Starting /dee2/code/volunteer_pipeline.sh SRR12670115 current disk space = 3057524166656 free memory = 1466210460 SRR12670115 SRAfilesize c96dbebe057ae9a3e16ec62abdbf89ea SRR12670115.sra SRR12670115.sra file validated SRR12670115 is paired end SRR12670115 is conventional basespace SRR12670115 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670115_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5905 37.0 37.0 37.0 37.0 37.0 2 36.47975 37.0 37.0 37.0 37.0 37.0 3 36.598 37.0 37.0 37.0 37.0 37.0 4 36.5995 37.0 37.0 37.0 37.0 37.0 5 36.627 37.0 37.0 37.0 37.0 37.0 6 36.634 37.0 37.0 37.0 37.0 37.0 7 36.5495 37.0 37.0 37.0 37.0 37.0 8 36.54 37.0 37.0 37.0 37.0 37.0 9 36.598 37.0 37.0 37.0 37.0 37.0 10-14 36.587900000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.5707 37.0 37.0 37.0 37.0 37.0 20-24 36.5433 37.0 37.0 37.0 37.0 37.0 25-29 36.5073 37.0 37.0 37.0 37.0 37.0 30-34 36.4887 37.0 37.0 37.0 37.0 37.0 35-39 36.479200000000006 37.0 37.0 37.0 37.0 37.0 40-44 36.432900000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.4181 37.0 37.0 37.0 37.0 37.0 50-54 36.4072 37.0 37.0 37.0 37.0 37.0 55-59 36.3806 37.0 37.0 37.0 37.0 37.0 60-64 36.3384 37.0 37.0 37.0 37.0 37.0 65-69 36.374199999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.3317 37.0 37.0 37.0 37.0 37.0 75-79 36.340999999999994 37.0 37.0 37.0 37.0 37.0 80-84 36.2621 37.0 37.0 37.0 37.0 37.0 85-89 36.266200000000005 37.0 37.0 37.0 37.0 37.0 90-94 36.2495 37.0 37.0 37.0 37.0 37.0 95-99 36.2314 37.0 37.0 37.0 37.0 37.0 100-104 36.2494 37.0 37.0 37.0 37.0 37.0 105-109 36.2533 37.0 37.0 37.0 37.0 37.0 110-114 36.1937 37.0 37.0 37.0 37.0 37.0 115-119 36.211 37.0 37.0 37.0 37.0 37.0 120-124 36.0984 37.0 37.0 37.0 37.0 37.0 125-129 36.067299999999996 37.0 37.0 37.0 37.0 37.0 130-134 36.0486 37.0 37.0 37.0 37.0 37.0 135-139 36.001400000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.8187 37.0 37.0 37.0 37.0 37.0 145-149 35.784000000000006 37.0 37.0 37.0 37.0 37.0 150-151 35.562 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 2.0 24 2.0 25 3.0 26 4.0 27 10.0 28 11.0 29 17.0 30 27.0 31 30.0 32 49.0 33 61.0 34 100.0 35 295.0 36 2955.0 37 434.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.925000000000004 11.700000000000001 5.375 40.0 2 17.874153923289047 12.333918275256957 37.954374529957384 31.837553271496617 3 17.5 17.325 28.975 36.199999999999996 4 22.325 25.025 23.7 28.95 5 22.5 31.525 23.95 22.025 6 20.0 33.675 26.200000000000003 20.125 7 15.2 25.174999999999997 42.575 17.05 8 17.325 25.025 31.45 26.200000000000003 9 18.2 23.674999999999997 34.75 23.375 10-14 19.950000000000003 30.635 26.82 22.595000000000002 15-19 19.845 27.79 28.09 24.275 20-24 20.8 27.77 28.15 23.28 25-29 20.330000000000002 27.79 28.395 23.485 30-34 20.05 28.244999999999997 28.244999999999997 23.46 35-39 20.47 27.915 27.815 23.799999999999997 40-44 20.11 28.965000000000003 26.86 24.065 45-49 20.599999999999998 28.044999999999998 27.42 23.935000000000002 50-54 20.53 27.944999999999997 28.155 23.369999999999997 55-59 20.474999999999998 27.785 27.900000000000002 23.84 60-64 20.64 27.685 28.244999999999997 23.43 65-69 20.985 27.839999999999996 28.199999999999996 22.975 70-74 21.709999999999997 27.950000000000003 27.325 23.015 75-79 20.200000000000003 28.634999999999998 27.310000000000002 23.855 80-84 20.47 28.37 27.675 23.485 85-89 21.09 28.79 27.045 23.075000000000003 90-94 20.974999999999998 28.775000000000002 26.5 23.75 95-99 21.385 27.925 26.919999999999998 23.77 100-104 21.3 27.875 27.62 23.205000000000002 105-109 21.575 28.725 26.534999999999997 23.165 110-114 21.21 28.665000000000003 26.450000000000003 23.674999999999997 115-119 20.94 29.04 26.365 23.655 120-124 21.105 28.33 26.119999999999997 24.445 125-129 21.44 28.49 25.94 24.13 130-134 21.385 28.410000000000004 25.724999999999998 24.48 135-139 21.26 28.93 25.14 24.67 140-144 21.224999999999998 28.34 24.709999999999997 25.724999999999998 145-149 21.865000000000002 27.775 25.540000000000003 24.82 150-151 21.2375 27.437499999999996 24.9375 26.387500000000003 >>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 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.5 23 3.0 24 4.0 25 3.5 26 4.0 27 5.5 28 7.5 29 9.0 30 11.0 31 19.0 32 28.5 33 34.0 34 46.5 35 67.0 36 87.5 37 105.0 38 124.0 39 139.0 40 171.5 41 209.5 42 231.5 43 248.0 44 283.5 45 288.0 46 245.0 47 242.0 48 241.5 49 221.5 50 187.5 51 163.0 52 139.0 53 98.0 54 88.5 55 79.0 56 48.5 57 31.5 58 27.0 59 20.0 60 13.5 61 7.5 62 5.0 63 3.0 64 2.0 65 1.5 66 1.0 67 1.5 68 0.5 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.5 75 0.5 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 0.27499999999999997 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 78.475 #Duplication Level Percentage of deduplicated Percentage of total 1 79.03791016247213 62.025 2 15.992354252946797 25.1 3 3.886588085377509 9.15 4 0.796431984708506 2.5 5 0.1911436763300414 0.75 6 0.06371455877668047 0.3 7 0.03185727938834024 0.17500000000000002 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 GTGGAATCTGTTAGTGGCGGTGATGGGTATCGGAGCTCCCCTTCCGGCGG 7 0.17500000000000002 No Hit GCAACCTTGAGACCTCAAAATGTCACGGTGTTCCTCGGGCACATCCGGCA 6 0.15 No Hit CTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACT 6 0.15 No Hit GTCTCGGCCAATCTTTACATACTCATCAAATCGCTCCTTCAAGTCTTCAG 5 0.125 No Hit CTGGAGAGTACTGTGTAGAGATGGCGTGAGGAGAGAGAGTAGAGAAGTGA 5 0.125 No Hit GTGGAGGGGCTGGTGGTAACTTGCGATCAGATTAAAAGGCCTAAAGATGA 5 0.125 No Hit GTAACTACATAATAATATTAGTAACGGCAATAATAGTGAAACAACATTCT 5 0.125 No Hit CCCATCATTAACAGAACAGTATATTTTAAAGCTCTCCTTCAATACCAGAG 5 0.125 No Hit CACGTTTCGATCCATTCAAAACACAGCATTTAACATGCCATAAACTTGTG 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 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.0625 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.16249999999999998 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.2625 0.0 0.0 0.0 0.0 68-69 0.30000000000000004 0.0 0.0 0.0 0.0 70-71 0.4125 0.0 0.0 0.0 0.0 72-73 0.48750000000000004 0.0 0.0 0.0 0.0 74-75 0.6125 0.0 0.0 0.0 0.0 76-77 0.65 0.0 0.0 0.0 0.0 78-79 0.7625 0.0 0.0 0.0 0.0 80-81 0.975 0.0 0.0 0.0 0.0 82-83 1.1375000000000002 0.0 0.0 0.0 0.0 84-85 1.5125000000000002 0.0 0.0 0.0 0.0 86-87 2.0375 0.0 0.0 0.0 0.0 88-89 2.5125 0.0 0.0 0.0 0.0 90-91 2.8875 0.0 0.0 0.0 0.0 92-93 3.2125 0.0 0.0 0.0 0.0 94-95 3.6875 0.0 0.0 0.0 0.0 96-97 4.324999999999999 0.0 0.0 0.0 0.0 98-99 4.8875 0.0 0.0 0.0 0.0 100-101 5.5375 0.0 0.0 0.0 0.0 102-103 6.125 0.0 0.0 0.0 0.0 104-105 7.15 0.0 0.0 0.0 0.0 106-107 8.15 0.0 0.0 0.0 0.0 108-109 9.025 0.0 0.0 0.0 0.0 110-111 9.825 0.0 0.0 0.0 0.0 112-113 10.75 0.0 0.0 0.0 0.0 114-115 11.65 0.0 0.0 0.0 0.0 116-117 12.7625 0.0 0.0 0.0 0.0 118-119 13.85 0.0 0.0 0.0 0.0 120-121 14.575 0.0 0.0 0.0 0.0 122-123 15.575 0.0 0.0 0.0 0.0 124-125 16.5 0.0 0.0 0.0 0.0 126-127 17.7875 0.0 0.0 0.0 0.0 128-129 18.9625 0.0 0.0 0.0 0.0 130-131 20.1875 0.0 0.0 0.0 0.0 132-133 21.375 0.0 0.0 0.0 0.0 134-135 22.2 0.0 0.0 0.0 0.0 136-137 23.575 0.0 0.0 0.0 0.0 138-139 24.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATGACC 10 0.006830828 145.0 7 GGGGGGG 30 0.0014437955 24.166668 140-144 TTTTTTT 40 0.0076550315 18.125 85-89 >>END_MODULE SRR12670115 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670115_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 36.4135 37.0 37.0 37.0 37.0 37.0 2 36.207 37.0 37.0 37.0 37.0 37.0 3 36.3145 37.0 37.0 37.0 37.0 37.0 4 36.323 37.0 37.0 37.0 37.0 37.0 5 36.4075 37.0 37.0 37.0 37.0 37.0 6 36.421 37.0 37.0 37.0 37.0 37.0 7 36.3925 37.0 37.0 37.0 37.0 37.0 8 36.396 37.0 37.0 37.0 37.0 37.0 9 36.344 37.0 37.0 37.0 37.0 37.0 10-14 36.451100000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.431200000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.3756 37.0 37.0 37.0 37.0 37.0 25-29 36.3343 37.0 37.0 37.0 37.0 37.0 30-34 36.3534 37.0 37.0 37.0 37.0 37.0 35-39 36.2504 37.0 37.0 37.0 37.0 37.0 40-44 36.2279 37.0 37.0 37.0 37.0 37.0 45-49 36.2401 37.0 37.0 37.0 37.0 37.0 50-54 36.2001 37.0 37.0 37.0 37.0 37.0 55-59 36.1854 37.0 37.0 37.0 37.0 37.0 60-64 36.147499999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.1425 37.0 37.0 37.0 37.0 37.0 70-74 36.0613 37.0 37.0 37.0 37.0 37.0 75-79 36.1305 37.0 37.0 37.0 37.0 37.0 80-84 36.066199999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.0402 37.0 37.0 37.0 37.0 37.0 90-94 36.056 37.0 37.0 37.0 37.0 37.0 95-99 36.011199999999995 37.0 37.0 37.0 37.0 37.0 100-104 35.90409999999999 37.0 37.0 37.0 37.0 37.0 105-109 35.8894 37.0 37.0 37.0 37.0 37.0 110-114 35.854200000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.8706 37.0 37.0 37.0 37.0 37.0 120-124 35.6968 37.0 37.0 37.0 37.0 37.0 125-129 35.6177 37.0 37.0 37.0 37.0 37.0 130-134 35.471500000000006 37.0 37.0 37.0 37.0 37.0 135-139 35.3352 37.0 37.0 37.0 37.0 37.0 140-144 35.1931 37.0 37.0 37.0 34.6 37.0 145-149 34.8055 37.0 37.0 37.0 25.0 37.0 150-151 34.46275 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 1.0 14 4.0 15 0.0 16 1.0 17 2.0 18 0.0 19 1.0 20 3.0 21 4.0 22 4.0 23 4.0 24 2.0 25 4.0 26 5.0 27 6.0 28 17.0 29 11.0 30 26.0 31 42.0 32 63.0 33 101.0 34 173.0 35 482.0 36 2693.0 37 349.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.975 24.099999999999998 7.324999999999999 26.6 2 24.224999999999998 26.025 32.65 17.1 3 20.075000000000003 26.474999999999998 32.85 20.599999999999998 4 23.974999999999998 34.975 22.7 18.35 5 25.05 36.6 23.1 15.25 6 21.75 39.4 21.6 17.25 7 20.4 22.475 37.574999999999996 19.55 8 20.025000000000002 26.424999999999997 28.025 25.525 9 22.85 24.25 30.15 22.75 10-14 23.150000000000002 29.175 26.465 21.21 15-19 23.46 27.46 27.450000000000003 21.63 20-24 23.71 28.175 27.665 20.45 25-29 23.155 28.12 27.805000000000003 20.919999999999998 30-34 23.215 27.825 28.115000000000002 20.845 35-39 23.345 27.634999999999998 28.055000000000003 20.965 40-44 22.86 27.700000000000003 28.16 21.279999999999998 45-49 23.535 27.11 28.555000000000003 20.8 50-54 22.91 27.794999999999998 28.555000000000003 20.74 55-59 22.84 28.655 27.12 21.385 60-64 23.665 27.37 27.845 21.12 65-69 23.794999999999998 27.93 27.295 20.979999999999997 70-74 24.505 28.4 26.395000000000003 20.7 75-79 23.494999999999997 27.845 27.485 21.175 80-84 23.95 28.01 27.224999999999998 20.815 85-89 24.12 28.465 26.43 20.985 90-94 24.16 28.01 27.250000000000004 20.580000000000002 95-99 24.36 28.515 26.465 20.66 100-104 25.105 28.57 26.505000000000003 19.82 105-109 24.905 27.655 27.265 20.175 110-114 25.264999999999997 28.03 26.77 19.935 115-119 25.85 28.275 26.355 19.52 120-124 26.56 28.499999999999996 25.685000000000002 19.255 125-129 26.939999999999998 28.535 25.590000000000003 18.935 130-134 27.650000000000002 28.384999999999998 24.62 19.345000000000002 135-139 28.134999999999998 27.834999999999997 25.169999999999998 18.86 140-144 28.294999999999998 27.375 24.6 19.73 145-149 29.78 26.840000000000003 25.169999999999998 18.21 150-151 30.0 27.6625 24.25 18.087500000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 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 1.0 11 1.5 12 0.5 13 0.0 14 0.0 15 0.5 16 1.0 17 0.5 18 0.0 19 1.5 20 2.5 21 1.0 22 0.5 23 2.5 24 3.5 25 3.0 26 2.0 27 2.0 28 4.0 29 6.5 30 13.0 31 17.5 32 20.5 33 30.0 34 47.0 35 70.5 36 87.5 37 117.5 38 146.0 39 164.0 40 183.5 41 205.0 42 220.5 43 242.5 44 272.0 45 280.5 46 261.0 47 235.5 48 222.5 49 207.0 50 188.5 51 150.5 52 123.0 53 104.5 54 87.0 55 71.5 56 47.0 57 34.0 58 32.0 59 26.5 60 13.5 61 8.5 62 9.0 63 7.5 64 3.5 65 1.0 66 2.5 67 2.5 68 1.0 69 0.5 70 0.5 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 0.5 85 0.5 86 0.0 87 0.0 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 0.0 97 0.0 98 0.0 99 0.0 100 2.0 >>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 78.375 #Duplication Level Percentage of deduplicated Percentage of total 1 79.23444976076554 62.1 2 15.661881977671452 24.55 3 3.923444976076555 9.225 4 0.7974481658692184 2.5 5 0.3189792663476874 1.25 6 0.0 0.0 7 0.03189792663476874 0.17500000000000002 8 0.03189792663476874 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 AGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 8 0.2 No Hit AAATCGTTGATTTCTGCACTGATTTTTTCTCTGAACAACAACTCCAACAG 7 0.17500000000000002 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit CAGAGCGTCTTCCAAGACCTGGCCAAGGACAGGATAAGGGCCACAGCCGG 5 0.125 No Hit AGTTAGCCTCCATCCAAAATTTATAATGGCCAAAGCTATAACGGGCTTTA 5 0.125 No Hit AGTAGACTGGGCCAAGAGTGCTGGTGTGAAGCAGTTCCTGTTCATCAGCA 5 0.125 No Hit AAGCTGTTGGGGTTTGGGTCGTGTTGTTTCTTGCAGTGTTATAGATTTTA 5 0.125 No Hit CTTCATCCTCCTCCTCCTCCTCCTTCACCCCTCGAAATTCCCACCGTTCG 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit CTTTTCCTGAAGGCTATGTACCCCAACCAACTACAGAAGAAGAGAAAGGC 5 0.125 No Hit CACGAAACGGCTGACATTAATACCTTCAAATGGGGTGTGGCTGATCGTGG 5 0.125 No Hit ATTTTGGGTACCGGGAAGGTTTCCACAGTTAACACTGGCTATTCTAAGAG 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 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.0625 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.16249999999999998 0.0 0.0 0.0 0.0 58-59 0.1875 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.2875 0.0 0.0 0.0 0.0 68-69 0.32499999999999996 0.0 0.0 0.0 0.0 70-71 0.4375 0.0 0.0 0.0 0.0 72-73 0.5249999999999999 0.0 0.0 0.0 0.0 74-75 0.6625000000000001 0.0 0.0 0.0 0.0 76-77 0.6875 0.0 0.0 0.0 0.0 78-79 0.7875 0.0 0.0 0.0 0.0 80-81 1.0 0.0 0.0 0.0 0.0 82-83 1.1625 0.0 0.0 0.0 0.0 84-85 1.5625 0.0 0.0 0.0 0.0 86-87 2.1125 0.0 0.0 0.0 0.0 88-89 2.5875 0.0 0.0 0.0 0.0 90-91 2.9625 0.0 0.0 0.0 0.0 92-93 3.2875 0.0 0.0 0.0 0.0 94-95 3.8125 0.0 0.0 0.0 0.0 96-97 4.475 0.0 0.0 0.0 0.0 98-99 5.0375 0.0 0.0 0.0 0.0 100-101 5.7125 0.0 0.0 0.0 0.0 102-103 6.3125 0.0 0.0 0.0 0.0 104-105 7.324999999999999 0.0 0.0 0.0 0.0 106-107 8.35 0.0 0.0 0.0 0.0 108-109 9.2 0.0 0.0 0.0 0.0 110-111 9.975 0.0 0.0 0.0 0.0 112-113 10.8875 0.0 0.0 0.0 0.0 114-115 11.875 0.0 0.0 0.0 0.0 116-117 13.025 0.0 0.0 0.0 0.0 118-119 14.1375 0.0 0.0 0.0 0.0 120-121 14.8625 0.0 0.0 0.0 0.0 122-123 15.875 0.0 0.0 0.0 0.0 124-125 16.8 0.0 0.0 0.0 0.0 126-127 18.1375 0.0 0.0 0.0 0.0 128-129 19.35 0.0 0.0 0.0 0.0 130-131 20.6 0.0 0.0 0.0 0.0 132-133 21.8 0.0 0.0 0.0 0.0 134-135 22.612499999999997 0.0 0.0 0.0 0.0 136-137 23.975 0.0 0.0 0.0 0.0 138-139 25.049999999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCTGAGA 10 0.006830828 145.0 1 AAAAAAA 70 1.807628E-6 18.642857 95-99 >>END_MODULE Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858161 spots for SRR12670115.sra Written 858161 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra Read 858142 spots for SRR12670115.sra Written 858142 spots for SRR12670115.sra SRR ids: ['SRR12670115.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_58mcqr_8 SRR12670115.sra spots: 17162859 blocks: [[1, 858142], [858143, 1716284], [1716285, 2574426], [2574427, 3432568], [3432569, 4290710], [4290711, 5148852], [5148853, 6006994], [6006995, 6865136], [6865137, 7723278], [7723279, 8581420], [8581421, 9439562], [9439563, 10297704], [10297705, 11155846], [11155847, 12013988], [12013989, 12872130], [12872131, 13730272], [13730273, 14588414], [14588415, 15446556], [15446557, 16304698], [16304699, 17162859]] SRR12670115 file size 5810989 SRR12670115 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 SRR12670115 SRR12670115_1.fastq SRR12670115_2.fastq Input file: SRR12670115_1.fastq Paired file: SRR12670115_2.fastq trimmed: SRR12670115-trimmed-pair1.fastq, SRR12670115-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 Mon Feb 10 23:46:55 2025 >> started Mon Feb 10 23:47:14 2025 >> done (19.808s) 17162859 read pairs processed; of these: 108 ( 0.00%) short read pairs filtered out after trimming by size control 5592 ( 0.03%) empty read pairs filtered out after trimming by size control 17157159 (99.97%) read pairs available; of these: 5257716 (30.64%) trimmed read pairs available after processing 11899443 (69.36%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 12 0.00% 20 19 0.00% 21 27 0.00% 22 49 0.00% 23 51 0.00% 24 53 0.00% 25 67 0.00% 26 62 0.00% 27 97 0.00% 28 100 0.00% 29 84 0.00% 30 107 0.00% 31 105 0.00% 32 128 0.00% 33 147 0.00% 34 151 0.00% 35 143 0.00% 36 142 0.00% 37 168 0.00% 38 231 0.00% 39 230 0.00% 40 305 0.00% 41 291 0.00% 42 308 0.00% 43 315 0.00% 44 307 0.00% 45 346 0.00% 46 409 0.00% 47 501 0.00% 48 597 0.00% 49 639 0.00% 50 762 0.00% 51 849 0.00% 52 994 0.01% 53 1004 0.01% 54 1121 0.01% 55 1091 0.01% 56 1305 0.01% 57 1507 0.01% 58 1678 0.01% 59 2114 0.01% 60 2604 0.02% 61 2865 0.02% 62 3042 0.02% 63 3412 0.02% 64 3750 0.02% 65 3992 0.02% 66 4266 0.02% 67 4729 0.03% 68 5604 0.03% 69 6204 0.04% 70 7158 0.04% 71 8436 0.05% 72 9506 0.06% 73 10722 0.06% 74 11801 0.07% 75 12580 0.07% 76 13902 0.08% 77 14528 0.08% 78 16096 0.09% 79 17897 0.10% 80 19370 0.11% 81 21678 0.13% 82 24152 0.14% 83 26473 0.15% 84 28812 0.17% 85 31047 0.18% 86 32314 0.19% 87 34205 0.20% 88 35840 0.21% 89 37375 0.22% 90 40406 0.24% 91 43131 0.25% 92 46694 0.27% 93 48819 0.28% 94 51855 0.30% 95 54618 0.32% 96 55942 0.33% 97 57454 0.33% 98 58673 0.34% 99 60370 0.35% 100 62582 0.36% 101 63272 0.37% 102 66994 0.39% 103 69167 0.40% 104 70634 0.41% 105 73337 0.43% 106 73772 0.43% 107 74578 0.43% 108 74778 0.44% 109 75597 0.44% 110 75584 0.44% 111 76883 0.45% 112 79078 0.46% 113 80276 0.47% 114 82290 0.48% 115 83858 0.49% 116 84648 0.49% 117 85193 0.50% 118 85062 0.50% 119 83625 0.49% 120 85083 0.50% 121 84965 0.50% 122 86045 0.50% 123 87638 0.51% 124 88933 0.52% 125 88541 0.52% 126 89822 0.52% 127 89403 0.52% 128 88649 0.52% 129 88525 0.52% 130 88742 0.52% 131 87737 0.51% 132 87713 0.51% 133 88847 0.52% 134 88973 0.52% 135 89997 0.52% 136 90423 0.53% 137 89949 0.52% 138 89131 0.52% 139 90992 0.53% 140 89029 0.52% 141 87948 0.51% 142 88048 0.51% 143 88198 0.51% 144 89801 0.52% 145 89536 0.52% 146 89199 0.52% 147 89610 0.52% 148 88832 0.52% 149 87198 0.51% 150 88058 0.51% 151 11899443 69.36% 17157159 reads passed initial QC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=35 prefix-density=0.49 prefix-fanout=2.0 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAGCTTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCATGTTGGCTTGTACCGGGGTGCGGTTGACGGTGGCAACGGCTGCCGATGAGATCATAGAGGAGGAAGCCAT criterion=fanout-score sequence-density=0.03 sequence-density-rank=36 fanout-score=141.03 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=13.2 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=32 prefix-density=0.67 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=157.89 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=16.6 sequence=AGAGAGAGAGACAGAGAGAATGGCCACCACAGCAGCCCTCTCCAGCGCCATGGTCAGCACATCGTTTACTCGCCGGGTGCCAGTGACAAGCCTACGGGCACTTCCCAACGTGGGGGAGTCTCTTCTTGGCTTGAAAGCCAGTCGAGGAGGACGTGTTAAAGCAATGGCAG SRR12670115 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:47:55 Started mapping on | Feb 10 23:47:55 Finished on | Feb 10 23:49:29 Mapping speed, Million of reads per hour | 657.08 Number of input reads | 17157159 Average input read length | 282 UNIQUE READS: Uniquely mapped reads number | 16055512 Uniquely mapped reads % | 93.58% Average mapped length | 280.77 Number of splices: Total | 15184099 Number of splices: Annotated (sjdb) | 14867119 Number of splices: GT/AG | 14863780 Number of splices: GC/AG | 258378 Number of splices: AT/AC | 9387 Number of splices: Non-canonical | 52554 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.03% Deletion average length | 2.89 Insertion rate per base | 0.02% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 395834 % of reads mapped to multiple loci | 2.31% Number of reads mapped to too many loci | 116845 % of reads mapped to too many loci | 0.68% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.28% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 705813 705813 705813 N_multimapping 395834 395834 395834 N_noFeature 590813 15820923 698095 N_ambiguous 222498 883 94629 UnstrandedReadsAssigned:15242201 PositiveStrandReadsAssigned:233706 NegativeStrandReadsAssigned:15262788 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=130 echo kmer=125 SRR12670115 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: SRR12670115-trimmed-pair1.fastq SRR12670115-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,157,159 reads, 15,378,653 reads pseudoaligned [quant] estimated average fragment length: 192.002 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,120 rounds 52401 SRR12670115.ke.tsv 34699 SRR12670115.se.tsv 87100 total ==> SRR12670115.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1827 515 18.5992 Potri.005G024800.1.v4.1 1035 843.998 226 17.6682 Potri.004G059700.1.v4.1 961 770.043 9 0.771176 Potri.007G009000.2.v4.1 1416 1225 0 0 Potri.003G141000.2.v4.1 2943 2752 752.466 18.0412 Potri.016G087400.1.v4.1 270 112.214 665 391.021 Potri.015G069301.1.v4.1 564 378.002 0 0 Potri.010G195200.1.v4.1 1773 1582 46 1.91857 Potri.012G127500.1.v4.1 977 786.036 89 7.47091 ==> SRR12670115.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 225 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 289 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 10 SRR12670115 completed mapping pipeline successfully