Starting /dee2/code/volunteer_pipeline.sh SRR12768915 current disk space = 3057340461056 free memory = 1012570308 SRR12768915 SRAfilesize 54e6560b69db8d29d113d8745ef4e29d SRR12768915.sra SRR12768915.sra file validated SRR12768915 is paired end SRR12768915 is conventional basespace SRR12768915 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12768915_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.68 37.0 37.0 37.0 37.0 37.0 2 36.67 37.0 37.0 37.0 37.0 37.0 3 36.602 37.0 37.0 37.0 37.0 37.0 4 36.5405 37.0 37.0 37.0 37.0 37.0 5 36.436 37.0 37.0 37.0 37.0 37.0 6 36.447 37.0 37.0 37.0 37.0 37.0 7 36.475 37.0 37.0 37.0 37.0 37.0 8 36.4165 37.0 37.0 37.0 37.0 37.0 9 36.4295 37.0 37.0 37.0 37.0 37.0 10-14 36.406099999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.3667 37.0 37.0 37.0 37.0 37.0 20-24 36.3904 37.0 37.0 37.0 37.0 37.0 25-29 36.2033 37.0 37.0 37.0 37.0 37.0 30-34 36.1922 37.0 37.0 37.0 37.0 37.0 35-39 36.1634 37.0 37.0 37.0 37.0 37.0 40-44 36.1935 37.0 37.0 37.0 37.0 37.0 45-49 36.1788 37.0 37.0 37.0 37.0 37.0 50-54 36.149300000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.0205 37.0 37.0 37.0 37.0 37.0 60-64 36.048700000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.0115 37.0 37.0 37.0 37.0 37.0 70-74 35.705000000000005 37.0 37.0 37.0 37.0 37.0 75-79 35.2794 37.0 37.0 37.0 34.6 37.0 80-84 34.6727 37.0 37.0 37.0 25.0 37.0 85-89 33.9169 37.0 37.0 37.0 25.0 37.0 90-94 33.045899999999996 37.0 37.0 37.0 11.0 37.0 95-99 31.883699999999997 37.0 29.8 37.0 11.0 37.0 100-104 31.1844 37.0 25.0 37.0 11.0 37.0 105-109 30.590899999999998 37.0 25.0 37.0 11.0 37.0 110-114 30.6869 37.0 25.0 37.0 11.0 37.0 115-119 31.125099999999996 37.0 25.0 37.0 11.0 37.0 120-124 31.866200000000003 37.0 29.8 37.0 11.0 37.0 125-129 32.4371 37.0 37.0 37.0 11.0 37.0 130-134 33.014799999999994 37.0 37.0 37.0 11.0 37.0 135-139 33.312799999999996 37.0 37.0 37.0 11.0 37.0 140-144 33.841750000000005 37.0 37.0 37.0 25.0 37.0 145-149 34.2594 37.0 37.0 37.0 25.0 37.0 150 34.5385 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 0.0 22 3.0 23 5.0 24 12.0 25 27.0 26 27.0 27 45.0 28 47.0 29 48.0 30 63.0 31 85.0 32 144.0 33 352.0 34 1492.0 35 867.0 36 729.0 37 52.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 1.0820332159033719 95.16859587317565 2.415702063412179 1.3336688475088072 2 1.4500000000000002 1.875 6.275 90.4 3 12.125 70.5 9.925 7.449999999999999 4 18.725 33.775 32.550000000000004 14.95 5 33.35 22.8 28.875 14.975 6 27.650000000000002 24.7 31.225 16.425 7 23.775 25.974999999999998 33.650000000000006 16.6 8 24.375 24.775 32.525 18.325 9 28.65 25.1 31.474999999999998 14.774999999999999 10-14 26.255 25.115 31.135 17.495 15-19 25.39 25.77 31.0 17.84 20-24 25.230000000000004 24.965 31.324999999999996 18.48 25-29 24.695 26.255 30.835 18.215 30-34 24.93 27.33 29.82 17.919999999999998 35-39 25.405 28.205000000000002 29.294999999999998 17.095 40-44 25.535000000000004 29.65 27.26 17.555 45-49 25.540000000000003 29.865000000000002 25.779999999999998 18.815 50-54 26.155 30.23 23.855 19.759999999999998 55-59 24.725 30.825000000000003 23.315 21.135 60-64 24.065 30.044999999999998 22.585 23.305 65-69 21.82 29.82 23.365 24.995 70-74 19.805 28.349999999999998 24.975 26.87 75-79 18.990000000000002 27.49 26.075 27.445000000000004 80-84 18.9 25.319999999999997 27.185 28.595 85-89 18.685 23.599999999999998 28.444999999999997 29.270000000000003 90-94 19.03 22.08 30.825000000000003 28.065 95-99 20.905 21.42 30.59 27.084999999999997 100-104 24.705 21.245 29.25 24.8 105-109 31.47 19.759999999999998 26.279999999999998 22.49 110-114 38.86 18.58 23.255 19.305 115-119 45.375 17.825 20.505000000000003 16.295 120-124 51.72 16.35 17.84 14.09 125-129 57.879999999999995 14.035 15.634999999999998 12.45 130-134 62.419999999999995 12.33 14.02 11.23 135-139 66.645 12.1 12.46 8.795 140-144 70.3985199259963 10.640532026601331 10.735536776838842 8.225411270563528 145-149 73.88 9.19 9.44 7.489999999999999 150 76.325 8.450000000000001 7.925 7.3 >>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 1.0 9 2.0 10 1.5 11 2.0 12 2.5 13 1.5 14 1.0 15 1.5 16 2.5 17 4.0 18 4.0 19 4.5 20 4.0 21 2.5 22 3.5 23 4.0 24 4.0 25 5.5 26 5.5 27 6.0 28 7.0 29 14.5 30 18.0 31 19.0 32 30.5 33 33.0 34 32.0 35 36.0 36 50.0 37 66.0 38 75.0 39 92.5 40 117.0 41 146.0 42 174.0 43 203.0 44 240.0 45 279.5 46 320.0 47 345.0 48 348.5 49 328.0 50 275.5 51 212.0 52 167.0 53 126.5 54 74.5 55 41.0 56 25.0 57 12.5 58 7.0 59 6.0 60 5.0 61 4.0 62 3.0 63 1.0 64 1.5 65 1.0 66 0.0 67 0.0 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 0.65 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 0.005 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.775 #Duplication Level Percentage of deduplicated Percentage of total 1 88.39152491793494 74.05000000000001 2 8.654133094598627 14.499999999999998 3 1.4920919128618322 3.75 4 0.6266786034019696 2.1 5 0.2984183825723664 1.25 6 0.1492091912861832 0.75 7 0.17905102954341987 1.05 8 0.029841838257236648 0.2 9 0.029841838257236648 0.22499999999999998 >10 0.1492091912861832 2.125 >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 ACATGTTAGTGCTCCATGATCTTGAGAAGGAAACCTTGTCATTCCTTCCA 25 0.625 No Hit ACTATGCGACCAGATCTCTGATGCGGTGCTCGATGCTTGCCTTGAGCAGG 19 0.475 No Hit ACGTGTTGCTGTTGATATTTAATTTGGTAATTTGATGTCAATTTTCTGAT 16 0.4 No Hit ACATCCCAATTTCAGACTGTGAGTAACCCTGTAAGGAGATCGGAAGAGCA 15 0.375 No Hit ACAAAACCTTTGGGAATTGGAATATGATCCTCGTTGTAGTTTCTCTCAAG 10 0.25 No Hit ACGTGTTCTTTTGAAGATTGTTGTTCGATTGTTACCTGAGAAAAGAAGAT 9 0.22499999999999998 No Hit ACAAACTATGCGACCAGATCTCTGATGCGGTGCTCGATGCTTGCCTTGAG 8 0.2 No Hit ACGTGTCATTTATCTGGTTTGATCAATTCTGAAGCTATTATTTGTTTCCA 7 0.17500000000000002 No Hit ACATGGGAGACTGTCAAGCTTCTCAAGCCCAATGCCTAAGTCTTTGGGAT 7 0.17500000000000002 No Hit ACATTGGATTTGTTTCTGACGACGTTGGTCTTGATGCTGAGATCGGAAGA 7 0.17500000000000002 No Hit ACGTGTGATCTTTGGTATTGTAATAAAAAAAATAGATCGGAAGAGCACAC 7 0.17500000000000002 No Hit ACAGAATAACTACTCTGAAGAGGCTGAAACCGATATGGTTGATGAGATCG 7 0.17500000000000002 No Hit ACAAAAGAGGAACTAATGAAGGTGCTCTGACTAGAGTTGTCGCTAGATCG 7 0.17500000000000002 No Hit ACATCATTAGCAACTGAAATGGGAAGATTGGTCTCTGAAGGGTATGTGCT 6 0.15 No Hit ACAAACGTGTTGCTGTTGATATTTAATTTGGTAATTTGATGTCAATTTTC 6 0.15 No Hit ACTCTGTTGTGATTTTGATCTTTTCTTGATTAGGTTCATATTGTGATTTT 6 0.15 No Hit ACAAGTAGGAGCTCGAATTTCCCCGATCGTTCAAAGATCGGAAGAGCACA 6 0.15 No Hit ACAGCAGCAAAATGTAGTAATGTGTTCTTTGGACGAAAGATCGGAAGAGC 6 0.15 No Hit ACAAGATCTTCACGATGAATCTTTCTGCTCCATTTATCTGCGAGTTCTTC 5 0.125 No Hit ACAGACGTGGTTCCGAGGATGTAAGCAAAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) ACAACGATCAAGAGCGACTGTGCTATTCCTGCAATTCTTGCAAAGCTGGT 5 0.125 No Hit ACAAAACTGTATGGAGTCTATTAAACTTCTATGCCTACGTGAAAAACCAC 5 0.125 No Hit ACCGGTGCTGAAAGGAAAGAGGCTGCTGAGAGTACTCTCACTGCTTAGAT 5 0.125 No Hit ACCATGTCTGTTGGTACGTGTGATCTTTGGTATTGTAATAAAAAAAATAG 5 0.125 No Hit ACTGATAGTAGGAAGTGTACTTCCTTTTGTGTTTTTGTTTGGCTGCTATG 5 0.125 No Hit ACACTGTAGGAGATAGTTCAGGCTGGGCAATTGGTATGGATTATAGCACC 5 0.125 No Hit ACAAGGCCTATGGGATGACTGCATTTGAATATCATGGCACGGATCCAAGA 5 0.125 No Hit ACTCTGTTGTGATTTTGATCTTTTCTTCATTAGGTTCATATTGTGATTTT 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.0625 0.0 0.0 0.0 0.0 12-13 0.30000000000000004 0.0 0.0 0.0 0.0 14-15 0.48750000000000004 0.0 0.0 0.0 0.0 16-17 0.525 0.0 0.0 0.0 0.0 18-19 0.5375000000000001 0.0 0.0 0.0 0.0 20-21 0.6375 0.0 0.0 0.0 0.0 22-23 0.8500000000000001 0.0 0.0 0.0 0.0 24-25 1.2375 0.0 0.0 0.0 0.0 26-27 1.7625000000000002 0.0 0.0 0.0 0.0 28-29 2.7625 0.0 0.0 0.0 0.0 30-31 4.125 0.0 0.0 0.0 0.0 32-33 5.8875 0.0 0.0 0.0 0.0 34-35 8.3625 0.0 0.0 0.0 0.0 36-37 11.1625 0.0 0.0 0.0 0.0 38-39 13.899999999999999 0.0 0.0 0.0 0.0 40-41 16.8875 0.0 0.0 0.0125 0.0 42-43 19.875 0.0 0.0 0.025 0.0 44-45 23.3375 0.0 0.0 0.025 0.0 46-47 27.0375 0.0 0.0 0.025 0.0 48-49 30.2125 0.0 0.0 0.025 0.0 50-51 33.6375 0.0 0.0 0.025 0.0 52-53 37.2625 0.0 0.0 0.025 0.0 54-55 40.1375 0.0 0.0 0.025 0.0 56-57 43.4 0.0 0.0 0.025 0.0 58-59 46.2125 0.0 0.0 0.025 0.0 60-61 48.6125 0.0 0.0 0.025 0.0 62-63 50.7625 0.0 0.0 0.025 0.0 64-65 52.650000000000006 0.0 0.0 0.025 0.0 66-67 54.675 0.0 0.0 0.025 0.0 68-69 56.6 0.0 0.0 0.025 0.0 70-71 58.925 0.0 0.0 0.025 0.0 72-73 60.825 0.0 0.0 0.025 0.0 74-75 62.6875 0.0 0.0 0.025 0.0 76-77 64.225 0.0 0.0 0.025 0.0 78-79 65.48750000000001 0.0 0.0 0.025 0.0 80-81 66.75 0.0 0.0 0.025 0.0 82-83 67.7625 0.0 0.0 0.025 0.0 84-85 68.4625 0.0 0.0 0.025 0.0 86-87 69.3375 0.0 0.0 0.025 0.0 88-89 70.25 0.0 0.0 0.025 0.0 90-91 71.375 0.0 0.0 0.025 0.0 92-93 72.2375 0.0 0.0 0.025 0.0 94-95 73.0625 0.0 0.0 0.025 0.0 96-97 73.8625 0.0 0.0 0.025 0.0 98-99 74.4375 0.0 0.0 0.025 0.0 100-101 75.0625 0.0 0.0 0.025 0.0 102-103 75.4625 0.0 0.0 0.025 0.0 104-105 76.25 0.0 0.0 0.025 0.0 106-107 76.75 0.0 0.0 0.025 0.0 108-109 77.2 0.0 0.0 0.025 0.0 110-111 77.6125 0.0 0.0 0.025 0.0 112-113 78.025 0.0 0.0 0.025 0.0 114-115 78.625 0.0 0.0 0.025 0.0 116-117 79.2125 0.0 0.0 0.025 0.0 118-119 79.9625 0.0 0.0 0.025 0.0 120-121 80.5625 0.0 0.0 0.025 0.0 122-123 80.8375 0.0 0.0 0.025 0.0 124-125 81.2375 0.0 0.0 0.025 0.0 126-127 81.82499999999999 0.0 0.0 0.025 0.0 128-129 82.275 0.0 0.0 0.025 0.0 130-131 82.4875 0.0 0.0 0.025 0.0 132-133 82.80000000000001 0.0 0.0 0.025 0.0 134-135 83.05000000000001 0.0 0.0 0.025 0.0 136-137 83.25 0.0 0.0 0.025 0.0 138 83.425 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATGATG 10 0.006973645 144.0 2 ACATGTG 10 0.006973645 144.0 1 ACATGGA 15 1.1730364E-4 144.0 1 ACAGAAC 10 0.006973645 144.0 1 ACATGAT 20 1.9452218E-6 144.0 1 CATTTTG 10 0.006973645 144.0 2 ACATCGG 10 0.006973645 144.0 1 ATTTTGT 10 0.006973645 144.0 3 ACAACTT 10 0.006973645 144.0 1 ACATTTT 20 3.687869E-4 108.0 1 GGGGGGG 6000 0.0 5.3040004 140-144 >>END_MODULE SRR12768915 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12768915_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.843 37.0 37.0 37.0 37.0 37.0 2 35.955 37.0 37.0 37.0 37.0 37.0 3 36.2665 37.0 37.0 37.0 37.0 37.0 4 36.4425 37.0 37.0 37.0 37.0 37.0 5 36.4635 37.0 37.0 37.0 37.0 37.0 6 36.562 37.0 37.0 37.0 37.0 37.0 7 36.6145 37.0 37.0 37.0 37.0 37.0 8 36.647 37.0 37.0 37.0 37.0 37.0 9 36.511 37.0 37.0 37.0 37.0 37.0 10-14 36.61094999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.441 37.0 37.0 37.0 37.0 37.0 20-24 36.3993 37.0 37.0 37.0 37.0 37.0 25-29 36.390499999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.378499999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.299549999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.303700000000006 37.0 37.0 37.0 37.0 37.0 45-49 36.241 37.0 37.0 37.0 37.0 37.0 50-54 36.230599999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.1827 37.0 37.0 37.0 37.0 37.0 60-64 36.1637 37.0 37.0 37.0 37.0 37.0 65-69 36.0256 37.0 37.0 37.0 37.0 37.0 70-74 35.947500000000005 37.0 37.0 37.0 37.0 37.0 75-79 35.8554 37.0 37.0 37.0 37.0 37.0 80-84 35.754450000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.304899999999996 37.0 37.0 37.0 37.0 37.0 90-94 34.863099999999996 37.0 37.0 37.0 27.4 37.0 95-99 34.122550000000004 37.0 37.0 37.0 25.0 37.0 100-104 33.467949999999995 37.0 37.0 37.0 13.8 37.0 105-109 32.74625 37.0 37.0 37.0 11.0 37.0 110-114 32.21905 37.0 37.0 37.0 11.0 37.0 115-119 31.806600000000003 37.0 37.0 37.0 11.0 37.0 120-124 31.743900000000004 37.0 32.2 37.0 11.0 37.0 125-129 31.623999999999995 37.0 32.2 37.0 11.0 37.0 130-134 31.42145 37.0 25.0 37.0 11.0 37.0 135-139 31.63825 37.0 29.8 37.0 11.0 37.0 140-144 31.838399999999996 37.0 34.6 37.0 11.0 37.0 145-149 31.849200000000003 37.0 34.6 37.0 11.0 37.0 150 32.22925 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 1.0 18 0.0 19 1.0 20 0.0 21 2.0 22 15.0 23 11.0 24 17.0 25 20.0 26 16.0 27 22.0 28 29.0 29 47.0 30 104.0 31 199.0 32 262.0 33 331.0 34 497.0 35 1004.0 36 1334.0 37 87.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 17.5 22.55 34.050000000000004 25.900000000000002 2 15.875 29.299999999999997 21.65 33.175 3 12.525 23.175 40.1 24.2 4 17.75 26.474999999999998 29.049999999999997 26.724999999999998 5 19.125 31.25 26.3 23.325000000000003 6 17.05 30.575000000000003 28.475 23.9 7 17.625 28.199999999999996 26.275 27.900000000000002 8 17.2 33.375 27.0 22.425 9 17.1 31.075000000000003 28.1 23.724999999999998 10-14 18.63593179658983 29.951497574878744 25.861293064653236 25.551277563878195 15-19 17.645 30.53 26.575 25.25 20-24 18.815 31.169999999999998 25.874999999999996 24.14 25-29 18.09 30.525000000000002 26.419999999999998 24.965 30-34 19.725 29.15 27.58 23.544999999999998 35-39 20.776038801940096 29.91649582479124 27.031351567578376 22.276113805690283 40-44 22.285 28.15 26.71 22.855 45-49 22.53 28.365000000000002 27.075 22.03 50-54 23.07 27.965 27.800000000000004 21.165 55-59 24.265 27.994999999999997 26.619999999999997 21.12 60-64 23.580000000000002 28.335 27.095000000000002 20.990000000000002 65-69 24.435000000000002 27.62 27.49 20.455000000000002 70-74 25.27 25.55 28.21 20.97 75-79 27.16 23.735 28.235 20.87 80-84 27.01635081754088 24.011200560028 27.75638781939097 21.21606080304015 85-89 26.255 24.575 28.294999999999998 20.875 90-94 26.200000000000003 26.075 28.335 19.39 95-99 28.32641632081604 27.05635281764088 26.606330316515823 18.01090054502725 100-104 30.09150457522876 27.68638431921596 25.891294564728234 16.330816540827044 105-109 34.45172258612931 26.676333816690835 24.951247562378118 13.920696034801741 110-114 41.16705835291764 24.8262413120656 21.626081304065202 12.380619030951548 115-119 47.18 22.33 19.42 11.07 120-124 51.665000000000006 20.419999999999998 17.645 10.27 125-129 56.705000000000005 19.36 15.495000000000001 8.44 130-134 61.23306165308266 17.030851542577132 14.280714035701786 7.455372768638433 135-139 65.04825241262063 14.72073603680184 13.230661533076654 7.0003500175008755 140-144 68.83500000000001 13.364999999999998 11.465 6.335 145-149 71.72717271727173 12.016201620162017 10.716071607160716 5.540554055405541 150 74.69367341835459 11.0527631907977 9.177294323580895 5.076269067266817 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 9.0 1 5.5 2 2.5 3 3.5 4 2.5 5 2.5 6 3.0 7 2.0 8 1.5 9 2.0 10 2.5 11 1.0 12 0.5 13 1.0 14 2.5 15 2.0 16 2.5 17 4.5 18 4.5 19 3.5 20 3.0 21 3.0 22 2.5 23 6.0 24 6.0 25 3.0 26 3.5 27 7.5 28 10.5 29 10.5 30 14.0 31 16.0 32 16.5 33 22.0 34 30.0 35 40.0 36 52.5 37 70.5 38 82.0 39 91.5 40 110.0 41 132.5 42 186.5 43 229.5 44 275.0 45 312.0 46 311.0 47 315.5 48 332.0 49 306.5 50 233.5 51 183.0 52 166.5 53 126.0 54 73.0 55 62.5 56 44.0 57 18.5 58 10.0 59 7.0 60 4.0 61 3.5 62 4.0 63 3.0 64 1.5 65 1.0 66 0.5 67 0.5 68 0.5 69 0.5 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 0.5 82 0.5 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 0.5 >>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 0.005 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.005 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 0.005 85-89 0.0 90-94 0.0 95-99 0.005 100-104 0.005 105-109 0.005 110-114 0.005 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.005 135-139 0.005 140-144 0.0 145-149 0.01 150 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.325 #Duplication Level Percentage of deduplicated Percentage of total 1 88.53885388538853 73.775 2 8.310831083108312 13.850000000000001 3 1.8901890189018902 4.725 4 0.4800480048004801 1.6 5 0.15001500150015 0.625 6 0.15001500150015 0.75 7 0.21002100210021002 1.225 8 0.030003000300030006 0.2 9 0.06000600060006001 0.44999999999999996 >10 0.18001800180018002 2.8000000000000003 >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 CCTGCTCAAGGCAAGCATCGAGCACCGCATCAGAGATCTGGTCGCATAGT 26 0.65 No Hit TGGAAGGAATGACAAGGTTTCCTTCTCAAGATCATGGAGCACTAACATGT 24 0.6 No Hit AGTTCACAATCCAAAGCCTAATCAGAAAATTGACATCAAATTACCAAATT 24 0.6 No Hit CCTTACAGGGTTACTCACAGTCTGAAATTGGGATGTGATCGTCGGACTGT 15 0.375 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 12 0.3 No Hit GCTTTCTTGAGAGAAACTACAACGAGGATCATATTCCAATTCCCAAAGGT 11 0.27499999999999997 No Hit TCTTTTCTCAGGTAACAATCGAACAACAATCTTCAAAAGAACACGTGATC 9 0.22499999999999998 No Hit TTTCCTCAGCCATACTGATCAAAATCACAATATGAACCTAATCAAGAAAA 9 0.22499999999999998 No Hit ATTTTTTTTATTACAATACCAAAGATCACACGTGATCGTCGGACTGTAGA 8 0.2 No Hit CATCAACCATATCGGTTTCAGCCTCTTCAGAGTAGTTATTCTGTGATCGT 7 0.17500000000000002 No Hit AAATGGAAACAAATAATAGCTTCAGAATTGATCAAACCAGATAAATGACA 7 0.17500000000000002 No Hit TTGAACGATCGGGGAAATTCGAGCTCCTACTTGTGATCGTCGGACTGTAG 7 0.17500000000000002 No Hit CTGGGTCCTGCTCAAGGCAGGCATCGAGCACTGCATCAGAGATCTGGTCA 7 0.17500000000000002 No Hit AGCGACAACTCTAGTCAGAGCACCTTCATTAGTTCCTCTTTTGTGATCGT 7 0.17500000000000002 No Hit AAGGGGCCACCCACCCATTCCCCTTAGCCCTCTCACTCCCTAAGCTAAGG 7 0.17500000000000002 No Hit CAGCATCAAGACCAACGTCGTCAGAAACAAATCCAATGTGATCGTCGGAC 7 0.17500000000000002 No Hit ATCAAGCCAATCCCAAAGACTTAGGCATTGGGCTTGAGAAGCTTGACAGT 6 0.15 No Hit ATTTTTTTTATTACAATACCAAAGATCACACGTACCAACAGACATGGTGA 6 0.15 No Hit TTCGTCCAAAGAACACATTACTACATTTTGCTGCTGTGATCGTCGGACTG 6 0.15 No Hit ATCTTAATGCATGAGATTAGACCATTGAGGATAGCTAACGATTATAGACC 6 0.15 No Hit TAGCACATACCCTTCAGAGACCAATCTTCCCATTTCAGTTGCTAATGATG 6 0.15 No Hit ATGAAACCTCTGGTGCACTTTACGTGGTTTTTCACGTAGGCATAGAAGTT 5 0.125 No Hit TTTCCTCAGCCATACTGATCAAAATCACAATATGAACCTAATGAAGAAAA 5 0.125 No Hit AAGCAGTGAGAGTACTCTCAGCAGCCTCTTTCCTTTCAGCACCGGTGATC 5 0.125 No Hit TTGCTTACATCCTCGGAACCACGTCTGTGATCGTCGGACTGTAGAACTCT 5 0.125 Illumina DpnII expression Sequencing Primer (100% over 22bp) TAATGACCGAGACCTTCCTCCAACTCTTCCTCAGGTTGGCTAGCAAACCA 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 0.025 0.0 0.0 2 0.0 0.0 0.025 0.0 0.0 3 0.0 0.0 0.025 0.0 0.0 4 0.0 0.0 0.025 0.0 0.0 5 0.0 0.0 0.025 0.0 0.0 6 0.0 0.0 0.025 0.0 0.0 7 0.0 0.0 0.025 0.0 0.0 8 0.0 0.0 0.05 0.0 0.0 9 0.0 0.0 0.05 0.0 0.0 10-11 0.0 0.0 0.0875 0.0 0.0 12-13 0.0 0.0 0.325 0.0 0.0 14-15 0.0 0.0 0.5125 0.0 0.0 16-17 0.0 0.0 0.55 0.0 0.0 18-19 0.0 0.0 0.5625 0.0 0.0 20-21 0.0 0.0 0.6625 0.0 0.0 22-23 0.0 0.0 0.8999999999999999 0.0 0.0 24-25 0.0 0.0 1.2125 0.0 0.0 26-27 0.0 0.0 1.7125 0.0 0.0 28-29 0.0 0.0 2.7 0.0 0.0 30-31 0.0 0.0 4.0125 0.0 0.0 32-33 0.0 0.0 5.762499999999999 0.0 0.0 34-35 0.0 0.0 8.2375 0.0 0.0 36-37 0.0 0.0 10.95 0.0 0.0 38-39 0.0 0.0 13.75 0.0 0.0 40-41 0.0 0.0 16.7125 0.0 0.0 42-43 0.0 0.0 19.612499999999997 0.0 0.0 44-45 0.0 0.0 23.049999999999997 0.0 0.0 46-47 0.0 0.0 26.8375 0.0 0.0 48-49 0.0 0.0 30.075 0.0 0.0 50-51 0.0 0.0 33.4875 0.0 0.0 52-53 0.0 0.0 37.0375 0.0 0.0 54-55 0.0 0.0 39.8875 0.0 0.0 56-57 0.0 0.0 43.2 0.0 0.0 58-59 0.0 0.0 45.95 0.0 0.0 60-61 0.0 0.0 48.3375 0.0 0.0 62-63 0.0 0.0 50.475 0.0 0.0 64-65 0.0 0.0 52.3 0.0 0.0 66-67 0.0 0.0 54.2625 0.0 0.0 68-69 0.0 0.0 56.1875 0.0 0.0 70-71 0.0 0.0 58.4625 0.0 0.0 72-73 0.0 0.0 60.275000000000006 0.0 0.0 74-75 0.0 0.0 62.1375 0.0 0.0 76-77 0.0 0.0 63.7125 0.0 0.0 78-79 0.0 0.0 64.9625 0.0 0.0 80-81 0.0 0.0 66.1875 0.0 0.0 82-83 0.0 0.0 67.1625 0.0 0.0 84-85 0.0 0.0 67.9375 0.0 0.0 86-87 0.0 0.0 68.7625 0.0 0.0 88-89 0.0 0.0 69.6875 0.0 0.0 90-91 0.0 0.0 70.8 0.0 0.0 92-93 0.0 0.0 71.6625 0.0 0.0 94-95 0.0 0.0 72.5375 0.0 0.0 96-97 0.0 0.0 73.32499999999999 0.0 0.0 98-99 0.0 0.0 73.875 0.0 0.0 100-101 0.0 0.0 74.45 0.0 0.0 102-103 0.0 0.0 74.8375 0.0 0.0 104-105 0.0 0.0 75.625 0.0 0.0 106-107 0.0 0.0 76.125 0.0 0.0 108-109 0.0 0.0 76.55 0.0 0.0 110-111 0.0 0.0 76.9625 0.0 0.0 112-113 0.0 0.0 77.375 0.0 0.0 114-115 0.0 0.0 77.9875 0.0 0.0 116-117 0.0 0.0 78.5625 0.0 0.0 118-119 0.0 0.0 79.2625 0.0 0.0 120-121 0.0 0.0 79.9125 0.0 0.0 122-123 0.0 0.0 80.175 0.0 0.0 124-125 0.0 0.0 80.6 0.0 0.0 126-127 0.0 0.0 81.1875 0.0 0.0 128-129 0.0 0.0 81.6625 0.0 0.0 130-131 0.0 0.0 81.8625 0.0 0.0 132-133 0.0 0.0 82.15 0.0 0.0 134-135 0.0 0.0 82.375 0.0 0.0 136-137 0.0 0.0 82.57499999999999 0.0 0.0 138 0.0 0.0 82.85 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGTCCT 10 0.006973645 144.0 3 CTGGGTC 10 0.006973645 144.0 1 CCTGCTC 10 0.006973645 144.0 7 GGTCCTG 10 0.006973645 144.0 4 ATTGGCC 10 0.006973645 144.0 7 TGCTCAA 10 0.006973645 144.0 9 TGGGTCC 10 0.006973645 144.0 2 CTGCTCA 10 0.006973645 144.0 8 AAAGCTC 10 0.006973645 144.0 7 >>END_MODULE Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543635 spots for SRR12768915.sra Written 2543635 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra Read 2543631 spots for SRR12768915.sra Written 2543631 spots for SRR12768915.sra SRR ids: ['SRR12768915.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bbgdgaht SRR12768915.sra spots: 50872624 blocks: [[1, 2543631], [2543632, 5087262], [5087263, 7630893], [7630894, 10174524], [10174525, 12718155], [12718156, 15261786], [15261787, 17805417], [17805418, 20349048], [20349049, 22892679], [22892680, 25436310], [25436311, 27979941], [27979942, 30523572], [30523573, 33067203], [33067204, 35610834], [35610835, 38154465], [38154466, 40698096], [40698097, 43241727], [43241728, 45785358], [45785359, 48328989], [48328990, 50872624]] SRR12768915 file size 17167682 SRR12768915 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 SRR12768915 SRR12768915_1.fastq SRR12768915_2.fastq Input file: SRR12768915_1.fastq Paired file: SRR12768915_2.fastq trimmed: SRR12768915-trimmed-pair1.fastq, SRR12768915-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 22:29:56 2025 >> started Mon Feb 10 22:30:49 2025 >> done (53.162s) 50872624 read pairs processed; of these: 211630 ( 0.42%) short read pairs filtered out after trimming by size control 11159 ( 0.02%) empty read pairs filtered out after trimming by size control 50649835 (99.56%) read pairs available; of these: 43619516 (86.12%) trimmed read pairs available after processing 7030319 (13.88%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 23878 0.05% 19 34370 0.07% 20 36591 0.07% 21 65521 0.13% 22 66776 0.13% 23 83079 0.16% 24 149535 0.30% 25 123012 0.24% 26 169419 0.33% 27 208357 0.41% 28 318086 0.63% 29 288325 0.57% 30 451484 0.89% 31 399630 0.79% 32 388437 0.77% 33 721004 1.42% 34 734334 1.45% 35 638507 1.26% 36 829643 1.64% 37 676595 1.34% 38 684166 1.35% 39 878122 1.73% 40 661396 1.31% 41 793311 1.57% 42 785776 1.55% 43 814663 1.61% 44 942774 1.86% 45 919214 1.81% 46 1071797 2.12% 47 798318 1.58% 48 955685 1.89% 49 796900 1.57% 50 1116107 2.20% 51 878903 1.74% 52 822388 1.62% 53 707480 1.40% 54 793419 1.57% 55 678943 1.34% 56 664607 1.31% 57 668544 1.32% 58 549579 1.09% 59 625651 1.24% 60 640580 1.26% 61 528542 1.04% 62 549409 1.08% 63 496615 0.98% 64 524026 1.03% 65 501896 0.99% 66 587588 1.16% 67 426237 0.84% 68 464590 0.92% 69 491389 0.97% 70 702355 1.39% 71 426143 0.84% 72 495328 0.98% 73 469333 0.93% 74 471355 0.93% 75 348810 0.69% 76 343303 0.68% 77 311238 0.61% 78 376464 0.74% 79 282816 0.56% 80 307336 0.61% 81 319302 0.63% 82 241449 0.48% 83 246933 0.49% 84 315390 0.62% 85 239029 0.47% 86 231457 0.46% 87 241032 0.48% 88 229018 0.45% 89 218722 0.43% 90 285997 0.56% 91 204210 0.40% 92 207369 0.41% 93 213448 0.42% 94 213552 0.42% 95 193117 0.38% 96 242682 0.48% 97 164538 0.32% 98 172528 0.34% 99 206751 0.41% 100 154168 0.30% 101 150254 0.30% 102 179927 0.36% 103 157969 0.31% 104 147500 0.29% 105 152942 0.30% 106 139824 0.28% 107 144139 0.28% 108 158962 0.31% 109 145728 0.29% 110 156995 0.31% 111 138048 0.27% 112 123660 0.24% 113 141454 0.28% 114 129611 0.26% 115 125946 0.25% 116 115869 0.23% 117 132479 0.26% 118 126628 0.25% 119 108119 0.21% 120 108033 0.21% 121 109582 0.22% 122 100364 0.20% 123 101797 0.20% 124 112270 0.22% 125 92226 0.18% 126 104961 0.21% 127 94734 0.19% 128 95509 0.19% 129 90097 0.18% 130 89932 0.18% 131 89830 0.18% 132 105197 0.21% 133 78815 0.16% 134 81122 0.16% 135 89256 0.18% 136 81554 0.16% 137 77819 0.15% 138 88074 0.17% 139 74705 0.15% 140 93921 0.19% 141 75217 0.15% 142 72398 0.14% 143 70391 0.14% 144 93234 0.18% 145 76290 0.15% 146 75928 0.15% 147 74881 0.15% 148 73435 0.14% 149 71519 0.14% 150 7030319 13.88% 50649835 reads passed initial QC criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=1.74 fanout-score-rank=13 prefix-density=0.93 prefix-fanout=1.0 sequence=ATCTCTGATGCGGTGCTCGATGCTTGCCTTGAGCAGGACCCAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=63.71 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=5.9 sequence=TTTTTCTTCATTTTACGTGTTCTTTTGAAGATTGTTGTTCGATTGTTACCTGAGAAAAGA criterion=sequence-density sequence-density=0.92 sequence-density-rank=1 fanout-score=2.30 fanout-score-rank=13 prefix-density=0.96 prefix-fanout=2.2 sequence=GCATCAGAGATCTGGTCGCATAGTTTGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=11.24 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=3.2 sequence=TTTTTTTTCTTTTCTCAGGTAACAATCGAACAACAATCTTCAAAAGAACACGTAAAATGAAGAAAA SRR12768915 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 22:31:23 Started mapping on | Feb 10 22:31:23 Finished on | Feb 10 22:34:39 Mapping speed, Million of reads per hour | 930.30 Number of input reads | 50649835 Average input read length | 151 UNIQUE READS: Uniquely mapped reads number | 41724007 Uniquely mapped reads % | 82.38% Average mapped length | 133.51 Number of splices: Total | 15061162 Number of splices: Annotated (sjdb) | 14802233 Number of splices: GT/AG | 14769105 Number of splices: GC/AG | 222669 Number of splices: AT/AC | 11646 Number of splices: Non-canonical | 57742 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.02% Deletion average length | 2.02 Insertion rate per base | 0.01% Insertion average length | 1.56 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1845147 % of reads mapped to multiple loci | 3.64% Number of reads mapped to too many loci | 326117 % of reads mapped to too many loci | 0.64% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 13.16% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7080681 7080681 7080681 N_multimapping 1845147 1845147 1845147 N_noFeature 1967374 2082133 41286250 N_ambiguous 467363 144061 886 UnstrandedReadsAssigned:39289270 PositiveStrandReadsAssigned:39497813 NegativeStrandReadsAssigned:436871 Dataset is classified positive stranded MeadianReadLen=61 20thPercentileLength=42 echo kmer=37 SRR12768915 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: SRR12768915-trimmed-pair1.fastq SRR12768915-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 50,649,835 reads, 38,367,046 reads pseudoaligned [quant] estimated average fragment length: 65.3701 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,177 rounds 52401 SRR12768915.ke.tsv 34699 SRR12768915.se.tsv 87100 total ==> SRR12768915.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1953.63 1000.53 20.3058 Potri.005G024800.1.v4.1 1035 970.63 312 12.7448 Potri.004G059700.1.v4.1 961 896.63 33 1.45927 Potri.007G009000.2.v4.1 1416 1351.63 0 0 Potri.003G141000.2.v4.1 2943 2878.63 819.533 11.2879 Potri.016G087400.1.v4.1 270 206.121 459 88.2927 Potri.015G069301.1.v4.1 564 499.635 0 0 Potri.010G195200.1.v4.1 1773 1708.63 145.49 3.37612 Potri.012G127500.1.v4.1 977 912.63 3007 130.639 ==> SRR12768915.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2018 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 436 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 51 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 10 SRR12768915 completed mapping pipeline successfully