Starting /dee2/code/volunteer_pipeline.sh SRR13695408 current disk space = 3051209547776 free memory = 1187925100 SRR13695408 SRAfilesize b91c202d38eb9072eccf3e8a8f19da69 SRR13695408.sra SRR13695408.sra file validated SRR13695408 is paired end SRR13695408 is conventional basespace SRR13695408 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695408_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 36.578 37.0 37.0 37.0 37.0 37.0 2 36.32075 37.0 37.0 37.0 37.0 37.0 3 36.517 37.0 37.0 37.0 37.0 37.0 4 36.608 37.0 37.0 37.0 37.0 37.0 5 36.5715 37.0 37.0 37.0 37.0 37.0 6 36.587 37.0 37.0 37.0 37.0 37.0 7 36.5125 37.0 37.0 37.0 37.0 37.0 8 36.574 37.0 37.0 37.0 37.0 37.0 9 36.5865 37.0 37.0 37.0 37.0 37.0 10-14 36.5412 37.0 37.0 37.0 37.0 37.0 15-19 36.5284 37.0 37.0 37.0 37.0 37.0 20-24 36.48 37.0 37.0 37.0 37.0 37.0 25-29 36.438900000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.424 37.0 37.0 37.0 37.0 37.0 35-39 36.4255 37.0 37.0 37.0 37.0 37.0 40-44 36.4124 37.0 37.0 37.0 37.0 37.0 45-49 36.3915 37.0 37.0 37.0 37.0 37.0 50-54 36.3157 37.0 37.0 37.0 37.0 37.0 55-59 36.2915 37.0 37.0 37.0 37.0 37.0 60-64 36.3463 37.0 37.0 37.0 37.0 37.0 65-69 36.2758 37.0 37.0 37.0 37.0 37.0 70-74 36.2497 37.0 37.0 37.0 37.0 37.0 75-79 36.2573 37.0 37.0 37.0 37.0 37.0 80-84 36.1971 37.0 37.0 37.0 37.0 37.0 85-89 36.1707 37.0 37.0 37.0 37.0 37.0 90-94 36.134699999999995 37.0 37.0 37.0 37.0 37.0 95-99 36.0469 37.0 37.0 37.0 37.0 37.0 100-104 36.1336 37.0 37.0 37.0 37.0 37.0 105-109 36.0593 37.0 37.0 37.0 37.0 37.0 110-114 36.0612 37.0 37.0 37.0 37.0 37.0 115-119 36.025999999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.9881 37.0 37.0 37.0 37.0 37.0 125-129 35.9135 37.0 37.0 37.0 37.0 37.0 130-134 35.8643 37.0 37.0 37.0 37.0 37.0 135-139 35.8562 37.0 37.0 37.0 37.0 37.0 140-144 35.690400000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.512899999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.311499999999995 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 0.0 22 0.0 23 0.0 24 0.0 25 7.0 26 10.0 27 14.0 28 15.0 29 17.0 30 23.0 31 29.0 32 55.0 33 98.0 34 112.0 35 310.0 36 2970.0 37 338.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.050000000000004 12.6 8.1 40.25 2 20.336429826763748 12.92995229726337 34.973637961335676 31.75997991463721 3 18.2 16.55 26.8 38.45 4 21.75 25.1 23.625 29.525000000000002 5 23.75 31.2 23.849999999999998 21.2 6 20.125 35.075 23.45 21.349999999999998 7 15.625 27.800000000000004 39.550000000000004 17.025000000000002 8 17.825 26.974999999999998 31.924999999999997 23.275000000000002 9 17.325 24.85 33.025 24.8 10-14 19.950000000000003 30.330000000000002 26.495 23.225 15-19 19.830000000000002 28.994999999999997 27.345000000000002 23.830000000000002 20-24 20.015 29.325000000000003 26.779999999999998 23.880000000000003 25-29 19.71 28.660000000000004 27.865000000000002 23.765 30-34 19.919999999999998 28.735 27.589999999999996 23.755000000000003 35-39 20.185 28.060000000000002 28.199999999999996 23.555 40-44 20.080000000000002 28.83 26.979999999999997 24.11 45-49 20.21 29.115000000000002 26.31 24.365000000000002 50-54 21.085 28.335 26.96 23.62 55-59 20.765 28.315 27.37 23.549999999999997 60-64 20.485 28.93 27.169999999999998 23.415 65-69 20.075000000000003 28.595 28.105000000000004 23.225 70-74 21.044999999999998 29.24 26.43 23.285 75-79 20.05 28.18 27.675 24.095 80-84 20.46 27.800000000000004 27.685 24.055 85-89 20.064999999999998 28.360000000000003 27.229999999999997 24.345 90-94 20.685000000000002 28.115000000000002 27.115000000000002 24.085 95-99 20.195 28.794999999999998 27.485 23.525 100-104 20.555 29.145 26.6 23.7 105-109 20.544999999999998 28.525 27.47 23.46 110-114 20.93 28.439999999999998 26.96 23.669999999999998 115-119 21.945 28.215 26.119999999999997 23.72 120-124 20.865000000000002 28.18 26.55 24.404999999999998 125-129 21.634999999999998 27.675 26.86 23.830000000000002 130-134 21.69 27.839999999999996 25.91 24.560000000000002 135-139 21.005 27.685 27.189999999999998 24.12 140-144 20.645 27.82 27.089999999999996 24.445 145-149 21.34 27.815 26.105 24.740000000000002 150-151 21.775 27.8375 26.05 24.337500000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.0 23 0.5 24 1.0 25 1.5 26 3.0 27 5.5 28 11.5 29 13.0 30 19.0 31 33.0 32 37.0 33 45.5 34 64.0 35 70.5 36 77.0 37 105.5 38 127.0 39 135.5 40 165.5 41 200.0 42 219.0 43 225.5 44 246.5 45 282.0 46 266.0 47 240.5 48 239.0 49 221.5 50 198.0 51 157.5 52 125.5 53 112.5 54 88.5 55 61.0 56 55.5 57 55.5 58 34.0 59 23.5 60 16.5 61 6.0 62 4.0 63 2.0 64 0.5 65 0.0 66 0.5 67 0.5 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.5 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.42500000000000004 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 71.15 #Duplication Level Percentage of deduplicated Percentage of total 1 73.19044272663388 52.075 2 17.427969079409696 24.8 3 6.28952916373858 13.425 4 2.2839072382290935 6.5 5 0.4216444132115249 1.5 6 0.31623330990864373 1.35 7 0.07027406886858749 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CGCTGCTTTGGCCAAGTGACACCAGGTTTCTCCTTCTCGTATACAGCTTC 7 0.17500000000000002 No Hit CCTTCGCCAAGCAAAGGCAAGTTCTCCGATAACACAATCTTGATCCGCTG 7 0.17500000000000002 No Hit CCCCAATGAAGTCACCTAATCCTATCCCACTACACTTCACCACCAACCCT 6 0.15 No Hit AGCATAAGAACCAGCACGAACGGTAAGGGAAGAAGGGGCGGTGGAGCGGC 6 0.15 No Hit CCTTCATATCAAAGATAAAATTCAACCTTTGGACATTATCTTGCCAAAAA 6 0.15 No Hit GCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTT 6 0.15 No Hit GCTTGTTATACCCATCCATGAAGTCAAAAGAGCTCTTGTACTCATCTGGC 6 0.15 No Hit CCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGAC 6 0.15 No Hit GTCATAATTTCTGTGAATGCTCCCACCTAGCGAATTCTCAATCGGTAAAA 6 0.15 No Hit CTCCTTGGCTGGAACTGCAGTGATTTTGTTTTTAGGATTCTCAAAGCTTC 6 0.15 No Hit GCTCGTCCGGAATGAGTTGGGTTGGCAGCACTTCAATGACAGCATCAGCA 6 0.15 No Hit CACAAATTTGCAAATCATAAATACACAAGGGGTAAGGTTAAAAGGGTTAG 5 0.125 No Hit GTTCAGGAGCTGGAGGAGGGACCTCGTCAGCTTTCTTATGTCCTGGCAAT 5 0.125 No Hit CAGGTACTAGATGTCCAGATAGATTTGAGTTTCCCAAGTCCAGGCGAGTG 5 0.125 No Hit CTCGCAATGAAAGAATCCAAATCTTTATAAGTATATGCAAACTTTGTCAT 5 0.125 No Hit GCGTGGGATTGAACAAACTGCTATTCACCACAAGTATTCCTATGTCTCTA 5 0.125 No Hit GGTGCTCCCACCAAAAATTGGTGATGGGGTACTTGGGTCCAACTCCGGTG 5 0.125 No Hit CCAACACTAGAACCTCAACACTCCTCATCAGCACAAACACAGCACCCACT 5 0.125 No Hit CTACTAGTTGTACTCCATTGAAATTCAAATCCAAGGGAGAACAAAATTAT 5 0.125 No Hit CCAATAATCTCAGCGCCCAATCCAGTGCCTGTGCTGTACCCATCAGCCAA 5 0.125 No Hit AGCTAGGGTAACAGCCCAGATTAGCAAGCCAGTCTTACCCCCAGCATAGA 5 0.125 No Hit CGGATGAAGAAGCTTTGCTAGGAAGAGGATTGTAGAGAAGACGAGAGAAT 5 0.125 No Hit GAGGTGGTTCAAGCAGTCTCACGGAACGAGGAAGCATAAACTCGGCGAAT 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.2375 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.32499999999999996 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.5249999999999999 0.0 0.0 0.0 0.0 92-93 0.7875000000000001 0.0 0.0 0.0 0.0 94-95 0.9625 0.0 0.0 0.0 0.0 96-97 1.0875 0.0 0.0 0.0 0.0 98-99 1.35 0.0 0.0 0.0 0.0 100-101 1.5875 0.0 0.0 0.0 0.0 102-103 2.075 0.0 0.0 0.0 0.0 104-105 2.3 0.0 0.0 0.0 0.0 106-107 2.7125 0.0 0.0 0.0 0.0 108-109 3.0375 0.0 0.0 0.0 0.0 110-111 3.375 0.0 0.0 0.0 0.0 112-113 3.6500000000000004 0.0 0.0 0.0 0.0 114-115 4.1 0.0 0.0 0.0 0.0 116-117 4.5 0.0 0.0 0.0 0.0 118-119 5.125 0.0 0.0 0.0 0.0 120-121 5.725 0.0 0.0 0.0 0.0 122-123 6.225 0.0 0.0 0.0 0.0 124-125 6.8 0.0 0.0 0.0 0.0 126-127 7.2125 0.0 0.0 0.0 0.0 128-129 8.075 0.0 0.0 0.0 0.0 130-131 8.837499999999999 0.0 0.0 0.0 0.0 132-133 9.600000000000001 0.0 0.0 0.0 0.0 134-135 10.350000000000001 0.0 0.0 0.0 0.0 136-137 10.962499999999999 0.0 0.0 0.0 0.0 138-139 11.4375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCTGGAG 10 0.006830828 145.0 9 GAGCTGG 10 0.006830828 145.0 7 TTCAGGA 10 0.006830828 145.0 2 CAGGAGC 10 0.006830828 145.0 4 AGCTGGA 10 0.006830828 145.0 8 >>END_MODULE SRR13695408 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695408_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.18075 37.0 37.0 37.0 37.0 37.0 2 36.109 37.0 37.0 37.0 37.0 37.0 3 36.036 37.0 37.0 37.0 37.0 37.0 4 36.2285 37.0 37.0 37.0 37.0 37.0 5 36.364 37.0 37.0 37.0 37.0 37.0 6 36.165 37.0 37.0 37.0 37.0 37.0 7 36.256 37.0 37.0 37.0 37.0 37.0 8 36.141 37.0 37.0 37.0 37.0 37.0 9 36.288 37.0 37.0 37.0 37.0 37.0 10-14 36.2909 37.0 37.0 37.0 37.0 37.0 15-19 36.2583 37.0 37.0 37.0 37.0 37.0 20-24 36.2441 37.0 37.0 37.0 37.0 37.0 25-29 36.1854 37.0 37.0 37.0 37.0 37.0 30-34 36.09245 37.0 37.0 37.0 37.0 37.0 35-39 36.09 37.0 37.0 37.0 37.0 37.0 40-44 36.1267 37.0 37.0 37.0 37.0 37.0 45-49 36.1308 37.0 37.0 37.0 37.0 37.0 50-54 36.0243 37.0 37.0 37.0 37.0 37.0 55-59 36.0015 37.0 37.0 37.0 37.0 37.0 60-64 36.0398 37.0 37.0 37.0 37.0 37.0 65-69 35.960499999999996 37.0 37.0 37.0 37.0 37.0 70-74 35.9413 37.0 37.0 37.0 37.0 37.0 75-79 35.884100000000004 37.0 37.0 37.0 37.0 37.0 80-84 35.9094 37.0 37.0 37.0 37.0 37.0 85-89 35.8584 37.0 37.0 37.0 37.0 37.0 90-94 35.7863 37.0 37.0 37.0 37.0 37.0 95-99 35.84225 37.0 37.0 37.0 37.0 37.0 100-104 35.8421 37.0 37.0 37.0 37.0 37.0 105-109 35.82625 37.0 37.0 37.0 37.0 37.0 110-114 35.750899999999994 37.0 37.0 37.0 37.0 37.0 115-119 35.7392 37.0 37.0 37.0 37.0 37.0 120-124 35.6666 37.0 37.0 37.0 37.0 37.0 125-129 35.674 37.0 37.0 37.0 37.0 37.0 130-134 35.5533 37.0 37.0 37.0 37.0 37.0 135-139 35.5923 37.0 37.0 37.0 37.0 37.0 140-144 35.421499999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.270799999999994 37.0 37.0 37.0 34.6 37.0 150-151 35.04175 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 5.0 15 3.0 16 1.0 17 2.0 18 1.0 19 0.0 20 0.0 21 2.0 22 2.0 23 3.0 24 7.0 25 3.0 26 11.0 27 13.0 28 8.0 29 16.0 30 18.0 31 36.0 32 63.0 33 109.0 34 193.0 35 561.0 36 2727.0 37 212.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.76950087785302 21.921244043140206 14.171055931778278 27.13819914722849 2 27.450000000000003 27.3 29.349999999999998 15.9 3 22.075 25.7 32.2 20.025000000000002 4 24.5 31.7 24.3 19.5 5 27.275 33.575 21.625 17.525 6 18.825 38.9 24.15 18.125 7 20.05 23.625 38.5 17.825 8 23.0 27.425 27.175 22.400000000000002 9 22.2 24.3 30.775000000000002 22.725 10-14 23.71 29.705 25.8 20.785 15-19 22.46 28.389999999999997 27.83 21.32 20-24 23.73237323732373 28.42784278427843 27.502750275027505 20.337033703370334 25-29 24.01700850425213 27.358679339669834 27.378689344672335 21.245622811405703 30-34 23.210802700675167 27.44186046511628 27.646911727931982 21.70042510627657 35-39 23.617361736173617 27.322732273227324 28.112811281128113 20.94709470947095 40-44 23.4370311093328 27.45823747124137 28.293488046413923 20.811243373011905 45-49 22.744548909781955 27.230446089217843 27.470494098819763 22.554510902180436 50-54 23.387338733873385 28.092809280928094 27.627762776277624 20.89208920892089 55-59 23.916958479239618 27.03351675837919 27.383691845922964 21.665832916458232 60-64 23.1973197319732 26.817681768176815 28.70787078707871 21.277127712771275 65-69 23.189999999999998 27.229999999999997 27.76 21.82 70-74 23.771885942971487 28.024012006003 27.5887943971986 20.615307653826914 75-79 22.58177453235971 28.0334100230069 27.223166950085027 22.161648494548363 80-84 22.770000000000003 28.110000000000003 27.229999999999997 21.89 85-89 23.984593837535016 28.281312525010005 26.595638255302124 21.13845538215286 90-94 23.3023302330233 28.0978097809781 27.35273527352735 21.247124712471248 95-99 24.121206060303017 27.86639331966598 26.981349067453376 21.03105155257763 100-104 23.581790895447725 27.763881940970485 28.36418209104552 20.290145072536266 105-109 24.886198789455253 26.837076684508027 27.427342304036817 20.8493822219999 110-114 24.187418741874186 28.06780678067807 27.532753275327533 20.212021202120212 115-119 25.11004401760704 27.991196478591434 26.790716286514606 20.108043217286912 120-124 24.652326163081543 28.534267133566782 26.753376688344172 20.060030015007506 125-129 25.33513405362145 27.801120448179272 26.365546218487395 20.498199279711883 130-134 25.23261630815408 26.853426713356676 27.848924462231118 20.06503251625813 135-139 25.80290145072536 27.598799399699853 26.468234117058532 20.13006503251626 140-144 25.842584258425845 26.94269426942694 26.912691269126913 20.3020302030203 145-149 26.103051525762883 27.48874437218609 26.228114057028513 20.18009004502251 150-151 26.625812906453227 27.138569284642323 26.550775387693847 19.684842421210604 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.5 20 0.5 21 0.0 22 1.5 23 1.5 24 1.0 25 2.5 26 2.0 27 1.0 28 2.0 29 4.0 30 5.0 31 15.5 32 25.5 33 26.5 34 31.0 35 59.0 36 96.0 37 98.5 38 114.0 39 164.0 40 193.5 41 201.0 42 243.0 43 278.5 44 291.0 45 301.5 46 283.0 47 249.0 48 218.5 49 200.0 50 177.5 51 143.0 52 121.0 53 114.5 54 91.5 55 66.0 56 48.0 57 32.5 58 21.5 59 19.5 60 16.5 61 6.5 62 5.5 63 5.5 64 2.0 65 0.5 66 0.5 67 2.0 68 2.0 69 1.0 70 1.0 71 0.5 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 0.5 83 0.5 84 0.0 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 90 0.5 91 1.0 92 0.5 93 0.5 94 0.5 95 0.0 96 0.0 97 0.5 98 0.5 99 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.325 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 0.01 25-29 0.05 30-34 0.025 35-39 0.01 40-44 0.03 45-49 0.02 50-54 0.01 55-59 0.05 60-64 0.01 65-69 0.0 70-74 0.05 75-79 0.03 80-84 0.0 85-89 0.04 90-94 0.01 95-99 0.005 100-104 0.05 105-109 0.045 110-114 0.01 115-119 0.04 120-124 0.05 125-129 0.04 130-134 0.05 135-139 0.05 140-144 0.01 145-149 0.05 150-151 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.25 #Duplication Level Percentage of deduplicated Percentage of total 1 73.15789473684211 52.125 2 17.859649122807017 25.45 3 5.859649122807017 12.525 4 2.3157894736842106 6.6000000000000005 5 0.3859649122807018 1.375 6 0.3157894736842105 1.35 7 0.07017543859649122 0.35000000000000003 8 0.0 0.0 9 0.03508771929824561 0.22499999999999998 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 9 0.22499999999999998 No Hit ATTTCTTTGATGCTTCGGTGAAGTTGGCAGTGAAGATGAAGGCTGAAACC 7 0.17500000000000002 No Hit GCAAGAAGAGAGGGGACAAATGCGATCAAGAAATTGATCTGTACACTGTT 7 0.17500000000000002 No Hit AGATGGCTTCCTCCTCTATGATCTCATCGGCAGCCGTTGCCACCGTCAAC 6 0.15 No Hit CATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAA 6 0.15 No Hit GGATAAAGTGATAACTGAAGAAGCCACCAAGAGGAGAGGAGAGGAGAGGA 6 0.15 No Hit CTTCTCATTTATCAAATTCAGTATCCAATGGGTCTCGCCTTCGCGTTGCT 6 0.15 No Hit GTCCACTTCCACCTTATTTGTGGCTTCTGACCAATTTGGTAAGGTTCCTC 6 0.15 No Hit CATTTCTCTGGACCATATGGAGAGGATGTTGTCTTTGTTGCCAATGATTG 6 0.15 No Hit GGTAGAGAGCAGATAAGATAGCAGACACAAATTGTTATTATAGGCTCTAT 6 0.15 No Hit CCAACGTGTGAGGGACCTCTTGGACTTCAGTATCTACTTGGACATTAGCA 6 0.15 No Hit CATGGGAGAGCACCGGCCTCGATCAATCTCCACCACAAACAGCAGCGCTC 6 0.15 No Hit CTTGCTAATCTGGGCTGTTACCCTAGCTGGCATTCTTGCCGGAGGTGCAC 5 0.125 No Hit ACAAAATATACAAGAGAGAACACGATGGCTCAAACCATGGTGCTCATGTC 5 0.125 No Hit CAGCAGTTCTTCCAGCTCTTCTAGCGACGAGGAGGAAGGTGACGATGAAG 5 0.125 No Hit AAGAGGTTCTCCCGAAATAGGTGAAATGATCACTAAAGCAATGATTGTAG 5 0.125 No Hit CTACGCTCCAAAAGGCTTGATGCGTGTCCCGCCAGACCAGTCCATGGCTG 5 0.125 No Hit GAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTT 5 0.125 No Hit TATTATCGGGAAATCACCAACTCCAAAAACTGTCTCCTCTGATACCAAGG 5 0.125 No Hit CTCTCTCTCCCAACCAAACCCTAAAAACTTGATTCCTCTCTCTCGAAGAG 5 0.125 No Hit GCTGGTATTTCAGGGGGTCACATTAACCCAGCAGTGACATTTGGGCTGTT 5 0.125 No Hit GGTGGCATGAACCTCAGGGATGGGTTAGATGCATCTGGAAGGAAGCCCAA 5 0.125 No Hit GGGTAGATCTTTGATTCCTGTCCTGTGCGAAGTGGTGAATGATAATATAG 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.2375 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.32499999999999996 0.0 0.0 0.0 0.0 88-89 0.4375 0.0 0.0 0.0 0.0 90-91 0.5249999999999999 0.0 0.0 0.0 0.0 92-93 0.7875000000000001 0.0 0.0 0.0 0.0 94-95 0.9625 0.0 0.0 0.0 0.0 96-97 1.0875 0.0 0.0 0.0 0.0 98-99 1.35 0.0 0.0 0.0 0.0 100-101 1.5875 0.0 0.0 0.0 0.0 102-103 2.075 0.0 0.0 0.0 0.0 104-105 2.3 0.0 0.0 0.0 0.0 106-107 2.7375 0.0 0.0 0.0 0.0 108-109 3.0875 0.0 0.0 0.0 0.0 110-111 3.425 0.0 0.0 0.0 0.0 112-113 3.7 0.0 0.0 0.0 0.0 114-115 4.15 0.0 0.0 0.0 0.0 116-117 4.575 0.0 0.0 0.0 0.0 118-119 5.225 0.0 0.0 0.0 0.0 120-121 5.825 0.0 0.0 0.0 0.0 122-123 6.325 0.0 0.0 0.0 0.0 124-125 6.875 0.0 0.0 0.0 0.0 126-127 7.2875 0.0 0.0 0.0 0.0 128-129 8.1875 0.0 0.0 0.0 0.0 130-131 8.95 0.0 0.0 0.0 0.0 132-133 9.7125 0.0 0.0 0.0 0.0 134-135 10.4625 0.0 0.0 0.0 0.0 136-137 11.087499999999999 0.0 0.0 0.0 0.0 138-139 11.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAGCAGT 10 0.006830828 145.0 1 >>END_MODULE Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885129 spots for SRR13695408.sra Written 885129 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra Read 885125 spots for SRR13695408.sra Written 885125 spots for SRR13695408.sra SRR ids: ['SRR13695408.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_614etrzf SRR13695408.sra spots: 17702504 blocks: [[1, 885125], [885126, 1770250], [1770251, 2655375], [2655376, 3540500], [3540501, 4425625], [4425626, 5310750], [5310751, 6195875], [6195876, 7081000], [7081001, 7966125], [7966126, 8851250], [8851251, 9736375], [9736376, 10621500], [10621501, 11506625], [11506626, 12391750], [12391751, 13276875], [13276876, 14162000], [14162001, 15047125], [15047126, 15932250], [15932251, 16817375], [16817376, 17702504]] SRR13695408 file size 5994384 SRR13695408 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 SRR13695408 SRR13695408_1.fastq SRR13695408_2.fastq Input file: SRR13695408_1.fastq Paired file: SRR13695408_2.fastq trimmed: SRR13695408-trimmed-pair1.fastq, SRR13695408-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 00:48:52 2025 >> started Wed Feb 12 00:49:13 2025 >> done (21.360s) 17702504 read pairs processed; of these: 99 ( 0.00%) short read pairs filtered out after trimming by size control 1978 ( 0.01%) empty read pairs filtered out after trimming by size control 17700427 (99.99%) read pairs available; of these: 2758825 (15.59%) trimmed read pairs available after processing 14941602 (84.41%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 1 0.00% 20 1 0.00% 21 0 0.00% 22 7 0.00% 23 1 0.00% 24 2 0.00% 25 2 0.00% 26 3 0.00% 27 1 0.00% 28 1 0.00% 29 1 0.00% 30 5 0.00% 31 6 0.00% 32 3 0.00% 33 2 0.00% 34 7 0.00% 35 8 0.00% 36 13 0.00% 37 8 0.00% 38 9 0.00% 39 13 0.00% 40 9 0.00% 41 15 0.00% 42 21 0.00% 43 17 0.00% 44 26 0.00% 45 17 0.00% 46 22 0.00% 47 29 0.00% 48 32 0.00% 49 46 0.00% 50 66 0.00% 51 87 0.00% 52 104 0.00% 53 77 0.00% 54 104 0.00% 55 132 0.00% 56 143 0.00% 57 169 0.00% 58 214 0.00% 59 241 0.00% 60 321 0.00% 61 328 0.00% 62 439 0.00% 63 499 0.00% 64 573 0.00% 65 627 0.00% 66 690 0.00% 67 823 0.00% 68 939 0.01% 69 1122 0.01% 70 1326 0.01% 71 1489 0.01% 72 1657 0.01% 73 2000 0.01% 74 2158 0.01% 75 2490 0.01% 76 2800 0.02% 77 3117 0.02% 78 3497 0.02% 79 3823 0.02% 80 4338 0.02% 81 4895 0.03% 82 5706 0.03% 83 6462 0.04% 84 7287 0.04% 85 7879 0.04% 86 8506 0.05% 87 9210 0.05% 88 9941 0.06% 89 10532 0.06% 90 11491 0.06% 91 12476 0.07% 92 13222 0.07% 93 14535 0.08% 94 15854 0.09% 95 16690 0.09% 96 17897 0.10% 97 19216 0.11% 98 19957 0.11% 99 20597 0.12% 100 21837 0.12% 101 22421 0.13% 102 23312 0.13% 103 25037 0.14% 104 25885 0.15% 105 26890 0.15% 106 28781 0.16% 107 29813 0.17% 108 30992 0.18% 109 32329 0.18% 110 32793 0.19% 111 33715 0.19% 112 34873 0.20% 113 35824 0.20% 114 37280 0.21% 115 38918 0.22% 116 39938 0.23% 117 41283 0.23% 118 42395 0.24% 119 43424 0.25% 120 44264 0.25% 121 45325 0.26% 122 45666 0.26% 123 47153 0.27% 124 49025 0.28% 125 49388 0.28% 126 51604 0.29% 127 52161 0.29% 128 53734 0.30% 129 54438 0.31% 130 55900 0.32% 131 56156 0.32% 132 56775 0.32% 133 57306 0.32% 134 58248 0.33% 135 59562 0.34% 136 60569 0.34% 137 61833 0.35% 138 62954 0.36% 139 65261 0.37% 140 64698 0.37% 141 65241 0.37% 142 66024 0.37% 143 66263 0.37% 144 67633 0.38% 145 68429 0.39% 146 68643 0.39% 147 70351 0.40% 148 72004 0.41% 149 72028 0.41% 150 73369 0.41% 151 14941602 84.41% 17700427 reads passed initial QC criterion=sequence-density sequence-density=0.64 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=26 prefix-density=0.63 prefix-fanout=2.0 sequence=GTGTTGTCGAATCC criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=139.69 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=11.2 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=18 prefix-density=0.60 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=25 fanout-score=46.16 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=1.8 sequence=AAGGAACTCAAACGCATAGCTTCCTACAAATACCCCAGCTAGCCAATACTCTCAACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCGTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGGCCTCTCTGCTGACCCAGAGACCTTTGCCAAGAACCGTGAGCTTGAAGTCATCCATTCCAGGTGGGCCATGCTTGGAGCTCTTGGATGCGTCTTCCCCGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAGGCTGTATGGTTCAAGGCTGGAGCCCA SRR13695408 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 00:49:55 Started mapping on | Feb 12 00:49:56 Finished on | Feb 12 00:51:48 Mapping speed, Million of reads per hour | 568.94 Number of input reads | 17700427 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 16837163 Uniquely mapped reads % | 95.12% Average mapped length | 292.91 Number of splices: Total | 16617738 Number of splices: Annotated (sjdb) | 16308570 Number of splices: GT/AG | 16262488 Number of splices: GC/AG | 293546 Number of splices: AT/AC | 9111 Number of splices: Non-canonical | 52593 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.74 Insertion rate per base | 0.02% Insertion average length | 2.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 393066 % of reads mapped to multiple loci | 2.22% Number of reads mapped to too many loci | 36355 % of reads mapped to too many loci | 0.21% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.37% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 470428 470428 470428 N_multimapping 393066 393066 393066 N_noFeature 453978 16441611 659076 N_ambiguous 286746 1493 95378 UnstrandedReadsAssigned:16096439 PositiveStrandReadsAssigned:394059 NegativeStrandReadsAssigned:16082709 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13695408 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: SRR13695408-trimmed-pair1.fastq SRR13695408-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,700,427 reads, 16,114,169 reads pseudoaligned [quant] estimated average fragment length: 230.747 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,087 rounds 52401 SRR13695408.ke.tsv 34699 SRR13695408.se.tsv 87100 total ==> SRR13695408.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1788.25 540 15.8167 Potri.005G024800.1.v4.1 1035 805.253 228 14.8305 Potri.004G059700.1.v4.1 961 731.314 7 0.501356 Potri.007G009000.2.v4.1 1416 1186.25 0 0 Potri.003G141000.2.v4.1 2943 2713.25 860 16.602 Potri.016G087400.1.v4.1 270 89.9456 887 516.531 Potri.015G069301.1.v4.1 564 340.308 0 0 Potri.010G195200.1.v4.1 1773 1543.25 100 3.39403 Potri.012G127500.1.v4.1 977 747.292 52 3.64473 ==> SRR13695408.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 142 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 327 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 16 SRR13695408 completed mapping pipeline successfully