Starting /dee2/code/volunteer_pipeline.sh SRR12670176 current disk space = 3055681847296 free memory = 1149550064 SRR12670176 SRAfilesize e10cba0efd1fc0677988cf27df6e67a6 SRR12670176.sra SRR12670176.sra file validated SRR12670176 is paired end SRR12670176 is conventional basespace SRR12670176 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670176_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6525 37.0 37.0 37.0 37.0 37.0 2 36.4815 37.0 37.0 37.0 37.0 37.0 3 36.6455 37.0 37.0 37.0 37.0 37.0 4 36.6135 37.0 37.0 37.0 37.0 37.0 5 36.7475 37.0 37.0 37.0 37.0 37.0 6 36.649 37.0 37.0 37.0 37.0 37.0 7 36.561 37.0 37.0 37.0 37.0 37.0 8 36.6115 37.0 37.0 37.0 37.0 37.0 9 36.648 37.0 37.0 37.0 37.0 37.0 10-14 36.646 37.0 37.0 37.0 37.0 37.0 15-19 36.6006 37.0 37.0 37.0 37.0 37.0 20-24 36.5544 37.0 37.0 37.0 37.0 37.0 25-29 36.560900000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.555 37.0 37.0 37.0 37.0 37.0 35-39 36.5077 37.0 37.0 37.0 37.0 37.0 40-44 36.478699999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.49210000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.4113 37.0 37.0 37.0 37.0 37.0 55-59 36.403 37.0 37.0 37.0 37.0 37.0 60-64 36.404999999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.34 37.0 37.0 37.0 37.0 37.0 70-74 36.3438 37.0 37.0 37.0 37.0 37.0 75-79 36.277100000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.3147 37.0 37.0 37.0 37.0 37.0 85-89 36.286 37.0 37.0 37.0 37.0 37.0 90-94 36.289300000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.28529999999999 37.0 37.0 37.0 37.0 37.0 100-104 36.2248 37.0 37.0 37.0 37.0 37.0 105-109 36.219199999999994 37.0 37.0 37.0 37.0 37.0 110-114 36.1778 37.0 37.0 37.0 37.0 37.0 115-119 36.2557 37.0 37.0 37.0 37.0 37.0 120-124 36.1368 37.0 37.0 37.0 37.0 37.0 125-129 36.059999999999995 37.0 37.0 37.0 37.0 37.0 130-134 36.0781 37.0 37.0 37.0 37.0 37.0 135-139 35.9928 37.0 37.0 37.0 37.0 37.0 140-144 35.87259999999999 37.0 37.0 37.0 37.0 37.0 145-149 35.773199999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.547 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 1.0 20 0.0 21 0.0 22 0.0 23 1.0 24 2.0 25 4.0 26 1.0 27 0.0 28 13.0 29 12.0 30 18.0 31 32.0 32 49.0 33 60.0 34 128.0 35 298.0 36 2962.0 37 418.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.275 11.0 8.55 41.175 2 20.902255639097746 12.68170426065163 35.31328320802005 31.102756892230577 3 18.4 16.875 27.05 37.675 4 22.95 24.349999999999998 23.45 29.25 5 23.125 28.999999999999996 24.349999999999998 23.525 6 21.65 34.599999999999994 23.25 20.5 7 16.525000000000002 26.075 40.625 16.775000000000002 8 18.025 25.275 32.375 24.325 9 16.875 23.425 35.725 23.974999999999998 10-14 20.4 28.935 27.455000000000002 23.21 15-19 20.8 27.779999999999998 27.565 23.855 20-24 20.435 28.435 27.615000000000002 23.515 25-29 20.505000000000003 27.205000000000002 27.785 24.505 30-34 20.169999999999998 28.16 27.87 23.799999999999997 35-39 20.745 27.794999999999998 27.62 23.84 40-44 21.105 28.415000000000003 26.775 23.705000000000002 45-49 21.22 28.15 26.840000000000003 23.79 50-54 20.455000000000002 27.595 27.665 24.285 55-59 21.11 27.405 27.125 24.36 60-64 21.33 28.335 26.955000000000002 23.380000000000003 65-69 20.71 27.08 28.165000000000003 24.044999999999998 70-74 21.025 27.805000000000003 27.16 24.01 75-79 21.135 27.52 27.865000000000002 23.48 80-84 21.385 27.99 26.665 23.96 85-89 21.33 27.400000000000002 27.175 24.095 90-94 20.849999999999998 27.83 27.13 24.19 95-99 22.025 27.235 26.950000000000003 23.79 100-104 21.92 28.07 26.625 23.385 105-109 22.105 28.225 26.21 23.46 110-114 21.63 27.794999999999998 26.779999999999998 23.794999999999998 115-119 22.115000000000002 27.339999999999996 26.279999999999998 24.265 120-124 21.375 27.755000000000003 26.229999999999997 24.64 125-129 22.075 28.205000000000002 25.485000000000003 24.235 130-134 21.715 27.22 25.64 25.424999999999997 135-139 21.37 27.644999999999996 25.814999999999998 25.169999999999998 140-144 21.6 26.895000000000003 26.3 25.205 145-149 20.87 26.575 26.334999999999997 26.22 150-151 21.837500000000002 26.5875 26.375 25.2 >>END_MODULE >>Per sequence GC content pass #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 0.5 15 0.5 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 0.5 25 1.0 26 0.5 27 2.0 28 6.0 29 7.5 30 10.0 31 14.5 32 22.0 33 35.0 34 46.5 35 54.0 36 74.0 37 87.5 38 97.5 39 123.5 40 167.0 41 205.0 42 218.0 43 249.5 44 266.0 45 274.0 46 272.0 47 249.0 48 230.5 49 231.5 50 211.0 51 161.5 52 137.0 53 126.5 54 104.0 55 66.0 56 54.0 57 59.5 58 44.5 59 29.5 60 28.0 61 16.5 62 6.5 63 4.0 64 3.0 65 1.0 66 1.0 67 1.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 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 0.0 2 0.25 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 80.27499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 81.62566178760511 65.525 2 14.107754593584554 22.650000000000002 3 2.9274369355341014 7.049999999999999 4 0.9342883836810962 3.0 5 0.3114294612270321 1.25 6 0.03114294612270321 0.15 7 0.03114294612270321 0.17500000000000002 8 0.03114294612270321 0.2 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 CCTGCATTTACAATGAACTTCATTAACTGGAAGAATTTAAATAGGAGTGA 8 0.2 No Hit CCCATCTGCAGTGAATGAGTTCGGACTCCTTGTATCTCTCCAGATTCTCA 7 0.17500000000000002 No Hit CTCTGTTCTTCATTAAACTTCCTTTGTTGCATCGGCAACAATAAGTTCAT 6 0.15 No Hit CAACCTTTGAGCCAAGGGCAGCAGCACCAATGAGCACAGTGAGTGCCAAT 5 0.125 No Hit CACGCCCTCGGAACTCAACAAAAACCTCTAGTGGCGCTTTTCCACCTCCA 5 0.125 No Hit TACGTCCAGAGTTTTCTTTCTTCTACTCAGAGTCAGAGTCTATATTTCCC 5 0.125 No Hit CTCCTTTTTCGCCTTTTGCAATCCCACCCTCTCATATTCGTTTAGGGGAC 5 0.125 No Hit CTCTTCTCCTAGCATACTCATATGCAAGATACTCGCCAATGCCTGAGGAT 5 0.125 No Hit CGACAGCTTTACATAACAAGGCATGCTCTCAAGTGCCCAGAGTAAATTAT 5 0.125 No Hit GGCAAAAGTTGGAGGTAAAAATCAGGGTTTTCGGTGGCAGGATCTTTTTT 5 0.125 No Hit TCTTCATCTTCCTGGAATGGAATTTGCTACAAGCGAGAGAGATATGAGTT 5 0.125 No Hit GTCCACATCCTTCCCTTCTAGTCCTTCTCCTTGAGTAAATGCATCATTTA 5 0.125 No Hit GGCGACGTTTTCTCATTTGCAGGAGCATGGATCACAGGTGCAGTTTGATC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.037500000000000006 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.32499999999999996 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.475 0.0 0.0 0.0 0.0 78-79 0.6125 0.0 0.0 0.0 0.0 80-81 0.675 0.0 0.0 0.0 0.0 82-83 0.775 0.0 0.0 0.0 0.0 84-85 0.875 0.0 0.0 0.0 0.0 86-87 1.225 0.0 0.0 0.0 0.0 88-89 1.3625 0.0 0.0 0.0 0.0 90-91 1.625 0.0 0.0 0.0 0.0 92-93 2.1 0.0 0.0 0.0 0.0 94-95 2.6125 0.0 0.0 0.0 0.0 96-97 3.25 0.0 0.0 0.0 0.0 98-99 3.775 0.0 0.0 0.0 0.0 100-101 4.2875 0.0 0.0 0.0 0.0 102-103 4.9875 0.0 0.0 0.0 0.0 104-105 5.8875 0.0 0.0 0.0 0.0 106-107 6.8 0.0 0.0 0.0 0.0 108-109 7.5625 0.0 0.0 0.0 0.0 110-111 8.4125 0.0 0.0 0.0 0.0 112-113 9.2625 0.0 0.0 0.0 0.0 114-115 10.4 0.0 0.0 0.0 0.0 116-117 11.475 0.0 0.0 0.0 0.0 118-119 12.425 0.0 0.0 0.0 0.0 120-121 12.9375 0.0 0.0 0.0 0.0 122-123 13.875 0.0 0.0 0.0 0.0 124-125 14.7375 0.0 0.0 0.0 0.0 126-127 15.575 0.0 0.0 0.0 0.0 128-129 16.487499999999997 0.0 0.0 0.0 0.0 130-131 17.4625 0.0 0.0 0.0 0.0 132-133 18.525 0.0 0.0 0.0 0.0 134-135 19.575 0.0 0.0 0.0 0.0 136-137 20.4875 0.0 0.0 0.0 0.0 138-139 21.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTCTAG 10 0.006830828 145.0 3 GGAAGAG 95 0.007278115 10.684211 140-144 >>END_MODULE SRR12670176 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670176_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.397 37.0 37.0 37.0 37.0 37.0 2 36.3745 37.0 37.0 37.0 37.0 37.0 3 36.304 37.0 37.0 37.0 37.0 37.0 4 36.3275 37.0 37.0 37.0 37.0 37.0 5 36.428 37.0 37.0 37.0 37.0 37.0 6 36.349 37.0 37.0 37.0 37.0 37.0 7 36.3555 37.0 37.0 37.0 37.0 37.0 8 36.395 37.0 37.0 37.0 37.0 37.0 9 36.3925 37.0 37.0 37.0 37.0 37.0 10-14 36.4004 37.0 37.0 37.0 37.0 37.0 15-19 36.3875 37.0 37.0 37.0 37.0 37.0 20-24 36.325700000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.305 37.0 37.0 37.0 37.0 37.0 30-34 36.29350000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.263 37.0 37.0 37.0 37.0 37.0 40-44 36.2332 37.0 37.0 37.0 37.0 37.0 45-49 36.25410000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.244800000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.16160000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.1622 37.0 37.0 37.0 37.0 37.0 65-69 36.1383 37.0 37.0 37.0 37.0 37.0 70-74 36.15989999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.1505 37.0 37.0 37.0 37.0 37.0 80-84 36.0825 37.0 37.0 37.0 37.0 37.0 85-89 36.0493 37.0 37.0 37.0 37.0 37.0 90-94 36.1016 37.0 37.0 37.0 37.0 37.0 95-99 36.041700000000006 37.0 37.0 37.0 37.0 37.0 100-104 36.016000000000005 37.0 37.0 37.0 37.0 37.0 105-109 36.013999999999996 37.0 37.0 37.0 37.0 37.0 110-114 35.9065 37.0 37.0 37.0 37.0 37.0 115-119 35.924699999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.7464 37.0 37.0 37.0 37.0 37.0 125-129 35.6476 37.0 37.0 37.0 37.0 37.0 130-134 35.415499999999994 37.0 37.0 37.0 34.6 37.0 135-139 35.3409 37.0 37.0 37.0 37.0 37.0 140-144 34.9707 37.0 37.0 37.0 25.0 37.0 145-149 34.604 37.0 37.0 37.0 25.0 37.0 150-151 34.15025 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 4.0 14 2.0 15 2.0 16 1.0 17 0.0 18 3.0 19 0.0 20 2.0 21 1.0 22 4.0 23 3.0 24 3.0 25 5.0 26 8.0 27 9.0 28 13.0 29 18.0 30 25.0 31 39.0 32 46.0 33 98.0 34 180.0 35 520.0 36 2669.0 37 344.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.574999999999996 21.425 11.65 29.349999999999998 2 27.200000000000003 26.1 28.749999999999996 17.95 3 22.625 28.7 28.975 19.7 4 25.224999999999998 32.85 21.875 20.05 5 24.6 34.150000000000006 22.45 18.8 6 21.725 38.125 23.474999999999998 16.675 7 20.349999999999998 22.525000000000002 36.75 20.375 8 22.825 25.1 27.200000000000003 24.875 9 21.8 25.55 30.125 22.525000000000002 10-14 23.97 28.485 25.15 22.395 15-19 23.74 27.735 27.01 21.515 20-24 24.490000000000002 28.389999999999997 26.265 20.855 25-29 24.125 28.04 26.779999999999998 21.055 30-34 23.735 28.08 27.145000000000003 21.04 35-39 24.02 27.900000000000002 26.284999999999997 21.795 40-44 23.965 28.139999999999997 26.96 20.935000000000002 45-49 23.385 28.01 27.025 21.58 50-54 24.39 28.384999999999998 26.575 20.65 55-59 23.799999999999997 27.529999999999998 26.91 21.759999999999998 60-64 24.295 27.544999999999998 26.97 21.19 65-69 23.74 27.02 27.77 21.47 70-74 23.64 27.029999999999998 26.97 22.36 75-79 23.805 28.01 27.05 21.135 80-84 23.7 27.21 27.46 21.63 85-89 24.195 27.529999999999998 27.155 21.12 90-94 24.42 28.585 25.72 21.275 95-99 24.705 28.46 25.919999999999998 20.915 100-104 24.310000000000002 27.875 26.375 21.44 105-109 25.465 27.805000000000003 26.700000000000003 20.03 110-114 26.085 27.900000000000002 26.0 20.015 115-119 25.7 28.07 25.8 20.43 120-124 26.305 28.305000000000003 25.685000000000002 19.705000000000002 125-129 26.88 27.58 25.869999999999997 19.67 130-134 27.22 28.044999999999998 24.915000000000003 19.82 135-139 27.74 26.445 26.08 19.735 140-144 28.410000000000004 26.21 26.69 18.69 145-149 29.360000000000003 25.590000000000003 25.91 19.139999999999997 150-151 29.6625 25.474999999999998 25.724999999999998 19.1375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 1.0 10 1.0 11 0.5 12 0.5 13 1.0 14 1.5 15 0.5 16 0.0 17 0.5 18 1.0 19 0.5 20 0.0 21 0.0 22 0.0 23 0.5 24 0.5 25 0.0 26 3.0 27 7.5 28 5.5 29 2.5 30 4.0 31 7.5 32 11.5 33 21.5 34 29.5 35 35.5 36 51.5 37 72.0 38 105.0 39 143.5 40 192.5 41 204.5 42 214.0 43 253.0 44 273.0 45 288.0 46 275.0 47 275.5 48 270.5 49 226.0 50 199.5 51 162.5 52 133.5 53 118.0 54 99.5 55 88.0 56 62.5 57 44.5 58 31.5 59 21.5 60 13.0 61 7.5 62 5.0 63 3.5 64 5.5 65 4.0 66 2.0 67 1.0 68 1.0 69 0.5 70 0.0 71 0.5 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 1.0 79 0.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.5 86 1.0 87 0.5 88 0.0 89 0.0 90 0.0 91 0.0 92 0.5 93 1.0 94 0.5 95 0.0 96 0.5 97 0.5 98 0.0 99 0.0 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.0 #Duplication Level Percentage of deduplicated Percentage of total 1 81.5625 65.25 2 13.96875 22.35 3 3.03125 7.2749999999999995 4 1.0 3.2 5 0.28125 1.125 6 0.125 0.6 7 0.0 0.0 8 0.03125 0.2 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 AGTATTAGACGAACAGTATATGTTTCTGACATTGATCAACATGTAACTGA 8 0.2 No Hit CACACTTGTTCACGGGTTCTAAGAGAATGGCCACCAATACATTGATGAGC 6 0.15 No Hit CAAGCCTTTGCTTGGAAATGGATTCGATCACGAACTCAACCAATTTCTTA 6 0.15 No Hit GTCAGACAATCATTGCTGGTGTAGCTCCAGTTAGGATGTTCTACGAGAGC 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit GCTAAAAGAGGTTAACAAACAAGGGAAAGAGGTCTTTTATGACTATGAGG 5 0.125 No Hit AAGGACTTTTCGAGCAGGGTCCTTTAGTCTTCGTCAGATAAAATTTGCAA 5 0.125 No Hit GACCATCCTCGTGCTCGCCTAGCTCCAAAGTTATAGAAACAATCCCTGGG 5 0.125 No Hit AACATTTTTCAGCAAAAGAAAGTTAACTAGTTGGCCTACAGTGTCTTCAC 5 0.125 No Hit GAAACTGAATACCTGACAAAACGAATTCAAGATGGTGGAACAGAAGTTGT 5 0.125 No Hit AAATCAGCGGCATCTTCGGATACCAAGAAAGGAGGAGGGTCATCTTCTGG 5 0.125 No Hit ATCGACCTTTTCTAGTTGAAGGTAGTGAAGCAAAGAGACATGGCCTCCAC 5 0.125 No Hit GAAAAAAATAAACTTGATTCAGCATTGGTACTGATGATCACAAAAGCATG 5 0.125 No Hit ATGGATTTGATCCACAAAGTCCTGAACATTGTACTTCCTCCTATAACATT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.037500000000000006 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.3375 0.0 0.0 0.0 0.0 74-75 0.4375 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.6375 0.0 0.0 0.0 0.0 80-81 0.7 0.0 0.0 0.0 0.0 82-83 0.8 0.0 0.0 0.0 0.0 84-85 0.8999999999999999 0.0 0.0 0.0 0.0 86-87 1.25 0.0 0.0 0.0 0.0 88-89 1.3875 0.0 0.0 0.0 0.0 90-91 1.6375 0.0 0.0 0.0 0.0 92-93 2.1 0.0 0.0 0.0 0.0 94-95 2.6125 0.0 0.0 0.0 0.0 96-97 3.25 0.0 0.0 0.0 0.0 98-99 3.775 0.0 0.0 0.0 0.0 100-101 4.2875 0.0 0.0 0.0 0.0 102-103 4.975 0.0 0.0 0.0 0.0 104-105 5.8375 0.0 0.0 0.0 0.0 106-107 6.775 0.0 0.0 0.0 0.0 108-109 7.5375 0.0 0.0 0.0 0.0 110-111 8.3875 0.0 0.0 0.0 0.0 112-113 9.2375 0.0 0.0 0.0 0.0 114-115 10.4125 0.0 0.0 0.0 0.0 116-117 11.525 0.0 0.0 0.0 0.0 118-119 12.4875 0.0 0.0 0.0 0.0 120-121 13.037500000000001 0.0 0.0 0.0 0.0 122-123 14.0125 0.0 0.0 0.0 0.0 124-125 14.925 0.0 0.0 0.0 0.0 126-127 15.8 0.0 0.0 0.0 0.0 128-129 16.737499999999997 0.0 0.0 0.0 0.0 130-131 17.737499999999997 0.0 0.0 0.0 0.0 132-133 18.8 0.0 0.0 0.0 0.0 134-135 19.8625 0.0 0.0 0.0 0.0 136-137 20.7125 0.0 0.0 0.0 0.0 138-139 21.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATTTTC 10 0.006830828 145.0 9 >>END_MODULE Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713199 spots for SRR12670176.sra Written 713199 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra Read 713195 spots for SRR12670176.sra Written 713195 spots for SRR12670176.sra SRR ids: ['SRR12670176.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_p21vfpm7 SRR12670176.sra spots: 14263904 blocks: [[1, 713195], [713196, 1426390], [1426391, 2139585], [2139586, 2852780], [2852781, 3565975], [3565976, 4279170], [4279171, 4992365], [4992366, 5705560], [5705561, 6418755], [6418756, 7131950], [7131951, 7845145], [7845146, 8558340], [8558341, 9271535], [9271536, 9984730], [9984731, 10697925], [10697926, 11411120], [11411121, 12124315], [12124316, 12837510], [12837511, 13550705], [13550706, 14263904]] SRR12670176 file size 4825798 SRR12670176 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 SRR12670176 SRR12670176_1.fastq SRR12670176_2.fastq Input file: SRR12670176_1.fastq Paired file: SRR12670176_2.fastq trimmed: SRR12670176-trimmed-pair1.fastq, SRR12670176-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 08:35:25 2025 >> started Tue Feb 11 08:35:42 2025 >> done (16.683s) 14263904 read pairs processed; of these: 89 ( 0.00%) short read pairs filtered out after trimming by size control 9925 ( 0.07%) empty read pairs filtered out after trimming by size control 14253890 (99.93%) read pairs available; of these: 3500162 (24.56%) trimmed read pairs available after processing 10753728 (75.44%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 7 0.00% 20 9 0.00% 21 18 0.00% 22 22 0.00% 23 35 0.00% 24 39 0.00% 25 29 0.00% 26 44 0.00% 27 51 0.00% 28 53 0.00% 29 67 0.00% 30 82 0.00% 31 66 0.00% 32 85 0.00% 33 88 0.00% 34 103 0.00% 35 104 0.00% 36 86 0.00% 37 140 0.00% 38 135 0.00% 39 170 0.00% 40 183 0.00% 41 192 0.00% 42 208 0.00% 43 225 0.00% 44 224 0.00% 45 248 0.00% 46 262 0.00% 47 284 0.00% 48 314 0.00% 49 428 0.00% 50 511 0.00% 51 545 0.00% 52 633 0.00% 53 619 0.00% 54 726 0.01% 55 723 0.01% 56 776 0.01% 57 929 0.01% 58 1063 0.01% 59 1269 0.01% 60 1513 0.01% 61 1738 0.01% 62 1800 0.01% 63 2124 0.01% 64 2306 0.02% 65 2537 0.02% 66 2619 0.02% 67 2965 0.02% 68 3305 0.02% 69 3644 0.03% 70 4221 0.03% 71 4914 0.03% 72 5680 0.04% 73 6483 0.05% 74 6859 0.05% 75 7406 0.05% 76 8395 0.06% 77 8872 0.06% 78 9284 0.07% 79 10632 0.07% 80 11574 0.08% 81 13252 0.09% 82 14560 0.10% 83 16135 0.11% 84 17410 0.12% 85 19101 0.13% 86 20186 0.14% 87 21225 0.15% 88 21967 0.15% 89 23091 0.16% 90 24690 0.17% 91 26630 0.19% 92 28292 0.20% 93 30577 0.21% 94 32718 0.23% 95 34539 0.24% 96 35433 0.25% 97 36697 0.26% 98 37001 0.26% 99 37426 0.26% 100 39588 0.28% 101 39798 0.28% 102 41901 0.29% 103 43806 0.31% 104 45664 0.32% 105 47242 0.33% 106 48255 0.34% 107 48559 0.34% 108 47952 0.34% 109 48851 0.34% 110 48917 0.34% 111 49798 0.35% 112 51930 0.36% 113 51989 0.36% 114 53765 0.38% 115 55531 0.39% 116 56581 0.40% 117 56466 0.40% 118 56385 0.40% 119 55505 0.39% 120 55830 0.39% 121 56786 0.40% 122 57542 0.40% 123 58074 0.41% 124 59506 0.42% 125 59742 0.42% 126 60887 0.43% 127 61121 0.43% 128 60156 0.42% 129 59504 0.42% 130 60112 0.42% 131 59095 0.41% 132 60151 0.42% 133 61926 0.43% 134 61057 0.43% 135 62167 0.44% 136 63288 0.44% 137 62970 0.44% 138 62366 0.44% 139 62730 0.44% 140 61688 0.43% 141 61968 0.43% 142 61876 0.43% 143 61996 0.43% 144 63323 0.44% 145 63956 0.45% 146 64229 0.45% 147 63976 0.45% 148 64895 0.46% 149 63321 0.44% 150 63839 0.45% 151 10753728 75.44% 14253890 reads passed initial QC criterion=sequence-density sequence-density=0.56 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=27 prefix-density=0.55 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=53.06 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=6.3 sequence=AAACAGAATATTTACTTTTAGCGCAAGTTTCAATTCATGAGCTCGTTACATCACAAGTTAACATTACAAGCCAATAGTCCCAGCACAGAAAAAACTCTTTTGTTGCTCACTTTCCGGGAACGAAGTTTGTGGCATATGCCCAGGCGTTGTTGTTTACTGGGTCAGAAAGGTGGTCAGCCAGGTTCTCCAGTGGTCCCTTTCCGGTCACAATGGCCTGGACAAAGAATCCGAACATTGAGAACATAGCCAACCT criterion=sequence-density sequence-density=0.77 sequence-density-rank=1 fanout-score=2.13 fanout-score-rank=26 prefix-density=0.77 prefix-fanout=2.1 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=11.88 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=1.4 sequence=AGTACTGAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCACACTTTCCTTCTTTTCCAACAGAAAATGTCTTGCTGTGGAGGAAACTGTGG SRR12670176 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:36:27 Started mapping on | Feb 11 08:36:27 Finished on | Feb 11 08:38:08 Mapping speed, Million of reads per hour | 508.06 Number of input reads | 14253890 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 13307963 Uniquely mapped reads % | 93.36% Average mapped length | 285.53 Number of splices: Total | 13259744 Number of splices: Annotated (sjdb) | 13002968 Number of splices: GT/AG | 12983490 Number of splices: GC/AG | 230042 Number of splices: AT/AC | 8036 Number of splices: Non-canonical | 38176 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.02% Deletion average length | 3.06 Insertion rate per base | 0.02% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 333285 % of reads mapped to multiple loci | 2.34% Number of reads mapped to too many loci | 68177 % of reads mapped to too many loci | 0.48% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.67% % of reads unmapped: other | 0.15% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 612642 612642 612642 N_multimapping 333285 333285 333285 N_noFeature 352634 13086180 428613 N_ambiguous 223414 784 77201 UnstrandedReadsAssigned:12731915 PositiveStrandReadsAssigned:220999 NegativeStrandReadsAssigned:12802149 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=141 echo kmer=137 SRR12670176 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: SRR12670176-trimmed-pair1.fastq SRR12670176-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,253,890 reads, 12,846,820 reads pseudoaligned [quant] estimated average fragment length: 208.054 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,064 rounds 52401 SRR12670176.ke.tsv 34699 SRR12670176.se.tsv 87100 total ==> SRR12670176.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1810.95 462 17.2427 Potri.005G024800.1.v4.1 1035 827.946 327 26.6941 Potri.004G059700.1.v4.1 961 753.973 4 0.35857 Potri.007G009000.2.v4.1 1416 1208.95 0 0 Potri.003G141000.2.v4.1 2943 2735.95 843 20.8252 Potri.016G087400.1.v4.1 270 104.569 607.641 392.749 Potri.015G069301.1.v4.1 564 361.672 0 0 Potri.010G195200.1.v4.1 1773 1565.95 99 4.27295 Potri.012G127500.1.v4.1 977 769.968 117 10.2703 ==> SRR12670176.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 251 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 256 Potri.001G212900.v4.1 12 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 9 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 6 SRR12670176 completed mapping pipeline successfully