Starting /dee2/code/volunteer_pipeline.sh SRR13695412 current disk space = 3050831249408 free memory = 1539942468 SRR13695412 SRAfilesize d346b7eabe91cbe1fface80639a553e6 SRR13695412.sra SRR13695412.sra file validated SRR13695412 is paired end SRR13695412 is conventional basespace SRR13695412 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695412_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 36.585 37.0 37.0 37.0 37.0 37.0 2 36.34375 37.0 37.0 37.0 37.0 37.0 3 36.5495 37.0 37.0 37.0 37.0 37.0 4 36.6085 37.0 37.0 37.0 37.0 37.0 5 36.617 37.0 37.0 37.0 37.0 37.0 6 36.65 37.0 37.0 37.0 37.0 37.0 7 36.5645 37.0 37.0 37.0 37.0 37.0 8 36.6275 37.0 37.0 37.0 37.0 37.0 9 36.621 37.0 37.0 37.0 37.0 37.0 10-14 36.604 37.0 37.0 37.0 37.0 37.0 15-19 36.5741 37.0 37.0 37.0 37.0 37.0 20-24 36.547900000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.4892 37.0 37.0 37.0 37.0 37.0 30-34 36.4824 37.0 37.0 37.0 37.0 37.0 35-39 36.492000000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.5135 37.0 37.0 37.0 37.0 37.0 45-49 36.4171 37.0 37.0 37.0 37.0 37.0 50-54 36.409000000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.4226 37.0 37.0 37.0 37.0 37.0 60-64 36.3739 37.0 37.0 37.0 37.0 37.0 65-69 36.327200000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.3374 37.0 37.0 37.0 37.0 37.0 75-79 36.32000000000001 37.0 37.0 37.0 37.0 37.0 80-84 36.2615 37.0 37.0 37.0 37.0 37.0 85-89 36.291900000000005 37.0 37.0 37.0 37.0 37.0 90-94 36.2102 37.0 37.0 37.0 37.0 37.0 95-99 36.1759 37.0 37.0 37.0 37.0 37.0 100-104 36.161899999999996 37.0 37.0 37.0 37.0 37.0 105-109 36.131600000000006 37.0 37.0 37.0 37.0 37.0 110-114 36.1245 37.0 37.0 37.0 37.0 37.0 115-119 36.0219 37.0 37.0 37.0 37.0 37.0 120-124 36.0464 37.0 37.0 37.0 37.0 37.0 125-129 35.956599999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.9307 37.0 37.0 37.0 37.0 37.0 135-139 35.797799999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.757400000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.55669999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.155 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 7.0 26 2.0 27 9.0 28 12.0 29 11.0 30 27.0 31 28.0 32 52.0 33 77.0 34 108.0 35 336.0 36 3023.0 37 306.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.425 11.4 8.225 39.95 2 19.774153074027602 13.124215809284816 37.39021329987453 29.71141781681305 3 18.675 17.849999999999998 27.325 36.15 4 22.425 22.85 22.575 32.15 5 23.724999999999998 29.4 25.35 21.525 6 21.675 33.575 23.95 20.8 7 16.05 28.050000000000004 40.125 15.775 8 18.0 27.150000000000002 31.225 23.625 9 17.299999999999997 26.35 32.925 23.425 10-14 20.04 30.64 26.784999999999997 22.535 15-19 20.395 27.589999999999996 27.705000000000002 24.310000000000002 20-24 19.585 29.325000000000003 26.979999999999997 24.11 25-29 20.04 29.020000000000003 27.250000000000004 23.69 30-34 20.155 29.38 27.025 23.44 35-39 20.169999999999998 27.92 27.450000000000003 24.46 40-44 20.599999999999998 28.21 26.889999999999997 24.3 45-49 20.79 27.900000000000002 27.815 23.494999999999997 50-54 20.605 28.884999999999998 26.955000000000002 23.555 55-59 20.294999999999998 28.854999999999997 27.37 23.48 60-64 21.15 27.825 27.68 23.345 65-69 20.39 28.42 26.695 24.495 70-74 20.979999999999997 28.310000000000002 27.49 23.22 75-79 19.939999999999998 28.105000000000004 27.865000000000002 24.09 80-84 20.24 27.77 27.894999999999996 24.095 85-89 20.49 27.950000000000003 27.875 23.685000000000002 90-94 21.240000000000002 26.865 27.715 24.18 95-99 20.525 28.225 27.245 24.005000000000003 100-104 21.0 27.74 27.725 23.535 105-109 21.560000000000002 27.400000000000002 27.735 23.305 110-114 21.63 27.515 27.200000000000003 23.655 115-119 21.495 27.6 27.38 23.525 120-124 20.625 27.925 27.29 24.16 125-129 21.565 27.26 26.924999999999997 24.25 130-134 21.695 28.470000000000002 26.369999999999997 23.465 135-139 21.055 28.044999999999998 26.41 24.490000000000002 140-144 20.46 28.294999999999998 27.015 24.23 145-149 21.88 28.04 25.814999999999998 24.265 150-151 21.45 28.075 26.625 23.849999999999998 >>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 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 2.0 18 3.0 19 1.0 20 0.5 21 0.5 22 1.5 23 2.5 24 1.5 25 2.5 26 3.0 27 5.5 28 11.5 29 10.0 30 11.0 31 21.5 32 33.0 33 41.0 34 53.5 35 75.5 36 100.0 37 118.0 38 125.5 39 153.5 40 156.5 41 179.0 42 223.0 43 217.5 44 221.5 45 242.5 46 255.5 47 264.5 48 258.0 49 217.0 50 192.5 51 173.5 52 124.5 53 101.0 54 104.0 55 70.5 56 48.5 57 52.0 58 41.5 59 33.0 60 18.5 61 9.0 62 7.5 63 4.0 64 1.5 65 1.5 66 1.5 67 0.0 68 0.0 69 0.5 70 1.0 71 0.5 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 0.375 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 warn #Total Deduplicated Percentage 69.1 #Duplication Level Percentage of deduplicated Percentage of total 1 71.02026049204052 49.075 2 19.13892908827786 26.450000000000003 3 6.1143270622286545 12.675 4 2.532561505065123 7.000000000000001 5 0.723589001447178 2.5 6 0.21707670043415342 0.8999999999999999 7 0.0723589001447178 0.35000000000000003 8 0.1447178002894356 0.8 9 0.0 0.0 >10 0.0361794500723589 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 GTTGTTTGGCAAAATTATATCACCACAAAGCTGGCTGATCGGCTTGATCT 10 0.25 No Hit GGTGAGCATAACATGTCCGTGCTAGCTATTACAAGACAAACCCAAAAGGA 8 0.2 No Hit CCGTACAACATTAAATAAGTACACACAGAGGAAGAGTAATTATTTCGAAG 8 0.2 No Hit GCTTTACTCAAGAAGTTTTCCACTGACGCCCCTGCAGCCTCGGCCTTCCC 8 0.2 No Hit GCAGTATTTTCTTGTAGCAGGTCTCCATATATCACTAAGTGATATCCTTG 8 0.2 No Hit GCCTTCTCTTGTTGTCAACCTGAAGAACTCATCCTCGGCTGCATCAACGC 7 0.17500000000000002 No Hit GTACTCGCCATGGCTGGACGCCAGACTTGTTAGACAGCCTTGCATTTTCA 7 0.17500000000000002 No Hit CCCCTGTCCGTTTCTGTAACCTTAGAAAGAATAGAAGCAACCAAATCATC 6 0.15 No Hit CTCCGAGATCCCAAAGCTTTATCGTTACATTGCCTTTTGTAACTTTTCGC 6 0.15 No Hit CCCTCCACTGGTGGCACCATAACCATTTGTACCTTCCTCTAAGTTGTCAG 6 0.15 No Hit CCACAATATTAATACTAACTTCATTACCATCCTTCAAGATTGAACCGAGT 6 0.15 No Hit AGGATGATCACATGTTGCACGAGGAATCATAAAATCCCCGTGTGCACACA 6 0.15 No Hit GTCATCCTTGTATTTCAGGTATAATGGAATATCTAAAGCTCTCTCTGCAA 6 0.15 No Hit CTCTTCTCAGCAGACCCAATTGCTAGAATGCCTGATTGAGGAGGATTAAT 5 0.125 No Hit GTCCCTCGCTGATCTCTACCATATCAGCTTTTATCCTTTTGATGCTCCTA 5 0.125 No Hit GTGCTGTGACACCCTTTTCTTTCCTTCCAGTCCTATCAAGTGAGTGATAA 5 0.125 No Hit GCTTGGAGATCGGTGCGGTTACGGTAACGGAGTTTGGAGAGGAATTTTTG 5 0.125 No Hit GCACCGTAACCTCCTCCTCCACGACCAAAGCCAGGCCTTCCACCAGAGCC 5 0.125 No Hit GTTAAGGTGACCCACAGACTTTACCAGTAACAGGTGACCTAGAAGAAACC 5 0.125 No Hit GTCAAGCTAATCTCCTCAGTGCCACTGGTGAGAACAAGAGAGTTGATCAA 5 0.125 No Hit GCGGGACAAGAGCTCGGGGAAGACGCATCCAAGAGCTCCAAGCATGGCCC 5 0.125 No Hit CTGTGGAAACGTAGAAGATTGGTCATAATTGATCCAGGATGAAGTGAATT 5 0.125 No Hit CCCATATCTGTTCAGCAACATGGAGTGAAGGGCGAAATATAGATGGTCTC 5 0.125 No Hit AACAGATTCAAGATTAGCTCATCAGAAGGACATCTGCTTTTTCATAGTTT 5 0.125 No Hit CTTAGAAAGTGCTTCTCCTTACACACCCACAAGCCTAGAAAAGGAATTAG 5 0.125 No Hit CCCAGCGTCCAGAGTCAAAAATAAATAGAACTTATTTAACCGGATAATAC 5 0.125 No Hit GCATCATCACATGAGTCCTGGATTCCCCCCTCCACAAATGCCGCAGCTGA 5 0.125 No Hit GCCTTTCTCAATCTCTGCAATTTCTTCCCTAATGGAGATAAGCGCATCAC 5 0.125 No Hit GTCAAACTCATCTGCTTCCGCAAGCTGGTTGCTGTCTAACCACTGGATAG 5 0.125 No Hit GGGATGTCCAATACTTCATAGTATAGAATATCAGATGTCTGATTGTAGTG 5 0.125 No Hit TCAGCACCAACTTCCTCGTAATCCTTCTCAAGGGCAGCCAGATCTTCACG 5 0.125 No Hit GTTGTCGCCCCAGTCTTCTCCCCAAGAGTTCTTGATCAGCCAATATGGGA 5 0.125 No Hit GGACCATTCATCAGTGTTGTAGATAGGGCTGTAGCCATCCACATTAGCAC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 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 0.075 0.0 0.0 0.0 0.0 70-71 0.0875 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.3375 0.0 0.0 0.0 0.0 86-87 0.44999999999999996 0.0 0.0 0.0 0.0 88-89 0.525 0.0 0.0 0.0 0.0 90-91 0.6 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 0.9375 0.0 0.0 0.0 0.0 98-99 1.25 0.0 0.0 0.0 0.0 100-101 1.475 0.0 0.0 0.0 0.0 102-103 1.7999999999999998 0.0 0.0 0.0 0.0 104-105 2.0375 0.0 0.0 0.0 0.0 106-107 2.175 0.0 0.0 0.0 0.0 108-109 2.4749999999999996 0.0 0.0 0.0 0.0 110-111 2.775 0.0 0.0 0.0 0.0 112-113 3.2874999999999996 0.0 0.0 0.0 0.0 114-115 3.6 0.0 0.0 0.0 0.0 116-117 3.9625000000000004 0.0 0.0 0.0 0.0 118-119 4.425000000000001 0.0 0.0 0.0 0.0 120-121 4.825 0.0 0.0 0.0 0.0 122-123 5.125 0.0 0.0 0.0 0.0 124-125 5.475 0.0 0.0 0.0 0.0 126-127 6.15 0.0 0.0 0.0 0.0 128-129 6.7 0.0 0.0 0.0 0.0 130-131 7.525 0.0 0.0 0.0 0.0 132-133 8.1 0.0 0.0 0.0 0.0 134-135 8.625 0.0 0.0 0.0 0.0 136-137 9.2125 0.0 0.0 0.0 0.0 138-139 10.1125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13695412 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695412_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 36.221 37.0 37.0 37.0 37.0 37.0 2 36.181 37.0 37.0 37.0 37.0 37.0 3 36.263 37.0 37.0 37.0 37.0 37.0 4 36.291 37.0 37.0 37.0 37.0 37.0 5 36.3035 37.0 37.0 37.0 37.0 37.0 6 36.3365 37.0 37.0 37.0 37.0 37.0 7 36.3265 37.0 37.0 37.0 37.0 37.0 8 36.3985 37.0 37.0 37.0 37.0 37.0 9 36.401 37.0 37.0 37.0 37.0 37.0 10-14 36.365 37.0 37.0 37.0 37.0 37.0 15-19 36.2937 37.0 37.0 37.0 37.0 37.0 20-24 36.299800000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.25449999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.2247 37.0 37.0 37.0 37.0 37.0 35-39 36.19029999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.195 37.0 37.0 37.0 37.0 37.0 45-49 36.1415 37.0 37.0 37.0 37.0 37.0 50-54 36.1023 37.0 37.0 37.0 37.0 37.0 55-59 36.076499999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.095600000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.050799999999995 37.0 37.0 37.0 37.0 37.0 70-74 35.9882 37.0 37.0 37.0 37.0 37.0 75-79 35.9664 37.0 37.0 37.0 37.0 37.0 80-84 35.9816 37.0 37.0 37.0 37.0 37.0 85-89 35.9076 37.0 37.0 37.0 37.0 37.0 90-94 35.928200000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.9358 37.0 37.0 37.0 37.0 37.0 100-104 35.87140000000001 37.0 37.0 37.0 37.0 37.0 105-109 35.8918 37.0 37.0 37.0 37.0 37.0 110-114 35.7978 37.0 37.0 37.0 37.0 37.0 115-119 35.7369 37.0 37.0 37.0 37.0 37.0 120-124 35.7161 37.0 37.0 37.0 37.0 37.0 125-129 35.691300000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.611000000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.580400000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.5052 37.0 37.0 37.0 37.0 37.0 145-149 35.3925 37.0 37.0 37.0 37.0 37.0 150-151 35.093 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 4.0 14 5.0 15 2.0 16 2.0 17 1.0 18 2.0 19 3.0 20 0.0 21 4.0 22 1.0 23 5.0 24 3.0 25 4.0 26 10.0 27 9.0 28 14.0 29 8.0 30 25.0 31 35.0 32 51.0 33 87.0 34 190.0 35 471.0 36 2815.0 37 248.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.88565697091274 23.044132397191575 11.384152457372117 28.68605817452357 2 28.749999999999996 24.95 28.95 17.349999999999998 3 20.424999999999997 27.925 30.9 20.75 4 25.124999999999996 33.6 23.025000000000002 18.25 5 26.650000000000002 36.85 21.05 15.45 6 22.8 37.974999999999994 20.45 18.775 7 21.5 24.224999999999998 35.55 18.725 8 22.400000000000002 26.474999999999998 26.825 24.3 9 21.125 25.575 31.125000000000004 22.175 10-14 24.48 28.985 26.19 20.345 15-19 23.830000000000002 28.565 26.02 21.584999999999997 20-24 23.925 28.705000000000002 26.215 21.154999999999998 25-29 23.845 28.67 26.88 20.605 30-34 23.35 28.64 26.645000000000003 21.365000000000002 35-39 23.474999999999998 28.335 27.075 21.115000000000002 40-44 23.595 28.065 27.339999999999996 21.0 45-49 22.68 28.34 27.525 21.455 50-54 23.75 27.175 27.775 21.3 55-59 24.365000000000002 27.38 27.345000000000002 20.91 60-64 23.77 27.57 27.200000000000003 21.46 65-69 24.05 27.93 27.355 20.665 70-74 24.305 27.57 26.395000000000003 21.73 75-79 23.305 27.88 27.1 21.715 80-84 23.46 28.38 26.685 21.475 85-89 23.91 28.499999999999996 26.5 21.09 90-94 23.59 29.17 25.869999999999997 21.37 95-99 24.425 27.295 27.46 20.82 100-104 24.895 27.615000000000002 27.029999999999998 20.46 105-109 24.759999999999998 28.044999999999998 26.484999999999996 20.71 110-114 24.115000000000002 28.395 26.955000000000002 20.535 115-119 24.04 27.825 27.12 21.015 120-124 24.560000000000002 28.29 26.165 20.985 125-129 24.84 28.875 26.169999999999998 20.115 130-134 25.040000000000003 28.415000000000003 26.884999999999998 19.66 135-139 25.515 28.225 26.775 19.485 140-144 25.955000000000002 27.750000000000004 26.25 20.044999999999998 145-149 26.005 28.349999999999998 26.375 19.27 150-151 27.35 27.4125 26.2625 18.975 >>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 0.5 7 0.5 8 0.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 1.0 15 1.0 16 1.0 17 1.5 18 0.5 19 0.5 20 1.5 21 1.5 22 0.5 23 1.0 24 1.5 25 1.5 26 1.0 27 1.5 28 2.5 29 6.0 30 9.5 31 9.0 32 19.5 33 28.5 34 40.0 35 56.0 36 75.5 37 94.5 38 118.0 39 142.5 40 160.5 41 196.0 42 240.5 43 260.5 44 259.5 45 280.0 46 289.5 47 287.0 48 252.5 49 204.5 50 178.5 51 146.0 52 120.0 53 103.0 54 100.5 55 79.5 56 57.0 57 41.5 58 26.5 59 29.5 60 20.0 61 12.0 62 11.5 63 6.5 64 3.5 65 2.0 66 1.5 67 1.0 68 0.5 69 0.5 70 0.5 71 0.5 72 0.5 73 0.0 74 0.0 75 0.0 76 1.0 77 1.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 87 0.0 88 0.5 89 0.5 90 0.0 91 0.5 92 0.5 93 0.5 94 1.0 95 0.5 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 0.3 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 warn #Total Deduplicated Percentage 69.525 #Duplication Level Percentage of deduplicated Percentage of total 1 71.19741100323624 49.5 2 19.41747572815534 27.0 3 5.825242718446602 12.15 4 2.373247033441208 6.6000000000000005 5 0.7910823444804028 2.75 6 0.1438331535418914 0.6 7 0.0719165767709457 0.35000000000000003 8 0.1438331535418914 0.8 9 0.0 0.0 >10 0.03595828838547285 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 GTTTCGACGATAGTCGAGTTTCTCCAGTCAATGAAGCTGACATCAAGACC 10 0.25 No Hit CGTTGCAAATTACGTGGTGAAGCGTGTGCTCTACAAGTTTATTTGATGGT 8 0.2 No Hit GTTAATAGCTCCAAAGTACAAGGAATTATCCCAGAAGTATGATGATGTTG 8 0.2 No Hit GTTGGACCCCGTGGAAGGCTCTTCAGGAAGTTACTCACATGGATTGGATT 8 0.2 No Hit CCTGAAGATGGAAGAAGAAAAGTCTATGCAGAAGCTCTTGCAAAGGCAAA 8 0.2 No Hit AGCAGATGATGTCTTTTCACTGTTCGTAAGTGAGGAGGTTGATAAAGTGG 7 0.17500000000000002 No Hit GGAGAATGTTTGGGATCGTGCACTGTTGAAGAACTGCAACAAATCGAACA 7 0.17500000000000002 No Hit CGCTAATTTATCTACCAAAGGTTACTCAGCACTTCTTTCGGAACATCCAT 6 0.15 No Hit CATCAACAAGAATCAAACTTTGATTGAATCCCATCAAGAATTATCCGATG 6 0.15 No Hit GACGTAGTGATAATCATGATTCTTCAAGAAAGCGACACCGCAATGAAAGC 6 0.15 No Hit AGTTAGTGCTGTCTCGGACTGCAGTGATTCCCTAGAAAAGCCAGCAAAAA 6 0.15 No Hit GGGAAGGATTGTTATCGTATCATCAGAAGCTCACCGTTTTGCATACAGTG 5 0.125 No Hit GTTTCCTTCCCTTCTTCCTCAAGATAAAAAGGATTTGTAGTCTGAAATTC 5 0.125 No Hit ATATGGATAAACAATGCTGGCACAAATAAAGGTTTTAGACCCTTGTTGCA 5 0.125 No Hit GTTTGCACTGTATACACCACTCAGTCCCTTAATTCAACATGCTCAATCTC 5 0.125 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit GTGACGTTTCATTTTCATTTCAGTGTAGAAAGAGCAGAATCCCACCAATT 5 0.125 No Hit GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 5 0.125 No Hit CTCATCCTCATCGCCAAAGGAAATCTCTCAAACACATGCTGGATGATCAC 5 0.125 No Hit ATTGCCTTCTCTCCTTTATCCATGGCAGCTCGAGAATTGGTCGACTATGG 5 0.125 No Hit GTTACTTGTTTTCCACATCTACTGGTGGATCCTGATATACTCAATGATAA 5 0.125 No Hit GCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGC 5 0.125 No Hit TGCCAAGGTTCAGCGTGCTGTATGCATGATCAGCAACAACACAGCTGTGG 5 0.125 No Hit TTATTTCAATGAAGAAATGGAGGAATACGTGGAGATTCCAAGTGATGTTG 5 0.125 No Hit AAGGAGTTTACACCACCAGCACTTGTGGCAGTACTCCCATGGATGTGAAC 5 0.125 No Hit ATCTGTTGATTTTGCAGAGTTTGAACCAAAACTTGTTTACTAATACGGGT 5 0.125 No Hit AATGGACTATATGTCCCAGTTATTAGGGATGCAGACAAGAAAGGTCTATC 5 0.125 No Hit CCTAAGCCTGTTTCAGGCTAGCTTTCAAAAGAGTGATGAGTGATGTCCTT 5 0.125 No Hit GGCAAATTTGAGCTCTCTGGCATTCCTCCAGCACCTAGGGGTGTTCCTCA 5 0.125 No Hit CATAACTGTTACTCCCAGCAACCTAAACCTCAACCCATCAAGTACCGGGG 5 0.125 No Hit GGTCACCAGAAAGGCTAACAATGACATTACTTCCATTGCAAGCAATGGCG 5 0.125 No Hit CCTAAAGAAAAAAAAAAAATCACGCAAGAACAGAGAAAAAAAGAAAAGAA 5 0.125 No Hit GTAAATTAAATAAGTTTAGTCTGGCAACCTATTTTTAGGTTTGGCTACTT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 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 0.075 0.0 0.0 0.0 0.0 70-71 0.0875 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.3375 0.0 0.0 0.0 0.0 86-87 0.44999999999999996 0.0 0.0 0.0 0.0 88-89 0.525 0.0 0.0 0.0 0.0 90-91 0.6 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 0.9375 0.0 0.0 0.0 0.0 98-99 1.25 0.0 0.0 0.0 0.0 100-101 1.475 0.0 0.0 0.0 0.0 102-103 1.8375 0.0 0.0 0.0 0.0 104-105 2.0875000000000004 0.0 0.0 0.0 0.0 106-107 2.225 0.0 0.0 0.0 0.0 108-109 2.575 0.0 0.0 0.0 0.0 110-111 2.925 0.0 0.0 0.0 0.0 112-113 3.4124999999999996 0.0 0.0 0.0 0.0 114-115 3.725 0.0 0.0 0.0 0.0 116-117 4.0875 0.0 0.0 0.0 0.0 118-119 4.550000000000001 0.0 0.0 0.0 0.0 120-121 5.0 0.0 0.0 0.0 0.0 122-123 5.3 0.0 0.0 0.0 0.0 124-125 5.65 0.0 0.0 0.0 0.0 126-127 6.387499999999999 0.0 0.0 0.0 0.0 128-129 6.95 0.0 0.0 0.0 0.0 130-131 7.775 0.0 0.0 0.0 0.0 132-133 8.35 0.0 0.0 0.0 0.0 134-135 8.875 0.0 0.0 0.0 0.0 136-137 9.4625 0.0 0.0 0.0 0.0 138-139 10.3625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTCCA 10 0.006830828 145.0 9 GTTTTCC 10 0.006830828 145.0 8 >>END_MODULE Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729372 spots for SRR13695412.sra Written 729372 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra Read 729355 spots for SRR13695412.sra Written 729355 spots for SRR13695412.sra SRR ids: ['SRR13695412.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_6oph45ee SRR13695412.sra spots: 14587117 blocks: [[1, 729355], [729356, 1458710], [1458711, 2188065], [2188066, 2917420], [2917421, 3646775], [3646776, 4376130], [4376131, 5105485], [5105486, 5834840], [5834841, 6564195], [6564196, 7293550], [7293551, 8022905], [8022906, 8752260], [8752261, 9481615], [9481616, 10210970], [10210971, 10940325], [10940326, 11669680], [11669681, 12399035], [12399036, 13128390], [13128391, 13857745], [13857746, 14587117]] SRR13695412 file size 4935640 SRR13695412 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 SRR13695412 SRR13695412_1.fastq SRR13695412_2.fastq Input file: SRR13695412_1.fastq Paired file: SRR13695412_2.fastq trimmed: SRR13695412-trimmed-pair1.fastq, SRR13695412-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 Wed Feb 12 01:46:33 2025 >> started Wed Feb 12 01:46:49 2025 >> done (16.342s) 14587117 read pairs processed; of these: 93 ( 0.00%) short read pairs filtered out after trimming by size control 3266 ( 0.02%) empty read pairs filtered out after trimming by size control 14583758 (99.98%) read pairs available; of these: 2152246 (14.76%) trimmed read pairs available after processing 12431512 (85.24%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 0 0.00% 21 2 0.00% 22 0 0.00% 23 4 0.00% 24 4 0.00% 25 1 0.00% 26 2 0.00% 27 1 0.00% 28 0 0.00% 29 3 0.00% 30 1 0.00% 31 5 0.00% 32 4 0.00% 33 2 0.00% 34 10 0.00% 35 5 0.00% 36 6 0.00% 37 6 0.00% 38 8 0.00% 39 6 0.00% 40 7 0.00% 41 11 0.00% 42 18 0.00% 43 11 0.00% 44 22 0.00% 45 13 0.00% 46 27 0.00% 47 15 0.00% 48 43 0.00% 49 39 0.00% 50 52 0.00% 51 62 0.00% 52 56 0.00% 53 62 0.00% 54 57 0.00% 55 76 0.00% 56 84 0.00% 57 103 0.00% 58 154 0.00% 59 161 0.00% 60 203 0.00% 61 219 0.00% 62 275 0.00% 63 343 0.00% 64 356 0.00% 65 379 0.00% 66 469 0.00% 67 623 0.00% 68 620 0.00% 69 761 0.01% 70 842 0.01% 71 1025 0.01% 72 1158 0.01% 73 1401 0.01% 74 1556 0.01% 75 1812 0.01% 76 1898 0.01% 77 2255 0.02% 78 2494 0.02% 79 2794 0.02% 80 3247 0.02% 81 3626 0.02% 82 4092 0.03% 83 4577 0.03% 84 5263 0.04% 85 5923 0.04% 86 6311 0.04% 87 6770 0.05% 88 7361 0.05% 89 7963 0.05% 90 8650 0.06% 91 9242 0.06% 92 10101 0.07% 93 10941 0.08% 94 11771 0.08% 95 12728 0.09% 96 13469 0.09% 97 14501 0.10% 98 15180 0.10% 99 16011 0.11% 100 16738 0.11% 101 17448 0.12% 102 18627 0.13% 103 19507 0.13% 104 19989 0.14% 105 21485 0.15% 106 22458 0.15% 107 23376 0.16% 108 23956 0.16% 109 25104 0.17% 110 25429 0.17% 111 26328 0.18% 112 27265 0.19% 113 28136 0.19% 114 28998 0.20% 115 30514 0.21% 116 31664 0.22% 117 32693 0.22% 118 33444 0.23% 119 34155 0.23% 120 35119 0.24% 121 35662 0.24% 122 36120 0.25% 123 37551 0.26% 124 38588 0.26% 125 39129 0.27% 126 40421 0.28% 127 41492 0.28% 128 41813 0.29% 129 42646 0.29% 130 43906 0.30% 131 43921 0.30% 132 44402 0.30% 133 45580 0.31% 134 45849 0.31% 135 46152 0.32% 136 47860 0.33% 137 48313 0.33% 138 49185 0.34% 139 50626 0.35% 140 51059 0.35% 141 51683 0.35% 142 51051 0.35% 143 52032 0.36% 144 53172 0.36% 145 53509 0.37% 146 53702 0.37% 147 54487 0.37% 148 56048 0.38% 149 56370 0.39% 150 57127 0.39% 151 12431512 85.24% 14583758 reads passed initial QC criterion=sequence-density sequence-density=0.61 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=26 prefix-density=0.60 prefix-fanout=2.0 sequence=GTGTTGTCGAATCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=59.58 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=7.8 sequence=AAACAGAATATTTACTTTTAGCGCAAGTTTCAATTCATGAGCTCGTTACATCACAAGTTAACATTACAAGCCAATAGTCCCAGCACAGAAAAAACTCTTTTGTTGCTCACTTTCCGGGAACGAAGTTTGTGGCATATGCCCAGGCGTTGTTGTTTACTGGGTCAGAAAGGTGGTCAGCCAGGTTCTCCAGTGGTCCCTTTCCGGTCACAATGGCCTGGACAAAGAATCCGAACATTGAGAACATAGCCAACCT criterion=sequence-density sequence-density=0.57 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=22 prefix-density=0.58 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=19.40 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=2.0 sequence=CCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGG SRR13695412 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 01:47:29 Started mapping on | Feb 12 01:47:29 Finished on | Feb 12 01:49:03 Mapping speed, Million of reads per hour | 558.53 Number of input reads | 14583758 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 13713585 Uniquely mapped reads % | 94.03% Average mapped length | 293.23 Number of splices: Total | 13219883 Number of splices: Annotated (sjdb) | 12970202 Number of splices: GT/AG | 12929744 Number of splices: GC/AG | 244136 Number of splices: AT/AC | 7425 Number of splices: Non-canonical | 38578 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.82 Insertion rate per base | 0.02% Insertion average length | 2.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 328862 % of reads mapped to multiple loci | 2.25% Number of reads mapped to too many loci | 68618 % of reads mapped to too many loci | 0.47% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.12% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 541467 541467 541467 N_multimapping 328862 328862 328862 N_noFeature 381929 13405262 535555 N_ambiguous 242061 1305 86450 UnstrandedReadsAssigned:13089595 PositiveStrandReadsAssigned:307018 NegativeStrandReadsAssigned:13091580 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13695412 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: SRR13695412-trimmed-pair1.fastq SRR13695412-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,583,758 reads, 13,186,130 reads pseudoaligned [quant] estimated average fragment length: 235.953 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,129 rounds 52401 SRR13695412.ke.tsv 34699 SRR13695412.se.tsv 87100 total ==> SRR13695412.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1783.05 376 13.3674 Potri.005G024800.1.v4.1 1035 800.047 416 32.961 Potri.004G059700.1.v4.1 961 726.104 8 0.698414 Potri.007G009000.2.v4.1 1416 1181.05 0 0 Potri.003G141000.2.v4.1 2943 2708.05 486 11.3763 Potri.016G087400.1.v4.1 270 89.031 753 536.137 Potri.015G069301.1.v4.1 564 335.808 0 0 Potri.010G195200.1.v4.1 1773 1538.05 63 2.59653 Potri.012G127500.1.v4.1 977 742.068 107 9.14033 ==> SRR13695412.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 197 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 285 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR13695412 completed mapping pipeline successfully