Starting /dee2/code/volunteer_pipeline.sh SRR13165358 current disk space = 1542139121664 free memory = 1606701772 SRR13165358 SRAfilesize 31f9a27d2cd8e550f0614c7bcd143e1d SRR13165358.sra SRR13165358.sra file validated SRR13165358 is paired end SRR13165358 is conventional basespace SRR13165358 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165358_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 36.4445 37.0 37.0 37.0 37.0 37.0 2 36.19625 37.0 37.0 37.0 37.0 37.0 3 36.4745 37.0 37.0 37.0 37.0 37.0 4 36.539 37.0 37.0 37.0 37.0 37.0 5 36.4555 37.0 37.0 37.0 37.0 37.0 6 36.615 37.0 37.0 37.0 37.0 37.0 7 36.472 37.0 37.0 37.0 37.0 37.0 8 36.5215 37.0 37.0 37.0 37.0 37.0 9 36.5665 37.0 37.0 37.0 37.0 37.0 10-14 36.556999999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.50019999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.4554 37.0 37.0 37.0 37.0 37.0 25-29 36.4268 37.0 37.0 37.0 37.0 37.0 30-34 36.3981 37.0 37.0 37.0 37.0 37.0 35-39 36.3152 37.0 37.0 37.0 37.0 37.0 40-44 36.3446 37.0 37.0 37.0 37.0 37.0 45-49 36.28 37.0 37.0 37.0 37.0 37.0 50-54 36.297000000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.291599999999995 37.0 37.0 37.0 37.0 37.0 60-64 36.316 37.0 37.0 37.0 37.0 37.0 65-69 36.248599999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.243100000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.232299999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.163799999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.1947 37.0 37.0 37.0 37.0 37.0 90-94 36.0815 37.0 37.0 37.0 37.0 37.0 95-99 36.0737 37.0 37.0 37.0 37.0 37.0 100-104 36.1245 37.0 37.0 37.0 37.0 37.0 105-109 36.1103 37.0 37.0 37.0 37.0 37.0 110-114 36.060900000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.06060000000001 37.0 37.0 37.0 37.0 37.0 120-124 35.9166 37.0 37.0 37.0 37.0 37.0 125-129 35.9142 37.0 37.0 37.0 37.0 37.0 130-134 35.7966 37.0 37.0 37.0 37.0 37.0 135-139 35.6419 37.0 37.0 37.0 37.0 37.0 140-144 35.4028 37.0 37.0 37.0 37.0 37.0 145-149 35.110400000000006 37.0 37.0 37.0 29.8 37.0 150-151 34.71275 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 0.0 23 2.0 24 2.0 25 2.0 26 7.0 27 11.0 28 25.0 29 25.0 30 23.0 31 47.0 32 61.0 33 105.0 34 144.0 35 348.0 36 2760.0 37 435.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 53.1 10.025 5.375 31.5 2 22.532027128862094 10.27380055262497 33.55940718412459 33.634765134388346 3 20.1 15.075 26.950000000000003 37.875 4 25.474999999999998 22.775000000000002 21.2 30.55 5 27.025 27.275 22.525000000000002 23.175 6 24.15 30.525000000000002 21.65 23.674999999999997 7 18.35 25.124999999999996 39.725 16.8 8 20.275000000000002 22.225 31.225 26.275 9 19.925 22.15 31.374999999999996 26.55 10-14 23.59 25.990000000000002 25.7 24.72 15-19 24.415 24.025 24.825 26.735 20-24 23.799999999999997 25.245 25.314999999999998 25.64 25-29 23.71 24.995 25.415 25.88 30-34 24.27 25.055 25.235000000000003 25.44 35-39 24.575 25.05 24.595 25.779999999999998 40-44 24.169999999999998 24.515 24.57 26.745 45-49 23.855 24.834999999999997 24.990000000000002 26.32 50-54 23.76 25.46 24.955 25.825 55-59 24.5 24.08 25.380000000000003 26.040000000000003 60-64 24.32 24.195 24.905 26.58 65-69 24.055 25.52 24.765 25.66 70-74 24.425 25.169999999999998 24.32 26.085 75-79 24.154999999999998 24.884999999999998 25.314999999999998 25.645 80-84 23.905 24.795 24.474999999999998 26.825 85-89 24.42 25.03 24.265 26.284999999999997 90-94 24.515 24.675 24.57 26.240000000000002 95-99 24.610000000000003 24.705 24.77 25.915 100-104 25.445 24.23 24.38 25.945 105-109 24.575 25.365 24.099999999999998 25.96 110-114 24.85 25.055 24.44 25.655 115-119 24.795 24.975 24.16 26.07 120-124 24.4 25.305 24.349999999999998 25.945 125-129 24.13 24.89 23.82 27.16 130-134 25.06 25.759999999999998 23.68 25.5 135-139 24.645 25.66 23.150000000000002 26.545 140-144 24.55 24.81 24.48 26.16 145-149 25.240000000000002 24.585 23.625 26.55 150-151 25.8 26.150000000000002 23.1 24.95 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.0 24 1.5 25 0.5 26 0.5 27 1.5 28 3.0 29 6.5 30 11.5 31 15.5 32 16.5 33 20.5 34 28.5 35 35.5 36 49.5 37 62.5 38 61.5 39 73.5 40 116.5 41 128.5 42 148.5 43 187.0 44 191.0 45 186.0 46 171.5 47 179.5 48 203.5 49 187.5 50 165.0 51 140.5 52 118.0 53 117.5 54 97.0 55 95.5 56 95.0 57 85.5 58 87.5 59 75.5 60 73.0 61 67.5 62 67.5 63 63.5 64 60.5 65 64.5 66 52.0 67 38.5 68 35.5 69 44.5 70 44.0 71 39.0 72 42.0 73 36.5 74 25.0 75 21.5 76 17.5 77 15.5 78 10.5 79 5.5 80 5.0 81 2.0 82 0.5 83 0.5 84 0.0 85 0.0 86 0.5 87 0.5 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 0.475 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 71.45 #Duplication Level Percentage of deduplicated Percentage of total 1 73.61791462561231 52.6 2 17.179846046186146 24.55 3 6.263121063680896 13.425 4 1.9944016794961512 5.7 5 0.6298110566829951 2.25 6 0.2099370188943317 0.8999999999999999 7 0.06997900629811056 0.35000000000000003 8 0.0 0.0 9 0.03498950314905528 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 AGTAAAACAGTGAGGCATGCGGTATCTGTCCGACACACATTTGTATGGAC 9 0.22499999999999998 No Hit CTTCTCTCCCGATTTACCTAGAAGCAACTTCATCCAGTCACTCGTACCAC 7 0.17500000000000002 No Hit CGAGGAAACCTTTGCACGCCTCCGTTACCTTTTGGGAGGCCTACGCCCCA 7 0.17500000000000002 No Hit GTCCATCTTAATACGGAGCTGTCCTTGGTTGTTTATGCCTTGCCGGATTC 6 0.15 No Hit GCTGGAAAATAGCGAGTACATATACTCCATGGCATCGCATCCACATCAAT 6 0.15 No Hit GCCCTTGTGAAGAACCACCAGATGGATCAATAGCATGCCGTACATAATCA 6 0.15 No Hit GTTGAAGAGGTCTAGCTATCCTAATCCCTCAAACAAGGGCCACGAACATA 6 0.15 No Hit CCTGAAACCTATAACTTATGAAATTTTGGCATATTTGCAAAATGACTCGT 6 0.15 No Hit GTGCAAATCAAATTCAAAAAATCTTGGTAGAGGATATAGACAGAGCATTT 6 0.15 No Hit CCCATAGCTAAGCACGGTTATGAAAACAAGAGTACCGTCTACTTCTTCCT 5 0.125 No Hit GTATAATATTACATGTATATGTGTGTATATGTGTAGTCAGGGTTCAAATG 5 0.125 No Hit CGGGAATGCATTTACAAAATGTGATAGCTTATACTGGGCTTCATTCAAGA 5 0.125 No Hit ATAAATATTATTGCATCCCCAGGGAAAGCATCAACAGGATTAAAATGTTT 5 0.125 No Hit CCTCGGAGTCAGTATCCTTCATCTTCCTTGCCATCAGGTTCAGAAACTCC 5 0.125 No Hit ATCAGGTTCTTTGCCAGCACTTTTGGCTGTATCGATAGCTCTTTTCGGTA 5 0.125 No Hit GAGGGCTTGAGACCGCTGTACAACCCACCCCAGCCTTCCGTCTGAATCAG 5 0.125 No Hit CAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGT 5 0.125 No Hit GCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAGGCGGCCG 5 0.125 No Hit GTGATATCCATGTCACCAAAACCATGTGAAACCACCCAAGGGTAAAAGTG 5 0.125 No Hit CAGCTGGATTAGGCTGGTCAAGCAAGTCCTGTATCCCTACTAGAATCTGC 5 0.125 No Hit TTGCCATCCTTAAGTTTCCCTGCAGCCTCAAACTTGTTTTTTACTGCTAA 5 0.125 No Hit CCTCTCTCACCACAGCCCACATAAACCACAGTGTCGGAATTGGAGTACTT 5 0.125 No Hit GCCCCGTGTACACCAGCGGGTCCGAGTACTTGGCCAGCAGCGCCGCCGGG 5 0.125 No Hit TCGATATCACTATCACTGTCTGCATTATCTGCCTCAGCTCCACCACCAAC 5 0.125 No Hit CTCCGCTTGCTGCTGCTGCTGCTGCTGCTGCTTCTTGGTGTCGGCGCCGC 5 0.125 No Hit GATGAACTTCTCATGAAGCCGTCATTATCAGGGAGGCAGTCAGTGAGTCT 5 0.125 No Hit CTCGCGTCCAGCAGCCTCTGGTCACCCGTGTACGAGTGGGTGGTCGTCAT 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 0.025 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.1125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.21250000000000002 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.3125 0.0 0.0 0.0 0.0 78-79 0.38749999999999996 0.0 0.0 0.0 0.0 80-81 0.5125 0.0 0.0 0.0 0.0 82-83 0.7 0.0 0.0 0.0 0.0 84-85 0.975 0.0 0.0 0.0 0.0 86-87 1.1 0.0 0.0 0.0 0.0 88-89 1.2 0.0 0.0 0.0 0.0 90-91 1.375 0.0 0.0 0.0 0.0 92-93 1.725 0.0 0.0 0.0 0.0 94-95 2.1625 0.0 0.0 0.0 0.0 96-97 2.5625 0.0 0.0 0.0 0.0 98-99 3.025 0.0 0.0 0.0 0.0 100-101 3.625 0.0 0.0 0.0 0.0 102-103 4.1875 0.0 0.0 0.0 0.0 104-105 4.75 0.0 0.0 0.0 0.0 106-107 5.2375 0.0 0.0 0.0 0.0 108-109 5.6 0.0 0.0 0.0 0.0 110-111 6.25 0.0 0.0 0.0 0.0 112-113 6.8875 0.0 0.0 0.0 0.0 114-115 7.525 0.0 0.0 0.0 0.0 116-117 8.175 0.0 0.0 0.0 0.0 118-119 8.75 0.0 0.0 0.0 0.0 120-121 9.287500000000001 0.0 0.0 0.0 0.0 122-123 10.125 0.0 0.0 0.0 0.0 124-125 10.7125 0.0 0.0 0.0 0.0 126-127 11.325 0.0 0.0 0.0 0.0 128-129 11.9625 0.0 0.0 0.0 0.0 130-131 12.7625 0.0 0.0 0.0 0.0 132-133 13.475 0.0 0.0 0.0 0.0 134-135 14.3625 0.0 0.0 0.0 0.0 136-137 15.125 0.0 0.0 0.0 0.0 138-139 15.712499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTCCCA 10 0.006830828 145.0 7 CGGGGAC 10 0.006830828 145.0 1 CATCTTG 10 0.006830828 145.0 9 TCGGCCG 10 0.006830828 145.0 9 AACTTTT 10 0.006830828 145.0 9 GGCCCGA 10 0.006830828 145.0 145 AGAGTAA 10 0.006830828 145.0 4 ACCTCGG 10 0.006830828 145.0 6 CTCGGCC 10 0.006830828 145.0 8 CTAGAGT 10 0.006830828 145.0 2 GTAACTT 10 0.006830828 145.0 7 CCTAGAG 10 0.006830828 145.0 1 >>END_MODULE SRR13165358 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165358_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.016 37.0 37.0 37.0 37.0 37.0 2 36.0825 37.0 37.0 37.0 37.0 37.0 3 36.1215 37.0 37.0 37.0 37.0 37.0 4 36.113 37.0 37.0 37.0 37.0 37.0 5 36.2215 37.0 37.0 37.0 37.0 37.0 6 36.2225 37.0 37.0 37.0 37.0 37.0 7 36.1475 37.0 37.0 37.0 37.0 37.0 8 36.1735 37.0 37.0 37.0 37.0 37.0 9 36.209 37.0 37.0 37.0 37.0 37.0 10-14 36.205200000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.1824 37.0 37.0 37.0 37.0 37.0 20-24 36.1315 37.0 37.0 37.0 37.0 37.0 25-29 36.0994 37.0 37.0 37.0 37.0 37.0 30-34 36.05195 37.0 37.0 37.0 37.0 37.0 35-39 36.0218 37.0 37.0 37.0 37.0 37.0 40-44 36.05630000000001 37.0 37.0 37.0 37.0 37.0 45-49 35.99634999999999 37.0 37.0 37.0 37.0 37.0 50-54 35.970299999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.0073 37.0 37.0 37.0 37.0 37.0 60-64 35.9644 37.0 37.0 37.0 37.0 37.0 65-69 35.9167 37.0 37.0 37.0 37.0 37.0 70-74 35.869899999999994 37.0 37.0 37.0 37.0 37.0 75-79 35.9068 37.0 37.0 37.0 37.0 37.0 80-84 35.84675 37.0 37.0 37.0 37.0 37.0 85-89 35.84285 37.0 37.0 37.0 37.0 37.0 90-94 35.7312 37.0 37.0 37.0 37.0 37.0 95-99 35.81615000000001 37.0 37.0 37.0 37.0 37.0 100-104 35.7372 37.0 37.0 37.0 37.0 37.0 105-109 35.73595 37.0 37.0 37.0 37.0 37.0 110-114 35.64829999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.6426 37.0 37.0 37.0 37.0 37.0 120-124 35.4864 37.0 37.0 37.0 37.0 37.0 125-129 35.49135 37.0 37.0 37.0 37.0 37.0 130-134 35.310199999999995 37.0 37.0 37.0 34.6 37.0 135-139 35.2004 37.0 37.0 37.0 32.2 37.0 140-144 34.946299999999994 37.0 37.0 37.0 25.0 37.0 145-149 34.74929999999999 37.0 37.0 37.0 25.0 37.0 150-151 34.419250000000005 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 4.0 14 2.0 15 2.0 16 3.0 17 3.0 18 1.0 19 0.0 20 3.0 21 5.0 22 7.0 23 11.0 24 8.0 25 12.0 26 7.0 27 11.0 28 10.0 29 25.0 30 37.0 31 26.0 32 69.0 33 116.0 34 208.0 35 542.0 36 2664.0 37 223.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.96890672016048 18.78134403209629 8.625877632898696 24.623871614844532 2 31.55 22.400000000000002 26.474999999999998 19.575 3 23.65 23.674999999999997 29.4 23.275000000000002 4 27.625 30.85 19.900000000000002 21.625 5 29.575000000000003 33.025 18.224999999999998 19.175 6 23.474999999999998 35.449999999999996 17.65 23.425 7 22.2 19.825 33.425 24.55 8 24.775 22.425 23.625 29.175 9 23.65 22.425 25.5 28.425 10-14 26.595000000000002 26.735 22.305 24.365000000000002 15-19 25.505 24.959999999999997 24.39 25.145 20-24 25.622686806041813 25.27258177453236 23.76713013904171 25.337601280384114 25-29 25.897948974487246 24.662331165582792 24.297148574287146 25.142571285642823 30-34 25.443905366878404 25.138798579502826 24.18846596308708 25.228830090531684 35-39 26.512953886165853 25.047514254276283 23.777133139941984 24.662398719615886 40-44 26.000400160064025 25.835334133653458 23.85954381752701 24.304721888755502 45-49 25.964087430600713 25.1287950782774 24.038413444705647 24.868704046416244 50-54 27.443232969890968 24.742422726818045 23.291987596278886 24.5223567070121 55-59 26.52826413206603 25.277638819409702 23.70185092546273 24.49224612306153 60-64 25.54266279883965 25.157547264179254 24.17225167550265 25.127538261478442 65-69 26.695339067813563 25.550110022004404 23.26965393078616 24.484896979395877 70-74 26.89344672336168 24.21710855427714 24.352176088044022 24.537268634317158 75-79 25.80032012805122 24.414765906362547 24.019607843137255 25.765306122448976 80-84 26.961740435108776 24.71617904476119 24.221055263815956 24.10102525631408 85-89 27.647441348606872 24.01580711320094 23.43054374468511 24.90620779350708 90-94 26.758027408222468 25.767730319095726 23.617085125537663 23.857157147144143 95-99 27.56689172293073 24.726181545386346 23.960990247561888 23.74593648412103 100-104 27.303651825912954 25.34267133566783 23.43671835917959 23.916958479239618 105-109 27.492371567205243 24.97623930768846 23.795708068630884 23.735681056475414 110-114 27.8333500050015 26.192857857357204 23.181954586375912 22.791837551265377 115-119 28.19127651060424 25.360144057623053 22.97919167667067 23.46938775510204 120-124 27.738869434717362 25.722861430715362 23.36168084042021 23.176588294147074 125-129 27.63743684658096 26.386874093342005 23.395527987594416 22.580161072482618 130-134 28.484242121060532 25.1975987993997 23.036518259129565 23.281640820410203 135-139 29.439719859929962 26.21810905452726 22.30615307653827 22.0360180090045 140-144 29.998999699909973 25.27258177453236 23.30699209762929 21.421426427928377 145-149 30.7903951975988 24.542271135567784 23.03151575787894 21.635817908954476 150-151 30.040020010005 26.550775387693847 22.71135567783892 20.69784892446223 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 1.5 10 1.0 11 0.5 12 0.5 13 0.0 14 0.5 15 1.0 16 0.5 17 0.5 18 1.0 19 0.5 20 0.0 21 1.0 22 2.0 23 1.0 24 1.0 25 2.5 26 3.0 27 3.0 28 3.5 29 4.5 30 6.5 31 11.5 32 13.0 33 9.5 34 16.0 35 26.5 36 38.5 37 51.0 38 70.0 39 87.0 40 94.0 41 109.5 42 150.5 43 172.0 44 184.0 45 200.5 46 190.5 47 175.5 48 165.5 49 167.0 50 154.5 51 130.0 52 128.5 53 126.0 54 115.0 55 108.0 56 82.0 57 79.5 58 87.0 59 91.5 60 93.5 61 71.5 62 64.5 63 70.0 64 70.0 65 71.0 66 63.0 67 58.0 68 55.5 69 50.5 70 47.5 71 35.5 72 29.5 73 28.0 74 25.0 75 22.0 76 16.5 77 12.0 78 9.0 79 6.0 80 5.0 81 4.0 82 2.5 83 1.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 1.0 90 1.0 91 0.5 92 0.5 93 0.0 94 0.0 95 1.0 96 1.0 97 1.0 98 2.0 99 1.5 100 3.5 >>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 0.03 25-29 0.05 30-34 0.034999999999999996 35-39 0.03 40-44 0.04 45-49 0.034999999999999996 50-54 0.03 55-59 0.05 60-64 0.03 65-69 0.02 70-74 0.05 75-79 0.04 80-84 0.025 85-89 0.045 90-94 0.03 95-99 0.025 100-104 0.05 105-109 0.045 110-114 0.03 115-119 0.04 120-124 0.05 125-129 0.045 130-134 0.05 135-139 0.05 140-144 0.03 145-149 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 71.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 74.3562978427279 53.425 2 16.666666666666664 23.95 3 5.949895615866389 12.825000000000001 4 2.0876826722338206 6.0 5 0.5915100904662491 2.125 6 0.20876826722338201 0.8999999999999999 7 0.06958942240779402 0.35000000000000003 8 0.03479471120389701 0.2 9 0.03479471120389701 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 GTCTTTATGGTATATTTTGCAAGGAGTGTCCTTTAGGAACATACAAGAAC 9 0.22499999999999998 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit GCTTTTCCTGCGCAGCTTAGGTGGAAGGCGAAGAAGGCCCCCTTCCGGGG 7 0.17500000000000002 No Hit CCTACAGCTTTTCTTACAAGGTTCCGTTGCTATACTTTCAAGGTCATCAG 7 0.17500000000000002 No Hit GAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAA 6 0.15 No Hit GTTCGACACATGGGAGCTCTAAGTCCTCTCATCCGGTTAACTCCTATACA 6 0.15 No Hit CTTTGAAATGGACTTGAAACTTTCATTTTTCTGAAAGCATTGGCCATTTT 6 0.15 No Hit GTCTGAACTTACTTTTGACCTCAGACCTGAAATCAGAAAAAGTTCACTGC 6 0.15 No Hit CAAGGAGAGGCTGGATGACTACTACAAGAGGAATTACCAGGATTATTTCG 6 0.15 No Hit GGAGTACCCGGACGCCTACGTCCGCATCATCGGCTTCGACAACACCCGGC 6 0.15 No Hit GGGCGACATCCCCACCTACGTCGTGGGCGTCAATGCCGAGCTCTACTCCC 5 0.125 No Hit ATCCAGTACCAATTTGACTCGGAGTCAGACCAAGAAACAGAACACACAAG 5 0.125 No Hit GTATGATGGCGCCATGCAATCAGCTATCCAAAAGGTTCTTCCTCAAACTA 5 0.125 No Hit GGTCTGTCAACCTGATGGTCTGGCACTGCACCATCCCCGGAAAGCAGGGG 5 0.125 No Hit AGCAGATCGCCGAGTTCAAGGAGGCCTTCAGCCTCTTCGACAAGGATGGC 5 0.125 No Hit CTGACATCATGTGGCTTTGGAGTATATGCAATGGATTGGATAGGCCATGG 5 0.125 No Hit GGTTGCCAAATTTCTGGACCCGAGGCATTCTGCTCCGGGAGACAGCATTG 5 0.125 No Hit CGGCGAAGCGTGCGAAGAAGAAAGAGGAGGAGGAGGAGGAGAAGGCGCGT 5 0.125 No Hit AACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCCTCCAGG 5 0.125 No Hit GCTAGGTGTTGGAGATGCTATCACCAACGGAGATCTATATGCTACCGTAT 5 0.125 No Hit GTCATATATCATGTACACCAGTTTCTTCTGGCAACCCTGTTAGGCTATTA 5 0.125 No Hit CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 5 0.125 No Hit GGGCTGGCCGGCGCCGGCGGCGGCATCATCGCCCAGATCATCACCTACCC 5 0.125 No Hit GCTGCAAGCTCGACATGTTTGACCATATCAAAGATCAGAGATGAGGAGCT 5 0.125 No Hit CAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATA 5 0.125 No Hit GTTGTACAATTGCTCTGAATCTGTTATTTTCAGATGGGGCTAATGATGAA 5 0.125 No Hit GTTCTATCTAGAAGCGACTCCCGCACATTCTGTCTGGGTGTCAGAATTGC 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 0.025 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.1125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.21250000000000002 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.3 0.0 0.0 0.0 0.0 78-79 0.38749999999999996 0.0 0.0 0.0 0.0 80-81 0.5125 0.0 0.0 0.0 0.0 82-83 0.7 0.0 0.0 0.0 0.0 84-85 0.975 0.0 0.0 0.0 0.0 86-87 1.075 0.0 0.0 0.0 0.0 88-89 1.1875 0.0 0.0 0.0 0.0 90-91 1.375 0.0 0.0 0.0 0.0 92-93 1.725 0.0 0.0 0.0 0.0 94-95 2.175 0.0 0.0 0.0 0.0 96-97 2.5875 0.0 0.0 0.0 0.0 98-99 3.1125 0.0 0.0 0.0 0.0 100-101 3.7249999999999996 0.0 0.0 0.0 0.0 102-103 4.275 0.0 0.0 0.0 0.0 104-105 4.8375 0.0 0.0 0.0 0.0 106-107 5.3375 0.0 0.0 0.0 0.0 108-109 5.6875 0.0 0.0 0.0 0.0 110-111 6.325 0.0 0.0 0.0 0.0 112-113 6.9875 0.0 0.0 0.0 0.0 114-115 7.625 0.0 0.0 0.0 0.0 116-117 8.25 0.0 0.0 0.0 0.0 118-119 8.787500000000001 0.0 0.0 0.0 0.0 120-121 9.3125 0.0 0.0 0.0 0.0 122-123 10.1375 0.0 0.0 0.0 0.0 124-125 10.725 0.0 0.0 0.0 0.0 126-127 11.3625 0.0 0.0 0.0 0.0 128-129 11.9875 0.0 0.0 0.0 0.0 130-131 12.8125 0.0 0.0 0.0 0.0 132-133 13.525 0.0 0.0 0.0 0.0 134-135 14.412500000000001 0.0 0.0 0.0 0.0 136-137 15.175 0.0 0.0 0.0 0.0 138-139 15.787500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGGGCT 10 0.006830828 145.0 8 >>END_MODULE Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra Read 1353812 spots for SRR13165358.sra Written 1353812 spots for SRR13165358.sra Read 1353801 spots for SRR13165358.sra Written 1353801 spots for SRR13165358.sra SRR ids: ['SRR13165358.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_swdgypt7 SRR13165358.sra spots: 27076031 blocks: [[1, 1353801], [1353802, 2707602], [2707603, 4061403], [4061404, 5415204], [5415205, 6769005], [6769006, 8122806], [8122807, 9476607], [9476608, 10830408], [10830409, 12184209], [12184210, 13538010], [13538011, 14891811], [14891812, 16245612], [16245613, 17599413], [17599414, 18953214], [18953215, 20307015], [20307016, 21660816], [21660817, 23014617], [23014618, 24368418], [24368419, 25722219], [25722220, 27076031]] SRR13165358 file size 9179919 SRR13165358 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 SRR13165358 SRR13165358_1.fastq SRR13165358_2.fastq Input file: SRR13165358_1.fastq Paired file: SRR13165358_2.fastq trimmed: SRR13165358-trimmed-pair1.fastq, SRR13165358-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 16:03:01 2024 >> started Sat Dec 7 16:03:29 2024 >> done (27.958s) 27076031 read pairs processed; of these: 717 ( 0.00%) short read pairs filtered out after trimming by size control 37941 ( 0.14%) empty read pairs filtered out after trimming by size control 27037373 (99.86%) read pairs available; of these: 5308565 (19.63%) trimmed read pairs available after processing 21728808 (80.37%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 44 0.00% 19 43 0.00% 20 51 0.00% 21 73 0.00% 22 78 0.00% 23 94 0.00% 24 94 0.00% 25 109 0.00% 26 168 0.00% 27 181 0.00% 28 128 0.00% 29 187 0.00% 30 234 0.00% 31 192 0.00% 32 180 0.00% 33 213 0.00% 34 235 0.00% 35 249 0.00% 36 237 0.00% 37 269 0.00% 38 250 0.00% 39 255 0.00% 40 363 0.00% 41 353 0.00% 42 329 0.00% 43 361 0.00% 44 355 0.00% 45 393 0.00% 46 460 0.00% 47 437 0.00% 48 532 0.00% 49 655 0.00% 50 679 0.00% 51 820 0.00% 52 805 0.00% 53 947 0.00% 54 944 0.00% 55 1088 0.00% 56 1186 0.00% 57 1316 0.00% 58 1439 0.01% 59 1759 0.01% 60 1889 0.01% 61 2125 0.01% 62 2577 0.01% 63 2747 0.01% 64 2938 0.01% 65 3095 0.01% 66 3555 0.01% 67 3874 0.01% 68 4427 0.02% 69 4832 0.02% 70 5580 0.02% 71 6158 0.02% 72 7270 0.03% 73 8226 0.03% 74 8796 0.03% 75 9838 0.04% 76 10289 0.04% 77 11633 0.04% 78 12642 0.05% 79 13916 0.05% 80 15065 0.06% 81 16583 0.06% 82 18363 0.07% 83 20565 0.08% 84 23058 0.09% 85 24183 0.09% 86 26365 0.10% 87 26747 0.10% 88 28798 0.11% 89 30658 0.11% 90 32486 0.12% 91 35172 0.13% 92 37396 0.14% 93 40108 0.15% 94 42737 0.16% 95 44821 0.17% 96 47076 0.17% 97 48537 0.18% 98 49239 0.18% 99 51529 0.19% 100 53815 0.20% 101 55738 0.21% 102 57967 0.21% 103 59440 0.22% 104 62055 0.23% 105 63519 0.23% 106 65477 0.24% 107 66815 0.25% 108 68262 0.25% 109 69435 0.26% 110 69872 0.26% 111 71943 0.27% 112 74705 0.28% 113 74891 0.28% 114 79587 0.29% 115 79807 0.30% 116 81846 0.30% 117 81231 0.30% 118 83384 0.31% 119 84082 0.31% 120 85803 0.32% 121 86270 0.32% 122 87010 0.32% 123 89190 0.33% 124 91843 0.34% 125 92479 0.34% 126 93290 0.35% 127 94470 0.35% 128 94152 0.35% 129 95775 0.35% 130 95943 0.35% 131 96609 0.36% 132 97835 0.36% 133 99166 0.37% 134 99486 0.37% 135 100861 0.37% 136 101415 0.38% 137 100726 0.37% 138 101537 0.38% 139 103393 0.38% 140 103727 0.38% 141 103273 0.38% 142 105886 0.39% 143 105650 0.39% 144 106334 0.39% 145 109283 0.40% 146 110789 0.41% 147 114551 0.42% 148 111030 0.41% 149 112618 0.42% 150 109622 0.41% 151 21728808 80.37% 27037373 reads passed initial QC criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=2.25 fanout-score-rank=32 prefix-density=0.81 prefix-fanout=2.2 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCTTCGGTCGAGTGCTCGAACTTGCTTAGGAAGAAGATTAAGCTGAAGGCTTCTAGGCTTGTGTGTGCTTCTT criterion=fanout-score sequence-density=0.07 sequence-density-rank=31 fanout-score=28.60 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=7.5 sequence=TTTCTTCTCCGGCGCCATGCCGAGAACCACCACCTGGGCCTGGGTGCTGCTGGTGGTGCTGGCCTGCTCTGCCAGGTCTGGGTACATCTTCCCGCAAGTGCAGTTTGAGCCACAGTTGCAGCTTGATCCACAGCTGCAAGACATCT criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=3.45 fanout-score-rank=26 prefix-density=0.40 prefix-fanout=2.8 sequence=GCACCAGCTGCACCTGC criterion=fanout-score sequence-density=0.10 sequence-density-rank=19 fanout-score=126.24 fanout-score-rank=1 prefix-density=0.72 prefix-fanout=18.0 sequence=GCCGCCGCCGCCA SRR13165358 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 16:04:17 Started mapping on | Dec 07 16:04:17 Finished on | Dec 07 16:06:43 Mapping speed, Million of reads per hour | 666.67 Number of input reads | 27037373 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 25407933 Uniquely mapped reads % | 93.97% Average mapped length | 289.36 Number of splices: Total | 25853598 Number of splices: Annotated (sjdb) | 24241559 Number of splices: GT/AG | 25489683 Number of splices: GC/AG | 309926 Number of splices: AT/AC | 12600 Number of splices: Non-canonical | 41389 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.63 Insertion rate per base | 0.01% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 457349 % of reads mapped to multiple loci | 1.69% Number of reads mapped to too many loci | 73853 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.87% % of reads unmapped: other | 1.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1172415 1172415 1172415 N_multimapping 457349 457349 457349 N_noFeature 1052712 24690846 1288923 N_ambiguous 577987 4227 97901 UnstrandedReadsAssigned:23777234 PositiveStrandReadsAssigned:712860 NegativeStrandReadsAssigned:24021109 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13165358 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: SRR13165358-trimmed-pair1.fastq SRR13165358-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,037,373 reads, 24,353,093 reads pseudoaligned [quant] estimated average fragment length: 240.648 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,217 rounds 52973 SRR13165358.ke.tsv 35125 SRR13165358.se.tsv 88098 total ==> SRR13165358.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 696.757 0 0 PNS24247 1044 804.352 69.7382 5.15016 PNS24249 1928 1688.35 137.881 4.85108 PNS24246 1044 804.352 69.7382 5.15016 PNS24248 1044 804.352 69.7382 5.15016 PNS24244 1471 1231.35 126.904 6.12194 PNS24243 293 110.728 0 0 KQK14069 1603 1363.35 727.893 31.7143 KQK14071 474 253.44 21.1591 4.95926 ==> SRR13165358.se.tsv <== BRADI_1g14170v3 798 BRADI_1g53295v3 148 BRADI_1g59795v3 597 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 507 BRADI_1g74790v3 708 BRADI_1g09890v3 0 BRADI_1g77505v3 397 BRADI_1g48960v3 0 SRR13165358 completed mapping pipeline successfully