Starting /dee2/code/volunteer_pipeline.sh SRR18694439 current disk space = 1525920010240 free memory = 1553622328 SRR18694439 SRAfilesize a2ba67d90861a18b80edef8168dab900 SRR18694439.sra SRR18694439.sra file validated SRR18694439 is paired end SRR18694439 is conventional basespace SRR18694439 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694439_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 36.116 37.0 37.0 37.0 37.0 37.0 2 36.0825 37.0 37.0 37.0 37.0 37.0 3 36.3265 37.0 37.0 37.0 37.0 37.0 4 36.4595 37.0 37.0 37.0 37.0 37.0 5 36.575 37.0 37.0 37.0 37.0 37.0 6 36.515 37.0 37.0 37.0 37.0 37.0 7 36.4685 37.0 37.0 37.0 37.0 37.0 8 36.546 37.0 37.0 37.0 37.0 37.0 9 36.5765 37.0 37.0 37.0 37.0 37.0 10-14 36.6013 37.0 37.0 37.0 37.0 37.0 15-19 36.619 37.0 37.0 37.0 37.0 37.0 20-24 36.6083 37.0 37.0 37.0 37.0 37.0 25-29 36.527499999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.507799999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.6676 37.0 37.0 37.0 37.0 37.0 40-44 36.5903 37.0 37.0 37.0 37.0 37.0 45-49 36.41930000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.513 37.0 37.0 37.0 37.0 37.0 55-59 36.5259 37.0 37.0 37.0 37.0 37.0 60-64 36.49759999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.284299999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.38950000000001 37.0 37.0 37.0 37.0 37.0 75-79 36.4531 37.0 37.0 37.0 37.0 37.0 80-84 36.3885 37.0 37.0 37.0 37.0 37.0 85-89 36.179899999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.424699999999994 37.0 37.0 37.0 29.8 37.0 95-99 36.14489999999999 37.0 37.0 37.0 37.0 37.0 100-104 36.1258 37.0 37.0 37.0 37.0 37.0 105-109 36.1591 37.0 37.0 37.0 37.0 37.0 110-114 36.1491 37.0 37.0 37.0 37.0 37.0 115-119 36.498 37.0 37.0 37.0 37.0 37.0 120-124 36.539100000000005 37.0 37.0 37.0 37.0 37.0 125-129 36.5364 37.0 37.0 37.0 37.0 37.0 130-134 36.51370000000001 37.0 37.0 37.0 37.0 37.0 135-139 36.411300000000004 37.0 37.0 37.0 37.0 37.0 140-144 36.2621 37.0 37.0 37.0 37.0 37.0 145-149 36.2299 37.0 37.0 37.0 37.0 37.0 150-151 33.6185 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 2.0 26 3.0 27 3.0 28 3.0 29 5.0 30 10.0 31 17.0 32 37.0 33 49.0 34 109.0 35 350.0 36 3202.0 37 208.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.975 9.65 5.125 37.25 2 23.669678714859437 9.738955823293173 35.6425702811245 30.948795180722893 3 20.674999999999997 14.499999999999998 23.825 41.0 4 25.75 19.85 21.825 32.574999999999996 5 26.900000000000002 26.625 21.9 24.575 6 24.025 28.825 24.125 23.025000000000002 7 17.95 24.85 38.0 19.2 8 19.075 23.474999999999998 30.275000000000002 27.175 9 20.349999999999998 22.3 33.95 23.400000000000002 10-14 23.71 25.69 25.865 24.735 15-19 23.695 24.535 25.655 26.115 20-24 23.615 24.834999999999997 26.224999999999998 25.324999999999996 25-29 24.05 25.180000000000003 25.230000000000004 25.540000000000003 30-34 23.405 25.080000000000002 25.069999999999997 26.445 35-39 23.630000000000003 24.865000000000002 25.535000000000004 25.97 40-44 24.235 24.8 24.965 26.0 45-49 23.775 24.64 25.25 26.334999999999997 50-54 23.79 24.905 25.240000000000002 26.064999999999998 55-59 23.49 25.009999999999998 25.46 26.040000000000003 60-64 23.935000000000002 24.759999999999998 24.9 26.405 65-69 24.490000000000002 25.455 24.83 25.224999999999998 70-74 24.005000000000003 25.44 24.38 26.174999999999997 75-79 24.654999999999998 24.27 24.89 26.185000000000002 80-84 24.060000000000002 25.259999999999998 24.715 25.965 85-89 23.72 24.545 24.97 26.765 90-94 24.515 24.73 24.654999999999998 26.1 95-99 24.51 24.62 24.84 26.029999999999998 100-104 24.19 24.975 24.560000000000002 26.275 105-109 24.9 24.87 24.46 25.77 110-114 24.245 24.575 24.62 26.56 115-119 24.425 24.46 24.815 26.3 120-124 24.335 24.815 24.255 26.595000000000002 125-129 24.765 24.884999999999998 24.15 26.200000000000003 130-134 25.169999999999998 24.060000000000002 24.060000000000002 26.71 135-139 25.074999999999996 24.41 24.349999999999998 26.165 140-144 24.98 25.28 23.97 25.77 145-149 24.625 24.915000000000003 24.205 26.255 150-151 24.925 25.087500000000002 23.8875 26.1 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.5 5 0.5 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 1.0 27 2.0 28 2.0 29 2.0 30 7.5 31 17.0 32 17.5 33 23.5 34 30.0 35 33.5 36 52.0 37 51.0 38 65.0 39 93.0 40 104.0 41 136.0 42 161.5 43 165.0 44 173.5 45 183.5 46 185.0 47 196.5 48 183.5 49 159.5 50 149.0 51 143.0 52 140.0 53 124.5 54 102.0 55 87.0 56 105.5 57 102.5 58 85.5 59 91.0 60 85.5 61 74.0 62 65.0 63 66.5 64 77.0 65 69.0 66 61.5 67 57.0 68 52.0 69 48.0 70 42.0 71 34.5 72 22.5 73 18.0 74 14.5 75 13.5 76 10.0 77 4.0 78 2.5 79 2.0 80 0.5 81 0.0 82 0.5 83 0.5 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 0.4 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 84.5 #Duplication Level Percentage of deduplicated Percentage of total 1 85.6508875739645 72.375 2 11.627218934911243 19.650000000000002 3 1.982248520710059 5.025 4 0.4733727810650888 1.6 5 0.20710059171597633 0.8750000000000001 6 0.02958579881656805 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02958579881656805 0.325 >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 GGCCATCCTTGTGTTTCAGGTGGATTTCAGGCTCTCCAGCTGGTGCTTAA 13 0.325 No Hit TTCTGGCCAGGGCGGAGGATGAAGGGCATGGACAGCAGCATGGCGAGCTT 6 0.15 No Hit TGCAGATTTTGCTCCTACATACCTGTTGAGTCCGTGTAGCACAAGAAAAT 5 0.125 No Hit GCCTGCTGCAAACTTCTCAAACTCAAAGACTCCCATAGGTCCGTTCCAGA 5 0.125 No Hit GCGCCCTAGGCTCATGTCTAAGTAAAACGCTGAAGACCTCTGCTCTGGTC 5 0.125 No Hit CTCGCCGCAAGGTGGAGCGCAGAATCACCCCTCTTACCGGGGCTGTCCTT 5 0.125 No Hit GTCCAGTACCTCCCGTCGTAGTACCCAGGAGAGCTGTTGTGCTCACGGAA 5 0.125 No Hit GCCGTTCTCCGCGGCCATCTCCATCCCGCCGGAGCTCGCCTTGTGGGCGG 5 0.125 No Hit CCCGGTGATACACGCCTCGGCTGTGACAGTAATCCACTGCAGCAATGAGC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.1875 0.0 0.0 0.0 0.0 86-87 0.21250000000000002 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.3375 0.0 0.0 0.0 0.0 92-93 0.4 0.0 0.0 0.0 0.0 94-95 0.525 0.0 0.0 0.0 0.0 96-97 0.5625 0.0 0.0 0.0 0.0 98-99 0.7 0.0 0.0 0.0 0.0 100-101 0.75 0.0 0.0 0.0 0.0 102-103 0.95 0.0 0.0 0.0 0.0 104-105 1.25 0.0 0.0 0.0 0.0 106-107 1.4 0.0 0.0 0.0 0.0 108-109 1.5750000000000002 0.0 0.0 0.0 0.0 110-111 1.625 0.0 0.0 0.0 0.0 112-113 1.7125 0.0 0.0 0.0 0.0 114-115 1.9249999999999998 0.0 0.0 0.0 0.0 116-117 2.1500000000000004 0.0 0.0 0.0 0.0 118-119 2.425 0.0 0.0 0.0 0.0 120-121 2.7125000000000004 0.0 0.0 0.0 0.0 122-123 2.9875 0.0 0.0 0.0 0.0 124-125 3.2125 0.0 0.0 0.0 0.0 126-127 3.65 0.0 0.0 0.0 0.0 128-129 4.1875 0.0 0.0 0.0 0.0 130-131 4.5375 0.0 0.0 0.0 0.0 132-133 5.0125 0.0 0.0 0.0 0.0 134-135 5.3625 0.0 0.0 0.0 0.0 136-137 5.6625 0.0 0.0 0.0 0.0 138-139 6.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR18694439 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694439_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 34.0925 37.0 37.0 37.0 25.0 37.0 2 34.915 37.0 37.0 37.0 25.0 37.0 3 34.865 37.0 37.0 37.0 25.0 37.0 4 35.086 37.0 37.0 37.0 25.0 37.0 5 35.0575 37.0 37.0 37.0 25.0 37.0 6 34.922 37.0 37.0 37.0 25.0 37.0 7 35.1655 37.0 37.0 37.0 25.0 37.0 8 35.396 37.0 37.0 37.0 37.0 37.0 9 35.4225 37.0 37.0 37.0 37.0 37.0 10-14 35.3634 37.0 37.0 37.0 34.6 37.0 15-19 35.4512 37.0 37.0 37.0 34.6 37.0 20-24 35.2473 37.0 37.0 37.0 29.8 37.0 25-29 35.3865 37.0 37.0 37.0 32.2 37.0 30-34 35.639199999999995 37.0 37.0 37.0 37.0 37.0 35-39 35.4141 37.0 37.0 37.0 32.2 37.0 40-44 35.188399999999994 37.0 37.0 37.0 29.8 37.0 45-49 35.4602 37.0 37.0 37.0 37.0 37.0 50-54 34.8249 37.0 37.0 37.0 29.4 37.0 55-59 34.3579 37.0 37.0 37.0 25.0 37.0 60-64 34.913 37.0 37.0 37.0 27.4 37.0 65-69 34.0368 37.0 34.6 37.0 27.4 37.0 70-74 32.8264 37.0 29.8 37.0 22.2 37.0 75-79 33.4724 37.0 34.6 37.0 22.2 37.0 80-84 34.46040000000001 37.0 37.0 37.0 25.0 37.0 85-89 32.542500000000004 37.0 32.2 37.0 19.4 37.0 90-94 33.9495 37.0 37.0 37.0 25.0 37.0 95-99 33.8039 37.0 37.0 37.0 25.0 37.0 100-104 33.3975 37.0 37.0 37.0 25.0 37.0 105-109 34.1175 37.0 37.0 37.0 25.0 37.0 110-114 34.368700000000004 37.0 37.0 37.0 25.0 37.0 115-119 34.3377 37.0 37.0 37.0 25.0 37.0 120-124 33.9632 37.0 37.0 37.0 25.0 37.0 125-129 33.8258 37.0 37.0 37.0 25.0 37.0 130-134 33.6288 37.0 34.6 37.0 25.0 37.0 135-139 31.938300000000005 37.0 25.0 37.0 13.8 37.0 140-144 31.405900000000003 37.0 25.0 37.0 11.0 37.0 145-149 31.036099999999998 37.0 25.0 37.0 11.0 37.0 150-151 30.7775 37.0 25.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 2.0 15 0.0 16 2.0 17 1.0 18 3.0 19 5.0 20 4.0 21 4.0 22 5.0 23 13.0 24 10.0 25 14.0 26 16.0 27 22.0 28 37.0 29 50.0 30 75.0 31 183.0 32 245.0 33 527.0 34 1182.0 35 1413.0 36 187.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.975 20.4 7.55 29.075 2 30.95 22.900000000000002 26.275 19.875 3 22.6 26.0 27.900000000000002 23.5 4 26.35 30.725 19.6 23.325000000000003 5 28.599999999999998 32.5 18.25 20.65 6 23.65 36.375 17.175 22.8 7 23.799999999999997 19.875 32.525 23.799999999999997 8 23.474999999999998 22.575 24.349999999999998 29.599999999999998 9 25.4 20.825 29.175 24.6 10-14 26.395000000000003 25.045 23.235 25.324999999999996 15-19 25.88 24.9 24.05 25.169999999999998 20-24 26.845000000000002 24.895 23.735 24.525 25-29 26.365 24.59 24.115000000000002 24.93 30-34 26.290000000000003 24.64 24.19 24.88 35-39 25.895000000000003 24.990000000000002 24.305 24.81 40-44 26.529999999999998 24.154999999999998 24.125 25.19 45-49 26.529999999999998 24.905 23.385 25.180000000000003 50-54 25.72 24.565 24.895 24.82 55-59 26.855 24.815 23.205000000000002 25.124999999999996 60-64 26.395000000000003 24.62 23.72 25.264999999999997 65-69 27.08 24.67 23.595 24.654999999999998 70-74 26.745 24.665 23.77 24.82 75-79 27.665 22.88 24.485 24.97 80-84 26.490000000000002 25.019999999999996 23.785 24.705 85-89 23.77 27.49 23.919999999999998 24.82 90-94 26.07 25.185000000000002 23.39 25.355 95-99 26.43 25.595000000000002 23.665 24.310000000000002 100-104 27.075 24.959999999999997 23.145 24.82 105-109 25.590000000000003 25.69 24.279999999999998 24.44 110-114 26.445 25.6 23.794999999999998 24.16 115-119 26.384999999999998 25.480000000000004 23.669999999999998 24.465 120-124 26.150000000000002 25.264999999999997 24.560000000000002 24.025 125-129 26.82 25.595000000000002 24.13 23.455000000000002 130-134 27.055 25.41 23.945 23.59 135-139 27.275 25.095 24.11 23.52 140-144 27.51 25.28 24.15 23.06 145-149 27.089999999999996 25.55 24.255 23.105 150-151 25.5125 25.637500000000003 26.575 22.275 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 1.0 7 1.0 8 0.0 9 0.0 10 0.5 11 1.0 12 1.0 13 0.5 14 0.5 15 0.5 16 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 2.0 24 1.5 25 3.0 26 3.5 27 2.5 28 5.0 29 8.5 30 9.0 31 11.0 32 17.5 33 20.0 34 22.5 35 35.0 36 34.0 37 43.5 38 63.5 39 86.0 40 108.5 41 113.5 42 141.5 43 151.0 44 141.0 45 148.5 46 162.5 47 149.5 48 147.0 49 187.5 50 174.0 51 130.5 52 119.5 53 124.0 54 118.0 55 105.5 56 104.0 57 108.5 58 107.0 59 110.0 60 103.0 61 84.0 62 93.5 63 102.5 64 87.0 65 77.0 66 72.0 67 61.5 68 56.0 69 54.0 70 45.0 71 27.0 72 26.0 73 24.0 74 12.0 75 12.5 76 10.5 77 5.0 78 3.0 79 2.5 80 2.0 81 1.5 82 1.0 83 0.5 84 1.0 85 0.5 86 0.0 87 0.5 88 0.5 89 0.0 90 0.5 91 0.5 92 0.0 93 0.0 94 0.0 95 0.5 96 1.0 97 1.0 98 0.5 99 1.0 100 1.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.575 #Duplication Level Percentage of deduplicated Percentage of total 1 87.35027753432661 74.75 2 9.932807478819749 17.0 3 2.044989775051125 5.25 4 0.35056967572305 1.2 5 0.175284837861525 0.75 6 0.029214139643587496 0.15 7 0.029214139643587496 0.17500000000000002 8 0.029214139643587496 0.2 9 0.0 0.0 >10 0.05842827928717499 0.525 >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 CCTCTTGTTAGCTATCTACGTACGTGTACGATGGCTCCCACAGTGATGTC 11 0.27499999999999997 No Hit GAGAGAACCGTCGAAATATGCGAGTTTGACGGCAATCGTGACTGGGGAAG 10 0.25 No Hit AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 8 0.2 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit AGCTTGTTAGCTAGCTCGATAAGTACTGATTATTGGCAATGGCTTCCAAG 6 0.15 No Hit GCTGGGCTGGACGCGGACGAGGAGGAGGTCACCAGAGAGTTTCTACAGCT 5 0.125 No Hit ATGGACCCAACCTCCAACATGTTTGATCCACTCGCCACCGTCGACGATGG 5 0.125 No Hit GCCTCTCACCGTGGAGTCCCTCTTGAAGCAGATCGAGTATCTCATCCGCT 5 0.125 No Hit AGAACATTATCTATGATAGAACATAATAAATACTTCAGGGCCAACCATTA 5 0.125 No Hit GGACAAGTTTGCAGCAGATGCTGAAAGCAAGGTTGTCCCTGCCTCTGCCA 5 0.125 No Hit ATCAGTTCTTGGTTTGGAGATGGAAAGACAATCCAGCTCCCGGCTTGGAG 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.1875 0.0 0.0 0.0 0.0 86-87 0.21250000000000002 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.3375 0.0 0.0 0.0 0.0 92-93 0.4 0.0 0.0 0.0 0.0 94-95 0.525 0.0 0.0 0.0 0.0 96-97 0.575 0.0 0.0 0.0 0.0 98-99 0.7250000000000001 0.0 0.0 0.0 0.0 100-101 0.775 0.0 0.0 0.0 0.0 102-103 0.975 0.0 0.0 0.0 0.0 104-105 1.2625 0.0 0.0 0.0 0.0 106-107 1.3875000000000002 0.0 0.0 0.0 0.0 108-109 1.5499999999999998 0.0 0.0 0.0 0.0 110-111 1.6 0.0 0.0 0.0 0.0 112-113 1.6875 0.0 0.0 0.0 0.0 114-115 1.9 0.0 0.0 0.0 0.0 116-117 2.125 0.0 0.0 0.0 0.0 118-119 2.4 0.0 0.0 0.0 0.0 120-121 2.6875 0.0 0.0 0.0 0.0 122-123 2.9625 0.0 0.0 0.0 0.0 124-125 3.175 0.0 0.0 0.0 0.0 126-127 3.6 0.0 0.0 0.0 0.0 128-129 4.1375 0.0 0.0 0.0 0.0 130-131 4.487500000000001 0.0 0.0 0.0 0.0 132-133 4.9875 0.0 0.0 0.0 0.0 134-135 5.3375 0.0 0.0 0.0 0.0 136-137 5.637499999999999 0.0 0.0 0.0 0.0 138-139 6.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATAATGT 10 0.006830828 145.0 145 TTTTTTT 35 0.0035366106 20.714287 120-124 >>END_MODULE Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra Read 674235 spots for SRR18694439.sra Written 674235 spots for SRR18694439.sra Read 674232 spots for SRR18694439.sra Written 674232 spots for SRR18694439.sra SRR ids: ['SRR18694439.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vuux7kwu SRR18694439.sra spots: 13484643 blocks: [[1, 674232], [674233, 1348464], [1348465, 2022696], [2022697, 2696928], [2696929, 3371160], [3371161, 4045392], [4045393, 4719624], [4719625, 5393856], [5393857, 6068088], [6068089, 6742320], [6742321, 7416552], [7416553, 8090784], [8090785, 8765016], [8765017, 9439248], [9439249, 10113480], [10113481, 10787712], [10787713, 11461944], [11461945, 12136176], [12136177, 12810408], [12810409, 13484643]] SRR18694439 file size 4560971 SRR18694439 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 SRR18694439 SRR18694439_1.fastq SRR18694439_2.fastq Input file: SRR18694439_1.fastq Paired file: SRR18694439_2.fastq trimmed: SRR18694439-trimmed-pair1.fastq, SRR18694439-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 Dec 10 06:50:57 2024 >> started Tue Dec 10 06:51:13 2024 >> done (15.152s) 13484643 read pairs processed; of these: 159 ( 0.00%) short read pairs filtered out after trimming by size control 2721 ( 0.02%) empty read pairs filtered out after trimming by size control 13481763 (99.98%) read pairs available; of these: 1423818 (10.56%) trimmed read pairs available after processing 12057945 (89.44%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 8 0.00% 20 20 0.00% 21 13 0.00% 22 12 0.00% 23 21 0.00% 24 25 0.00% 25 35 0.00% 26 18 0.00% 27 21 0.00% 28 38 0.00% 29 43 0.00% 30 26 0.00% 31 27 0.00% 32 44 0.00% 33 29 0.00% 34 33 0.00% 35 27 0.00% 36 40 0.00% 37 37 0.00% 38 39 0.00% 39 42 0.00% 40 35 0.00% 41 44 0.00% 42 40 0.00% 43 46 0.00% 44 49 0.00% 45 49 0.00% 46 69 0.00% 47 48 0.00% 48 42 0.00% 49 67 0.00% 50 72 0.00% 51 82 0.00% 52 85 0.00% 53 106 0.00% 54 91 0.00% 55 101 0.00% 56 113 0.00% 57 126 0.00% 58 156 0.00% 59 190 0.00% 60 176 0.00% 61 191 0.00% 62 236 0.00% 63 280 0.00% 64 267 0.00% 65 264 0.00% 66 340 0.00% 67 359 0.00% 68 388 0.00% 69 482 0.00% 70 502 0.00% 71 598 0.00% 72 728 0.01% 73 874 0.01% 74 836 0.01% 75 962 0.01% 76 1160 0.01% 77 1174 0.01% 78 1413 0.01% 79 1491 0.01% 80 1709 0.01% 81 1898 0.01% 82 2132 0.02% 83 2453 0.02% 84 2536 0.02% 85 2954 0.02% 86 3213 0.02% 87 3266 0.02% 88 3736 0.03% 89 3876 0.03% 90 4277 0.03% 91 4653 0.03% 92 5096 0.04% 93 5681 0.04% 94 6000 0.04% 95 6612 0.05% 96 6685 0.05% 97 7164 0.05% 98 7410 0.05% 99 8004 0.06% 100 8494 0.06% 101 9097 0.07% 102 9629 0.07% 103 10134 0.08% 104 10574 0.08% 105 11215 0.08% 106 11833 0.09% 107 12361 0.09% 108 12892 0.10% 109 13610 0.10% 110 13927 0.10% 111 14662 0.11% 112 15286 0.11% 113 16165 0.12% 114 17085 0.13% 115 18143 0.13% 116 18622 0.14% 117 19227 0.14% 118 19639 0.15% 119 20410 0.15% 120 21469 0.16% 121 21598 0.16% 122 22353 0.17% 123 23499 0.17% 124 24559 0.18% 125 25129 0.19% 126 25778 0.19% 127 27141 0.20% 128 27459 0.20% 129 28499 0.21% 130 28943 0.21% 131 30061 0.22% 132 30844 0.23% 133 32047 0.24% 134 32819 0.24% 135 33746 0.25% 136 34480 0.26% 137 34409 0.26% 138 35367 0.26% 139 36410 0.27% 140 37171 0.28% 141 37859 0.28% 142 38631 0.29% 143 39801 0.30% 144 40791 0.30% 145 42251 0.31% 146 42780 0.32% 147 44075 0.33% 148 44946 0.33% 149 45277 0.34% 150 46319 0.34% 151 12057945 89.44% 13481763 reads passed initial QC criterion=sequence-density sequence-density=0.82 sequence-density-rank=1 fanout-score=2.84 fanout-score-rank=13 prefix-density=0.86 prefix-fanout=2.7 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.06 sequence-density-rank=31 fanout-score=121.00 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=15.6 sequence=CGGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAA criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=3.60 fanout-score-rank=11 prefix-density=0.66 prefix-fanout=3.2 sequence=GAGTTCAGCAAGGTCGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=25.53 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=4.5 sequence=TGCCTCCTCTTGTTAGCTATCTACGTACGTGTACGATGGCTCCCACAGTGATGTCGTCAGCGGCTACTGCCGTTGCTCCTTTCCAGGGCCTCAAGTCCACCGCCGGGCTCCCCATCGGCCGCCGCTCAGCCAGCGCTGGTCTCGGCAGCGTCTCCAACGGTGGAAGGATCAGGTGCATGCAGGTGTGGCC SRR18694439 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:51:58 Started mapping on | Dec 10 06:51:59 Finished on | Dec 10 06:53:27 Mapping speed, Million of reads per hour | 551.53 Number of input reads | 13481763 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 12530539 Uniquely mapped reads % | 92.94% Average mapped length | 295.67 Number of splices: Total | 12589329 Number of splices: Annotated (sjdb) | 11798361 Number of splices: GT/AG | 12413639 Number of splices: GC/AG | 148990 Number of splices: AT/AC | 4423 Number of splices: Non-canonical | 22277 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.01% Deletion average length | 2.44 Insertion rate per base | 0.01% Insertion average length | 2.53 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 195259 % of reads mapped to multiple loci | 1.45% Number of reads mapped to too many loci | 22706 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.57% % of reads unmapped: other | 1.87% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 755965 755965 755965 N_multimapping 195259 195259 195259 N_noFeature 576501 12174730 669086 N_ambiguous 312463 1633 49751 UnstrandedReadsAssigned:11641575 PositiveStrandReadsAssigned:354176 NegativeStrandReadsAssigned:11811702 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694439 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: SRR18694439-trimmed-pair1.fastq SRR18694439-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,481,763 reads, 11,982,230 reads pseudoaligned [quant] estimated average fragment length: 256.151 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,100 rounds 52973 SRR18694439.ke.tsv 35125 SRR18694439.se.tsv 88098 total ==> SRR18694439.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 681.267 0 0 PNS24247 1044 788.849 36.022 5.18526 PNS24249 1928 1672.85 11.2056 0.760634 PNS24246 1044 788.849 36.022 5.18526 PNS24248 1044 788.849 36.022 5.18526 PNS24244 1471 1215.85 60.7285 5.67166 PNS24243 293 95.0283 0 0 KQK14069 1603 1347.85 1100.93 92.7505 KQK14071 474 239.067 40.4649 19.2201 ==> SRR18694439.se.tsv <== BRADI_1g14170v3 1357 BRADI_1g53295v3 37 BRADI_1g59795v3 643 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 241 BRADI_1g74790v3 78 BRADI_1g09890v3 0 BRADI_1g77505v3 119 BRADI_1g48960v3 0 SRR18694439 completed mapping pipeline successfully