.0 0.0 0.0 0.0 104-105 8.425 0.0 0.0 0.0 0.0 106-107 9.775 0.0 0.0 0.0 0.0 108-109 11.45 0.0 0.0 0.0 0.0 110-111 12.725 0.0 0.0 0.0 0.0 112-113 13.9625 0.0 0.0 0.0 0.0 114-115 15.4125 0.0 0.0 0.0 0.0 116-117 17.225 0.0 0.0 0.0 0.0 118-119 18.85 0.0 0.0 0.0 0.0 120-121 20.8125 0.0 0.0 0.0 0.0 122-123 22.625 0.0 0.0 0.0 0.0 124-125 24.2875 0.0 0.0 0.0 0.0 126-127 25.975 0.0 0.0 0.0 0.0 128-129 27.7125 0.0 0.0 0.0 0.0 130-131 30.0625 0.0 0.0 0.0 0.0 132-133 32.425 0.0 0.0 0.0 0.0 134-135 34.6125 0.0 0.0 0.0 0.0 136-137 37.2625 0.0 0.0 0.0 0.0 138-139 39.6375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGGTTTG 10 0.006830828 145.0 7 ATCACTA 10 0.006830828 145.0 4 >>END_MODULE Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032611 spots for SRR28623304.sra Written 1032611 spots for SRR28623304.sra Read 1032616 spots for SRR28623304.sra Written 1032616 spots for SRR28623304.sra SRR ids: ['SRR28623304.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zwgkgqg3 SRR28623304.sra spots: 20652225 blocks: [[1, 1032611], [1032612, 2065222], [2065223, 3097833], [3097834, 4130444], [4130445, 5163055], [5163056, 6195666], [6195667, 7228277], [7228278, 8260888], [8260889, 9293499], [9293500, 10326110], [10326111, 11358721], [11358722, 12391332], [12391333, 13423943], [13423944, 14456554], [14456555, 15489165], [15489166, 16521776], [16521777, 17554387], [17554388, 18586998], [18586999, 19619609], [19619610, 20652225]] SRR28623304 file size 7622103 SRR28623304 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 SRR28623304 SRR28623304_1.fastq SRR28623304_2.fastq Input file: SRR28623304_1.fastq Paired file: SRR28623304_2.fastq trimmed: SRR28623304-trimmed-pair1.fastq, SRR28623304-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 Tue Feb 11 16:11:52 2025 >> started Tue Feb 11 16:12:26 2025 >> done (33.331s) 20652225 read pairs processed; of these: 19 ( 0.00%) short read pairs filtered out after trimming by size control 30461 ( 0.15%) empty read pairs filtered out after trimming by size control 20621745 (99.85%) read pairs available; of these: 11236467 (54.49%) trimmed read pairs available after processing 9385278 (45.51%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 1 0.00% 20 4 0.00% 21 0 0.00% 22 0 0.00% 23 1 0.00% 24 2 0.00% 25 6 0.00% 26 10 0.00% 27 7 0.00% 28 6 0.00% 29 9 0.00% 30 10 0.00% 31 22 0.00% 32 15 0.00% 33 29 0.00% 34 31 0.00% 35 36 0.00% 36 36 0.00% 37 36 0.00% 38 50 0.00% 39 72 0.00% 40 74 0.00% 41 85 0.00% 42 128 0.00% 43 117 0.00% 44 133 0.00% 45 124 0.00% 46 169 0.00% 47 189 0.00% 48 189 0.00% 49 232 0.00% 50 241 0.00% 51 304 0.00% 52 324 0.00% 53 468 0.00% 54 503 0.00% 55 568 0.00% 56 695 0.00% 57 768 0.00% 58 930 0.00% 59 1043 0.01% 60 1274 0.01% 61 1421 0.01% 62 1806 0.01% 63 2077 0.01% 64 2318 0.01% 65 2713 0.01% 66 3201 0.02% 67 3530 0.02% 68 4312 0.02% 69 4604 0.02% 70 5428 0.03% 71 6325 0.03% 72 7564 0.04% 73 9276 0.04% 74 10120 0.05% 75 10919 0.05% 76 12751 0.06% 77 14593 0.07% 78 15694 0.08% 79 18608 0.09% 80 20622 0.10% 81 23866 0.12% 82 25415 0.12% 83 29725 0.14% 84 33540 0.16% 85 37041 0.18% 86 40440 0.20% 87 46141 0.22% 88 47428 0.23% 89 51427 0.25% 90 54268 0.26% 91 62455 0.30% 92 66079 0.32% 93 72188 0.35% 94 78503 0.38% 95 80537 0.39% 96 82131 0.40% 97 81262 0.39% 98 86507 0.42% 99 88858 0.43% 100 92676 0.45% 101 101397 0.49% 102 113233 0.55% 103 109582 0.53% 104 117353 0.57% 105 119615 0.58% 106 120354 0.58% 107 128849 0.62% 108 126870 0.62% 109 139388 0.68% 110 148554 0.72% 111 141298 0.69% 112 151897 0.74% 113 148135 0.72% 114 165684 0.80% 115 170117 0.82% 116 168542 0.82% 117 177411 0.86% 118 173543 0.84% 119 177766 0.86% 120 184960 0.90% 121 183870 0.89% 122 189371 0.92% 123 199281 0.97% 124 204399 0.99% 125 214265 1.04% 126 206300 1.00% 127 205367 1.00% 128 223518 1.08% 129 210970 1.02% 130 220146 1.07% 131 230556 1.12% 132 252108 1.22% 133 239924 1.16% 134 246313 1.19% 135 266498 1.29% 136 253729 1.23% 137 249909 1.21% 138 249440 1.21% 139 247638 1.20% 140 243080 1.18% 141 244102 1.18% 142 261166 1.27% 143 249377 1.21% 144 251108 1.22% 145 240287 1.17% 146 234063 1.14% 147 247332 1.20% 148 238115 1.15% 149 248778 1.21% 150 253599 1.23% 151 9385278 45.51% 20621745 reads passed initial QC criterion=sequence-density sequence-density=3.55 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=32 prefix-density=3.52 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=32.67 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=1.0 sequence=AGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGAC criterion=sequence-density sequence-density=3.44 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=28 prefix-density=3.51 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=91.11 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=1.1 sequence=GTGAGACAGGTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAACCTAGTACGAG Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GTATTTAGCCTTG -y CAAGGCTAAATAC -o SRR28623304 SRR28623304_1.fastq SRR28623304_2.fastq Input file: SRR28623304_1.fastq Paired file: SRR28623304_2.fastq trimmed: SRR28623304-trimmed-pair1.fastq, SRR28623304-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): GTATTTAGCCTTG -- paired 3' end adapter sequence (-y): CAAGGCTAAATAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 16:14:10 2025 >> started Tue Feb 11 16:14:19 2025 >> done (9.098s) 10310873 read pairs processed; of these: 5433 ( 0.05%) short read pairs filtered out after trimming by size control 334 ( 0.00%) empty read pairs filtered out after trimming by size control 10305106 (99.94%) read pairs available; of these: 59 ( 0.00%) trimmed read pairs available after processing 10305047 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 1 0.00% 20 3 0.00% 21 0 0.00% 22 0 0.00% 23 1 0.00% 24 2 0.00% 25 2 0.00% 26 2 0.00% 27 4 0.00% 28 3 0.00% 29 3 0.00% 30 5 0.00% 31 13 0.00% 32 8 0.00% 33 13 0.00% 34 16 0.00% 35 14 0.00% 36 14 0.00% 37 21 0.00% 38 23 0.00% 39 37 0.00% 40 35 0.00% 41 43 0.00% 42 64 0.00% 43 62 0.00% 44 62 0.00% 45 63 0.00% 46 70 0.00% 47 98 0.00% 48 105 0.00% 49 130 0.00% 50 101 0.00% 51 159 0.00% 52 146 0.00% 53 238 0.00% 54 245 0.00% 55 269 0.00% 56 370 0.00% 57 389 0.00% 58 458 0.00% 59 524 0.01% 60 645 0.01% 61 667 0.01% 62 907 0.01% 63 1024 0.01% 64 1192 0.01% 65 1383 0.01% 66 1600 0.02% 67 1738 0.02% 68 2146 0.02% 69 2256 0.02% 70 2768 0.03% 71 3149 0.03% 72 3865 0.04% 73 4582 0.04% 74 5026 0.05% 75 5517 0.05% 76 6426 0.06% 77 7329 0.07% 78 7818 0.08% 79 9268 0.09% 80 10406 0.10% 81 11839 0.11% 82 12671 0.12% 83 14959 0.15% 84 16805 0.16% 85 18536 0.18% 86 20096 0.20% 87 23177 0.22% 88 23750 0.23% 89 25863 0.25% 90 27086 0.26% 91 31275 0.30% 92 33033 0.32% 93 36371 0.35% 94 39126 0.38% 95 40136 0.39% 96 40945 0.40% 97 40474 0.39% 98 42967 0.42% 99 44343 0.43% 100 46604 0.45% 101 50839 0.49% 102 56849 0.55% 103 54773 0.53% 104 58861 0.57% 105 59516 0.58% 106 60225 0.58% 107 64418 0.63% 108 63449 0.62% 109 69384 0.67% 110 73508 0.71% 111 70537 0.68% 112 75919 0.74% 113 74014 0.72% 114 82982 0.81% 115 85066 0.83% 116 84037 0.82% 117 88302 0.86% 118 85920 0.83% 119 89054 0.86% 120 92215 0.89% 121 91637 0.89% 122 94576 0.92% 123 99778 0.97% 124 102392 0.99% 125 107297 1.04% 126 103285 1.00% 127 102634 1.00% 128 111995 1.09% 129 105269 1.02% 130 108967 1.06% 131 114044 1.11% 132 125859 1.22% 133 120050 1.16% 134 123201 1.20% 135 132804 1.29% 136 126624 1.23% 137 125226 1.22% 138 124494 1.21% 139 123745 1.20% 140 121732 1.18% 141 122164 1.19% 142 130231 1.26% 143 124243 1.21% 144 126011 1.22% 145 120096 1.17% 146 116959 1.13% 147 123881 1.20% 148 118978 1.15% 149 123829 1.20% 150 126741 1.23% 151 4692912 45.54% criterion=sequence-density sequence-density=3.42 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=3.42 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=46.17 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=1.0 sequence=CCAGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGAC criterion=sequence-density sequence-density=3.30 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=29 prefix-density=3.37 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=99.76 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=1.0 sequence=CGTGAGACAGGTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAACCTAGTACGAG SRR28623304 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 16:15:10 Started mapping on | Feb 11 16:15:10 Finished on | Feb 11 16:18:20 Mapping speed, Million of reads per hour | 390.62 Number of input reads | 20615978 Average input read length | 272 UNIQUE READS: Uniquely mapped reads number | 13645166 Uniquely mapped reads % | 66.19% Average mapped length | 277.11 Number of splices: Total | 8384172 Number of splices: Annotated (sjdb) | 8146880 Number of splices: GT/AG | 8216316 Number of splices: GC/AG | 120506 Number of splices: AT/AC | 9546 Number of splices: Non-canonical | 37804 Mismatch rate per base, % | 0.56% Deletion rate per base | 0.03% Deletion average length | 2.80 Insertion rate per base | 0.08% Insertion average length | 3.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1436323 % of reads mapped to multiple loci | 6.97% Number of reads mapped to too many loci | 4704144 % of reads mapped to too many loci | 22.82% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.48% % of reads unmapped: other | 1.55% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5534489 5534489 5534489 N_multimapping 1436323 1436323 1436323 N_noFeature 2722415 13244038 2861027 N_ambiguous 333182 3801 67162 UnstrandedReadsAssigned:10589569 PositiveStrandReadsAssigned:397327 NegativeStrandReadsAssigned:10716977 Dataset is classified negative stranded MeadianReadLen=147 20thPercentileLength=120 echo kmer=115 SRR28623304 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR28623304-trimmed-pair1.fastq SRR28623304-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,615,978 reads, 13,211,304 reads pseudoaligned [quant] estimated average fragment length: 149.952 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,101 rounds 52401 SRR28623304.ke.tsv 34699 SRR28623304.se.tsv 87100 total ==> SRR28623304.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1869.05 2424 57.3755 Potri.005G024800.1.v4.1 1035 886.048 315 15.7278 Potri.004G059700.1.v4.1 961 812.048 18 0.980629 Potri.007G009000.2.v4.1 1416 1267.05 0 0 Potri.003G141000.2.v4.1 2943 2794.05 805.083 12.7474 Potri.016G087400.1.v4.1 270 121.339 377.372 137.589 Potri.015G069301.1.v4.1 564 415.075 0 0 Potri.010G195200.1.v4.1 1773 1624.05 470.993 12.8301 Potri.012G127500.1.v4.1 977 828.048 33 1.76308 ==> SRR28623304.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 23 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 101 Potri.001G212900.v4.1 15 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 313 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR28623304 completed mapping pipeline successfully