Starting /dee2/code/volunteer_pipeline.sh SRR12951290 current disk space = 1543499329536 free memory = 1602012028 SRR12951290 SRAfilesize cf72feb46945bd1392bea2e22aa8a558 SRR12951290.sra SRR12951290.sra file validated SRR12951290 is paired end SRR12951290 is conventional basespace SRR12951290 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951290_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.559 37.0 37.0 37.0 37.0 37.0 2 36.27325 37.0 37.0 37.0 37.0 37.0 3 36.5 37.0 37.0 37.0 37.0 37.0 4 36.5415 37.0 37.0 37.0 37.0 37.0 5 36.6315 37.0 37.0 37.0 37.0 37.0 6 36.62 37.0 37.0 37.0 37.0 37.0 7 36.517 37.0 37.0 37.0 37.0 37.0 8 36.605 37.0 37.0 37.0 37.0 37.0 9 36.5685 37.0 37.0 37.0 37.0 37.0 10-14 36.601 37.0 37.0 37.0 37.0 37.0 15-19 36.577 37.0 37.0 37.0 37.0 37.0 20-24 36.48290000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.5009 37.0 37.0 37.0 37.0 37.0 30-34 36.4781 37.0 37.0 37.0 37.0 37.0 35-39 36.453500000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.4098 37.0 37.0 37.0 37.0 37.0 45-49 36.401300000000006 37.0 37.0 37.0 37.0 37.0 50-54 36.4026 37.0 37.0 37.0 37.0 37.0 55-59 36.3402 37.0 37.0 37.0 37.0 37.0 60-64 36.339999999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.3116 37.0 37.0 37.0 37.0 37.0 70-74 36.3173 37.0 37.0 37.0 37.0 37.0 75-79 36.3494 37.0 37.0 37.0 37.0 37.0 80-84 36.326499999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.3275 37.0 37.0 37.0 37.0 37.0 90-94 36.3162 37.0 37.0 37.0 37.0 37.0 95-99 36.249700000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.291999999999994 37.0 37.0 37.0 37.0 37.0 105-109 36.25789999999999 37.0 37.0 37.0 37.0 37.0 110-114 36.2272 37.0 37.0 37.0 37.0 37.0 115-119 36.2034 37.0 37.0 37.0 37.0 37.0 120-124 36.1317 37.0 37.0 37.0 37.0 37.0 125-129 36.089999999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.9315 37.0 37.0 37.0 37.0 37.0 135-139 35.9033 37.0 37.0 37.0 37.0 37.0 140-144 35.6746 37.0 37.0 37.0 37.0 37.0 145-149 35.60799999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.1935 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 0.0 24 4.0 25 4.0 26 1.0 27 7.0 28 8.0 29 12.0 30 30.0 31 41.0 32 52.0 33 75.0 34 134.0 35 298.0 36 2830.0 37 502.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.4 10.05 4.125 34.425 2 21.62026586405819 11.562578379734136 34.08577878103837 32.731376975169304 3 21.55 14.325 25.874999999999996 38.25 4 25.5 21.349999999999998 21.3 31.85 5 25.95 26.375 24.45 23.225 6 27.175 28.95 21.85 22.025 7 18.825 26.3 35.375 19.5 8 22.7 24.15 27.775 25.374999999999996 9 21.175 20.349999999999998 32.45 26.025 10-14 23.915 25.88 24.42 25.785000000000004 15-19 24.23 24.34 24.445 26.985 20-24 23.810000000000002 24.779999999999998 25.955000000000002 25.455 25-29 24.099999999999998 25.124999999999996 24.625 26.150000000000002 30-34 23.5 25.979999999999997 24.665 25.855 35-39 23.175 25.39 25.419999999999998 26.015 40-44 24.404999999999998 25.3 24.529999999999998 25.765 45-49 23.825 24.825 25.424999999999997 25.924999999999997 50-54 24.195 24.745 24.445 26.615 55-59 24.175 24.335 24.72 26.77 60-64 24.33 24.45 24.884999999999998 26.334999999999997 65-69 23.885 24.884999999999998 25.040000000000003 26.19 70-74 24.595 24.86 25.074999999999996 25.47 75-79 24.4 25.025 24.32 26.255 80-84 25.39 25.115 23.799999999999997 25.695 85-89 25.255 24.95 24.01 25.785000000000004 90-94 25.535000000000004 24.775 23.7 25.990000000000002 95-99 24.425 24.83 24.535 26.21 100-104 24.815 24.435000000000002 24.735 26.015 105-109 25.81 24.490000000000002 23.53 26.169999999999998 110-114 24.73 24.905 23.919999999999998 26.445 115-119 24.905 24.87 23.265 26.96 120-124 25.064999999999998 25.575 22.585 26.775 125-129 24.4 25.27 23.56 26.77 130-134 24.08 25.330000000000002 23.875 26.715 135-139 23.985 25.05 23.0 27.965 140-144 23.61 24.705 24.099999999999998 27.584999999999997 145-149 24.7 25.055 22.825 27.42 150-151 23.849999999999998 25.137500000000003 23.425 27.5875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 1.0 25 1.0 26 0.0 27 0.0 28 0.5 29 3.0 30 6.0 31 8.0 32 10.0 33 13.0 34 17.5 35 32.5 36 46.5 37 45.5 38 58.0 39 97.0 40 125.0 41 132.5 42 153.0 43 176.0 44 183.5 45 179.0 46 185.5 47 201.5 48 187.0 49 151.0 50 138.0 51 134.5 52 134.0 53 135.5 54 117.5 55 112.5 56 104.5 57 93.0 58 91.5 59 87.5 60 80.5 61 67.0 62 56.0 63 63.5 64 71.0 65 61.0 66 56.0 67 61.0 68 52.0 69 46.5 70 53.0 71 48.0 72 38.0 73 24.0 74 15.5 75 11.5 76 8.5 77 6.0 78 5.5 79 4.5 80 2.5 81 2.0 82 1.5 83 1.0 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 0.325 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 82.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 83.98673100120627 69.625 2 12.635705669481304 20.95 3 2.623642943305187 6.525 4 0.4523522316043426 1.5 5 0.24125452352231602 1.0 6 0.030156815440289503 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.030156815440289503 0.25 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTACCAACCATCTCGTAT 10 0.25 TruSeq Adapter, Index 10 (97% over 37bp) GCGGCGAGAAAACAAAGGCAAGTATCTGAGTCATCTCATGAGTGCTTCTA 6 0.15 No Hit GTCATATGAGCCAAACTGCAGGCCAGCATATGGTATGATTTCAACAAGAG 5 0.125 No Hit GGGAGCAGCTAACTGGCTTCGGGTGTATCAGTATAGCATCTAATTCTTTG 5 0.125 No Hit CACACATCAGCAGTAGGCTGAAATTACAGCGGGGTATGCCGTGACAAAAA 5 0.125 No Hit GCCCGCGCGTCTGATCTTGGGGCCTTCCTTGAGCTGCTTCAGGATCACCT 5 0.125 No Hit GGCCAAAAGAGAAAAAAGGTATCGGATAGCATAGCAGAACAGACATGGGC 5 0.125 No Hit CAATATCGGAGGAAGCCAGTGGCTCCTCCAGCCTGAGGTTCTTGCTCTCC 5 0.125 No Hit CGGACATCTTCTAGTTTCCAGGCTTCCTCACAAACGCCTTTTGGACCTGC 5 0.125 No Hit CAGGAGACGTGATATGGTATTTGAGAAGAACTGCTGAAGAATAGCTACAC 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 0.0125 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 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 0.0625 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.225 0.0 0.0 0.0 0.0 74-75 0.275 0.0 0.0 0.0 0.0 76-77 0.4125 0.0 0.0 0.0 0.0 78-79 0.4875 0.0 0.0 0.0 0.0 80-81 0.75 0.0 0.0 0.0 0.0 82-83 1.1 0.0 0.0 0.0 0.0 84-85 1.4375 0.0 0.0 0.0 0.0 86-87 1.725 0.0 0.0 0.0 0.0 88-89 2.0625 0.0 0.0 0.0 0.0 90-91 2.2750000000000004 0.0 0.0 0.0 0.0 92-93 2.6 0.0 0.0 0.0 0.0 94-95 3.25 0.0 0.0 0.0 0.0 96-97 3.8 0.0 0.0 0.0 0.0 98-99 4.3375 0.0 0.0 0.0 0.0 100-101 5.15 0.0 0.0 0.0 0.0 102-103 5.85 0.0 0.0 0.0 0.0 104-105 6.512499999999999 0.0 0.0 0.0 0.0 106-107 7.3875 0.0 0.0 0.0 0.0 108-109 8.1125 0.0 0.0 0.0 0.0 110-111 8.7 0.0 0.0 0.0 0.0 112-113 9.6125 0.0 0.0 0.0 0.0 114-115 10.45 0.0 0.0 0.0 0.0 116-117 11.5125 0.0 0.0 0.0 0.0 118-119 12.337499999999999 0.0 0.0 0.0 0.0 120-121 13.225000000000001 0.0 0.0 0.0 0.0 122-123 14.212499999999999 0.0 0.0 0.0 0.0 124-125 15.325 0.0 0.0 0.0 0.0 126-127 16.225 0.0 0.0 0.0 0.0 128-129 17.0375 0.0 0.0 0.0 0.0 130-131 17.8875 0.0 0.0 0.0 0.0 132-133 18.7125 0.0 0.0 0.0 0.0 134-135 19.6875 0.0 0.0 0.0 0.0 136-137 20.5625 0.0 0.0 0.0 0.0 138-139 21.3375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12951290 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951290_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.295 37.0 37.0 37.0 37.0 37.0 2 36.2665 37.0 37.0 37.0 37.0 37.0 3 36.214 37.0 37.0 37.0 37.0 37.0 4 36.272 37.0 37.0 37.0 37.0 37.0 5 36.375 37.0 37.0 37.0 37.0 37.0 6 36.3205 37.0 37.0 37.0 37.0 37.0 7 36.277 37.0 37.0 37.0 37.0 37.0 8 36.4585 37.0 37.0 37.0 37.0 37.0 9 36.236 37.0 37.0 37.0 37.0 37.0 10-14 36.33899999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.31850000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.278600000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.1996 37.0 37.0 37.0 37.0 37.0 30-34 36.1735 37.0 37.0 37.0 37.0 37.0 35-39 36.1403 37.0 37.0 37.0 37.0 37.0 40-44 36.2154 37.0 37.0 37.0 37.0 37.0 45-49 36.154 37.0 37.0 37.0 37.0 37.0 50-54 36.089800000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.1197 37.0 37.0 37.0 37.0 37.0 60-64 36.1043 37.0 37.0 37.0 37.0 37.0 65-69 36.0338 37.0 37.0 37.0 37.0 37.0 70-74 36.0549 37.0 37.0 37.0 37.0 37.0 75-79 35.98010000000001 37.0 37.0 37.0 37.0 37.0 80-84 35.9525 37.0 37.0 37.0 37.0 37.0 85-89 35.958800000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.0439 37.0 37.0 37.0 37.0 37.0 95-99 35.935900000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.919200000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.8896 37.0 37.0 37.0 37.0 37.0 110-114 35.8056 37.0 37.0 37.0 37.0 37.0 115-119 35.8656 37.0 37.0 37.0 37.0 37.0 120-124 35.6926 37.0 37.0 37.0 37.0 37.0 125-129 35.528999999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.370799999999996 37.0 37.0 37.0 34.6 37.0 135-139 35.3464 37.0 37.0 37.0 37.0 37.0 140-144 35.029999999999994 37.0 37.0 37.0 27.4 37.0 145-149 34.6991 37.0 37.0 37.0 25.0 37.0 150-151 34.41425 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 4.0 14 4.0 15 3.0 16 1.0 17 3.0 18 0.0 19 2.0 20 1.0 21 3.0 22 3.0 23 7.0 24 3.0 25 6.0 26 13.0 27 17.0 28 15.0 29 11.0 30 16.0 31 31.0 32 71.0 33 106.0 34 187.0 35 500.0 36 2659.0 37 334.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.775 20.974999999999998 6.7250000000000005 26.525 2 28.725 23.724999999999998 26.724999999999998 20.825 3 23.9 25.674999999999997 27.474999999999998 22.95 4 26.775 30.075000000000003 20.925 22.225 5 27.250000000000004 31.724999999999998 20.075000000000003 20.95 6 25.05 33.650000000000006 20.424999999999997 20.875 7 25.4 19.225 33.0 22.375 8 24.25 21.95 24.55 29.25 9 23.974999999999998 20.925 26.8 28.299999999999997 10-14 26.815 24.545 23.26 25.380000000000003 15-19 26.484999999999996 24.23 23.625 25.66 20-24 26.634999999999998 24.7 23.27 25.395 25-29 26.83 24.845 23.29 25.035 30-34 25.985000000000003 24.625 23.580000000000002 25.81 35-39 26.619999999999997 24.915000000000003 23.365 25.1 40-44 26.590000000000003 24.865000000000002 23.325000000000003 25.22 45-49 26.369999999999997 24.75 23.36 25.52 50-54 26.169999999999998 24.425 23.815 25.590000000000003 55-59 26.655 24.385 23.44 25.52 60-64 26.19 24.425 23.665 25.72 65-69 26.669999999999998 25.005 23.474999999999998 24.85 70-74 25.82 24.11 24.595 25.474999999999998 75-79 26.965 24.965 23.615 24.455 80-84 27.155 24.79 23.45 24.605 85-89 27.18 24.89 23.335 24.595 90-94 27.68 24.535 23.515 24.27 95-99 26.840000000000003 24.63 23.794999999999998 24.735 100-104 27.665 25.130000000000003 22.759999999999998 24.445 105-109 27.785 24.93 22.785 24.5 110-114 28.335 25.259999999999998 23.025000000000002 23.380000000000003 115-119 28.73 24.92 22.97 23.380000000000003 120-124 29.085 25.22 22.759999999999998 22.935 125-129 29.220000000000002 25.55 22.255 22.975 130-134 29.520000000000003 25.81 22.085 22.585 135-139 29.799999999999997 24.985 22.85 22.365 140-144 30.675 24.865000000000002 22.415 22.045 145-149 31.735000000000003 25.28 22.515 20.47 150-151 31.4375 24.4375 22.45 21.675 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.5 7 0.5 8 0.5 9 1.5 10 1.0 11 0.0 12 0.5 13 0.5 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 1.5 23 1.5 24 0.5 25 1.5 26 2.0 27 2.0 28 2.5 29 2.0 30 4.5 31 7.0 32 7.0 33 13.0 34 19.0 35 25.5 36 41.5 37 50.0 38 55.5 39 70.0 40 99.0 41 135.5 42 144.5 43 141.0 44 162.0 45 172.5 46 171.5 47 188.0 48 182.5 49 164.5 50 155.5 51 142.0 52 140.5 53 133.5 54 103.5 55 92.5 56 98.0 57 88.5 58 79.5 59 87.5 60 80.5 61 69.5 62 67.5 63 73.0 64 77.5 65 68.0 66 75.0 67 72.0 68 65.5 69 62.5 70 55.5 71 51.5 72 40.5 73 36.0 74 31.0 75 21.0 76 13.5 77 10.0 78 5.0 79 3.0 80 3.5 81 1.0 82 0.0 83 0.0 84 0.0 85 0.5 86 1.0 87 1.0 88 0.5 89 0.0 90 0.0 91 1.0 92 1.0 93 0.0 94 0.0 95 2.0 96 2.0 97 1.0 98 2.5 99 2.5 100 4.0 >>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 82.875 #Duplication Level Percentage of deduplicated Percentage of total 1 84.07239819004525 69.675 2 12.39819004524887 20.549999999999997 3 2.7149321266968327 6.75 4 0.5429864253393665 1.7999999999999998 5 0.21116138763197587 0.8750000000000001 6 0.030165912518853696 0.15 7 0.0 0.0 8 0.030165912518853696 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 GCAGAAACATCCTTAACTGAGCTCCTCACTCACTCACTGCAGCTAGCCTC 8 0.2 No Hit AAAAGGCATTCTTTGCCCATAACAAACGGTAAACAAGATACATCACCTCG 6 0.15 No Hit AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 5 0.125 No Hit GGCAGAGTGGCTCCTCCTCCTCCCCCGAATCAGCAATTCAATCCTGCCCT 5 0.125 No Hit GTAGCTTTAGATCCTTCATGATCGCCGTGCAGCGTTGTGCCAGTAGTGTA 5 0.125 No Hit GGTGAGGCTGACAGGGCTGGGAGCCCGCGACAGCCTCCGTCTGGAGGCCG 5 0.125 No Hit CGGTCTGCACTTGTTGATATAATTCAAACTCGTGGTGTTCGAGGGCTTTA 5 0.125 No Hit GATCAAAGCATGCTGGCAGTGATAGTGAGGAGGAAGGAGGTCCTGTTCGT 5 0.125 No Hit GATCAAGTGAAGCAGACCATTCTGAAACTTCCTGGGTTCAAAGATGATGT 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 0.0125 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 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 0.0625 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.225 0.0 0.0 0.0 0.0 74-75 0.275 0.0 0.0 0.0 0.0 76-77 0.4125 0.0 0.0 0.0 0.0 78-79 0.4875 0.0 0.0 0.0 0.0 80-81 0.75 0.0 0.0 0.0 0.0 82-83 1.1 0.0 0.0 0.0 0.0 84-85 1.425 0.0 0.0 0.0 0.0 86-87 1.7000000000000002 0.0 0.0 0.0 0.0 88-89 2.0375 0.0 0.0 0.0 0.0 90-91 2.25 0.0 0.0 0.0 0.0 92-93 2.575 0.0 0.0 0.0 0.0 94-95 3.2249999999999996 0.0 0.0 0.0 0.0 96-97 3.7750000000000004 0.0 0.0 0.0 0.0 98-99 4.3125 0.0 0.0 0.0 0.0 100-101 5.125 0.0 0.0 0.0 0.0 102-103 5.8375 0.0 0.0 0.0 0.0 104-105 6.487500000000001 0.0 0.0 0.0 0.0 106-107 7.3875 0.0 0.0 0.0 0.0 108-109 8.1125 0.0 0.0 0.0 0.0 110-111 8.7125 0.0 0.0 0.0 0.0 112-113 9.6125 0.0 0.0 0.0 0.0 114-115 10.475000000000001 0.0 0.0 0.0 0.0 116-117 11.5375 0.0 0.0 0.0 0.0 118-119 12.375 0.0 0.0 0.0 0.0 120-121 13.2875 0.0 0.0 0.0 0.0 122-123 14.287500000000001 0.0 0.0 0.0 0.0 124-125 15.375 0.0 0.0 0.0 0.0 126-127 16.275 0.0 0.0 0.0 0.0 128-129 17.1125 0.0 0.0 0.0 0.0 130-131 17.975 0.0 0.0 0.0 0.0 132-133 18.7875 0.0 0.0 0.0 0.0 134-135 19.7375 0.0 0.0 0.0 0.0 136-137 20.6 0.0 0.0 0.0 0.0 138-139 21.4 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199942 spots for SRR12951290.sra Written 1199942 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra Read 1199926 spots for SRR12951290.sra Written 1199926 spots for SRR12951290.sra SRR ids: ['SRR12951290.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_w6lo_lj5 SRR12951290.sra spots: 23998536 blocks: [[1, 1199926], [1199927, 2399852], [2399853, 3599778], [3599779, 4799704], [4799705, 5999630], [5999631, 7199556], [7199557, 8399482], [8399483, 9599408], [9599409, 10799334], [10799335, 11999260], [11999261, 13199186], [13199187, 14399112], [14399113, 15599038], [15599039, 16798964], [16798965, 17998890], [17998891, 19198816], [19198817, 20398742], [20398743, 21598668], [21598669, 22798594], [22798595, 23998536]] SRR12951290 file size 8134052 SRR12951290 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 SRR12951290 SRR12951290_1.fastq SRR12951290_2.fastq Input file: SRR12951290_1.fastq Paired file: SRR12951290_2.fastq trimmed: SRR12951290-trimmed-pair1.fastq, SRR12951290-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 10:38:51 2024 >> started Sat Dec 7 10:39:17 2024 >> done (25.748s) 23998536 read pairs processed; of these: 271 ( 0.00%) short read pairs filtered out after trimming by size control 74329 ( 0.31%) empty read pairs filtered out after trimming by size control 23923936 (99.69%) read pairs available; of these: 5735184 (23.97%) trimmed read pairs available after processing 18188752 (76.03%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 18 0.00% 19 22 0.00% 20 22 0.00% 21 28 0.00% 22 34 0.00% 23 35 0.00% 24 43 0.00% 25 69 0.00% 26 78 0.00% 27 69 0.00% 28 65 0.00% 29 104 0.00% 30 83 0.00% 31 121 0.00% 32 108 0.00% 33 101 0.00% 34 110 0.00% 35 132 0.00% 36 146 0.00% 37 143 0.00% 38 173 0.00% 39 196 0.00% 40 209 0.00% 41 219 0.00% 42 267 0.00% 43 254 0.00% 44 258 0.00% 45 296 0.00% 46 323 0.00% 47 399 0.00% 48 514 0.00% 49 554 0.00% 50 699 0.00% 51 849 0.00% 52 847 0.00% 53 1022 0.00% 54 987 0.00% 55 1109 0.00% 56 1208 0.01% 57 1387 0.01% 58 1637 0.01% 59 1957 0.01% 60 2406 0.01% 61 2699 0.01% 62 3193 0.01% 63 3368 0.01% 64 3823 0.02% 65 3987 0.02% 66 4537 0.02% 67 4954 0.02% 68 5660 0.02% 69 6375 0.03% 70 7401 0.03% 71 8427 0.04% 72 9858 0.04% 73 11178 0.05% 74 11948 0.05% 75 13314 0.06% 76 14698 0.06% 77 15465 0.06% 78 16733 0.07% 79 18488 0.08% 80 20493 0.09% 81 22783 0.10% 82 25517 0.11% 83 27949 0.12% 84 30605 0.13% 85 32737 0.14% 86 34459 0.14% 87 35741 0.15% 88 37875 0.16% 89 39542 0.17% 90 42115 0.18% 91 45284 0.19% 92 47754 0.20% 93 50774 0.21% 94 54859 0.23% 95 57047 0.24% 96 58687 0.25% 97 60977 0.25% 98 61387 0.26% 99 63478 0.27% 100 64846 0.27% 101 66585 0.28% 102 68711 0.29% 103 71722 0.30% 104 74472 0.31% 105 75449 0.32% 106 78141 0.33% 107 78839 0.33% 108 79187 0.33% 109 79985 0.33% 110 80934 0.34% 111 81768 0.34% 112 84064 0.35% 113 86382 0.36% 114 88245 0.37% 115 91634 0.38% 116 90947 0.38% 117 91018 0.38% 118 91776 0.38% 119 91359 0.38% 120 91967 0.38% 121 92807 0.39% 122 92580 0.39% 123 94160 0.39% 124 96794 0.40% 125 97917 0.41% 126 98601 0.41% 127 99382 0.42% 128 98573 0.41% 129 98804 0.41% 130 98128 0.41% 131 97973 0.41% 132 98363 0.41% 133 100247 0.42% 134 100983 0.42% 135 101636 0.42% 136 101883 0.43% 137 100950 0.42% 138 101365 0.42% 139 102523 0.43% 140 100868 0.42% 141 100083 0.42% 142 100891 0.42% 143 100685 0.42% 144 101448 0.42% 145 103397 0.43% 146 102617 0.43% 147 102880 0.43% 148 102288 0.43% 149 101433 0.42% 150 101424 0.42% 151 18188752 76.03% 23923936 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=32 prefix-density=0.28 prefix-fanout=1.9 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.03 sequence-density-rank=33 fanout-score=453.18 fanout-score-rank=1 prefix-density=0.72 prefix-fanout=20.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=4.47 fanout-score-rank=21 prefix-density=0.28 prefix-fanout=3.8 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.09 sequence-density-rank=22 fanout-score=199.08 fanout-score-rank=1 prefix-density=0.81 prefix-fanout=22.5 sequence=CGGCGGCGGCGA SRR12951290 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:40:10 Started mapping on | Dec 07 10:40:10 Finished on | Dec 07 10:42:13 Mapping speed, Million of reads per hour | 700.21 Number of input reads | 23923936 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 22583840 Uniquely mapped reads % | 94.40% Average mapped length | 285.60 Number of splices: Total | 22065030 Number of splices: Annotated (sjdb) | 20615120 Number of splices: GT/AG | 21763404 Number of splices: GC/AG | 250868 Number of splices: AT/AC | 14150 Number of splices: Non-canonical | 36608 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.01% Deletion average length | 2.74 Insertion rate per base | 0.01% Insertion average length | 2.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 266832 % of reads mapped to multiple loci | 1.12% Number of reads mapped to too many loci | 47583 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.56% % of reads unmapped: other | 0.72% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1073264 1073264 1073264 N_multimapping 266832 266832 266832 N_noFeature 801621 22009873 994951 N_ambiguous 446819 3409 66888 UnstrandedReadsAssigned:21335400 PositiveStrandReadsAssigned:570558 NegativeStrandReadsAssigned:21522001 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=140 echo kmer=135 SRR12951290 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12951290-trimmed-pair1.fastq SRR12951290-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,923,936 reads, 21,798,068 reads pseudoaligned [quant] estimated average fragment length: 230.237 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,289 rounds 52973 SRR12951290.ke.tsv 35125 SRR12951290.se.tsv 88098 total ==> SRR12951290.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 707.259 0 0 PNS24247 1044 814.763 63.2989 5.3844 PNS24249 1928 1698.76 181.527 7.40597 PNS24246 1044 814.763 63.2989 5.3844 PNS24248 1044 814.763 63.2989 5.3844 PNS24244 1471 1241.76 102.576 5.72507 PNS24243 293 118.874 0 0 KQK14069 1603 1373.76 1814.66 91.5497 KQK14071 474 264.32 25.6538 6.72659 ==> SRR12951290.se.tsv <== BRADI_1g14170v3 1896 BRADI_1g53295v3 67 BRADI_1g59795v3 523 BRADI_1g07683v3 0 BRADI_1g00485v3 54 BRADI_1g20270v3 2531 BRADI_1g74790v3 269 BRADI_1g09890v3 26 BRADI_1g77505v3 391 BRADI_1g48960v3 1 SRR12951290 completed mapping pipeline successfully