Starting /dee2/code/volunteer_pipeline.sh SRR13695453 current disk space = 3049165623296 free memory = 1580678580 SRR13695453 SRAfilesize 51de741073236e27cb84c829e4639f2f SRR13695453.sra SRR13695453.sra file validated SRR13695453 is paired end SRR13695453 is conventional basespace SRR13695453 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695453_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 36.582 37.0 37.0 37.0 37.0 37.0 2 36.248 37.0 37.0 37.0 37.0 37.0 3 36.5255 37.0 37.0 37.0 37.0 37.0 4 36.565 37.0 37.0 37.0 37.0 37.0 5 36.585 37.0 37.0 37.0 37.0 37.0 6 36.63 37.0 37.0 37.0 37.0 37.0 7 36.453 37.0 37.0 37.0 37.0 37.0 8 36.5195 37.0 37.0 37.0 37.0 37.0 9 36.616 37.0 37.0 37.0 37.0 37.0 10-14 36.5464 37.0 37.0 37.0 37.0 37.0 15-19 36.5345 37.0 37.0 37.0 37.0 37.0 20-24 36.511500000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.4668 37.0 37.0 37.0 37.0 37.0 30-34 36.400600000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.3966 37.0 37.0 37.0 37.0 37.0 40-44 36.4448 37.0 37.0 37.0 37.0 37.0 45-49 36.3558 37.0 37.0 37.0 37.0 37.0 50-54 36.341899999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.3156 37.0 37.0 37.0 37.0 37.0 60-64 36.347699999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.2906 37.0 37.0 37.0 37.0 37.0 70-74 36.301500000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.251400000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.1631 37.0 37.0 37.0 37.0 37.0 85-89 36.2214 37.0 37.0 37.0 37.0 37.0 90-94 36.1178 37.0 37.0 37.0 37.0 37.0 95-99 36.0976 37.0 37.0 37.0 37.0 37.0 100-104 36.0952 37.0 37.0 37.0 37.0 37.0 105-109 36.039899999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.0179 37.0 37.0 37.0 37.0 37.0 115-119 36.0675 37.0 37.0 37.0 37.0 37.0 120-124 35.9695 37.0 37.0 37.0 37.0 37.0 125-129 35.901500000000006 37.0 37.0 37.0 37.0 37.0 130-134 35.8586 37.0 37.0 37.0 37.0 37.0 135-139 35.7634 37.0 37.0 37.0 37.0 37.0 140-144 35.688100000000006 37.0 37.0 37.0 37.0 37.0 145-149 35.595600000000005 37.0 37.0 37.0 37.0 37.0 150-151 35.3315 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 3.0 26 7.0 27 11.0 28 8.0 29 19.0 30 29.0 31 44.0 32 59.0 33 86.0 34 136.0 35 336.0 36 2911.0 37 350.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.275 11.600000000000001 7.675 39.45 2 20.211161387631975 13.22272498743087 35.570638511814984 30.995475113122172 3 18.875 17.75 28.4 34.975 4 24.2 23.799999999999997 23.474999999999998 28.525 5 24.575 30.9 23.9 20.625 6 21.45 34.775 22.975 20.8 7 15.0 26.424999999999997 41.375 17.2 8 17.575 26.525 31.55 24.349999999999998 9 16.475 24.175 33.825 25.525 10-14 20.54 29.28 27.750000000000004 22.43 15-19 20.119999999999997 27.925 28.22 23.735 20-24 20.150000000000002 28.244999999999997 27.655 23.95 25-29 19.8 28.12 27.639999999999997 24.44 30-34 19.919999999999998 28.38 27.74 23.96 35-39 19.43 28.615000000000002 28.444999999999997 23.51 40-44 19.215 28.915000000000003 27.875 23.995 45-49 19.405 28.349999999999998 28.345 23.9 50-54 19.675 28.970000000000002 27.744999999999997 23.61 55-59 19.855 28.610000000000003 27.96 23.575 60-64 20.255000000000003 28.185 27.83 23.73 65-69 19.564999999999998 28.349999999999998 28.249999999999996 23.835 70-74 20.04 28.335 28.384999999999998 23.24 75-79 20.265 28.625 27.634999999999998 23.474999999999998 80-84 20.57 29.154999999999998 26.805 23.47 85-89 20.995 28.544999999999998 27.339999999999996 23.119999999999997 90-94 19.785 28.28 28.155 23.78 95-99 19.67 28.449999999999996 28.04 23.84 100-104 19.61 28.1 28.299999999999997 23.990000000000002 105-109 20.665 27.794999999999998 28.515 23.025000000000002 110-114 20.080000000000002 28.21 28.51 23.200000000000003 115-119 20.48 28.48 28.110000000000003 22.93 120-124 19.82 28.185 28.215 23.78 125-129 19.42 27.61 28.67 24.3 130-134 20.635 27.955000000000002 27.255000000000003 24.154999999999998 135-139 21.33 28.13 26.779999999999998 23.76 140-144 21.0 28.345 27.045 23.61 145-149 21.3 28.035 27.150000000000002 23.515 150-151 21.1125 28.499999999999996 25.3 25.087500000000002 >>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 0.0 15 0.5 16 0.5 17 0.0 18 1.0 19 1.0 20 1.0 21 1.5 22 1.0 23 3.5 24 4.0 25 3.0 26 4.5 27 3.5 28 8.0 29 16.0 30 21.5 31 29.0 32 31.5 33 31.0 34 48.5 35 87.0 36 102.5 37 112.5 38 133.5 39 145.5 40 176.5 41 211.0 42 231.5 43 248.5 44 270.0 45 277.0 46 276.0 47 263.0 48 239.0 49 221.0 50 182.5 51 143.5 52 107.5 53 71.5 54 50.5 55 44.0 56 45.0 57 39.5 58 31.5 59 25.5 60 19.0 61 11.0 62 6.5 63 5.0 64 2.0 65 2.5 66 2.0 67 1.0 68 1.0 69 0.0 70 0.0 71 0.0 72 2.0 73 2.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.5499999999999999 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 69.825 #Duplication Level Percentage of deduplicated Percentage of total 1 71.24955245255997 49.75 2 19.011815252416756 26.55 3 6.337271750805586 13.275 4 2.4704618689581093 6.9 5 0.644468313641246 2.25 6 0.21482277121374865 0.8999999999999999 7 0.03580379520229145 0.17500000000000002 8 0.03580379520229145 0.2 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 GTGAGATTCTTGCAATGCAATCGGTCTGCCAAACATTAGCCCAAATTTCA 8 0.2 No Hit ACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACAT 7 0.17500000000000002 No Hit GCAAGAGTTGCATTGCGGGTATTCCTAGTTTATTGCCATTTTAACATGTC 6 0.15 No Hit CTTCGAAAGAACAGTTTTCTGCCACCACAGAATCCTGGTGACAATTTTAT 6 0.15 No Hit CTTTAGAATCACGGCCGTTCTTGGTACTCCCAGCTCCCTTCTTGTGAGCC 6 0.15 No Hit GCCTTCGACAACCTGTCACATCCAACAACCTTAGCTCCTTGAGCTCTCCT 6 0.15 No Hit CTGATAACATGCTGCATTCCACCAGCTCCAAATGAATGCCCACAAGGCAA 6 0.15 No Hit CAAAATTCTGCAAGTCTACATCTTCACCAAGATCTAGCTTGTCCAATTCT 6 0.15 No Hit GTGGGTAAACAACTGATGAGTAGAGAACACGATCAACCTATTCTTTATAA 5 0.125 No Hit ATAAGGCGTATCGGTCTTGATCTTCTTGACACCACTGGCTTCAATCTTGA 5 0.125 No Hit CCATGACATCAAGTAAACAAAGAAAAAAAAAACATTGCTGAAAAGAACTA 5 0.125 No Hit GCCGAGGTCCTAAAACACTTGTGTCAATAGTAGCCCCATAAGCTTCAGAG 5 0.125 No Hit CACCAGCCCAAGGTCCATAGCTATCAAATATTGTGTTGAGAATGGCAGTG 5 0.125 No Hit AGTCAAACAGGAGCACAAAGACAGGTTGACTTGAGGCCTTAAAGGATGAG 5 0.125 No Hit CATACCTTCTTGCTCAAAACATGGCAATGATTTTATCTTCACATTAAGTA 5 0.125 No Hit GCAAGAAGCATTACTTATAATGTTGGCAACCTCATGGTCGTAGTCCTTTT 5 0.125 No Hit CCTTTGTCATATTCAGTGACCCCATAGTTGTATGTCAACTCCAGCACAGC 5 0.125 No Hit GTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGT 5 0.125 No Hit GGCATTACTTTCACTGTTTATTCTGGGAGGCATTTGCCCTCAATATTTTT 5 0.125 No Hit GCAAAAGGAAAGAGAAAAACAAACGGTGGTTTATAATTCCTATTCATTAC 5 0.125 No Hit GCCTCATCAGAAGTTATGCCCAACTCCTGCCCAGGAATATTGGGACGCTG 5 0.125 No Hit GGCCTCCACAATGGTCGGATCTTGTCCTGACCACCTACATCCCAGACAGT 5 0.125 No Hit CCCATCTTGACTCTCTTGGATCGTTTGTGAATTAAATACTTTGTTATCAG 5 0.125 No Hit CATCAATATCAAAGGTACCTTCCGGTGGAGGTGCCAACATGTTAAATACA 5 0.125 No Hit ATCCAATACAAGCAAAAACTTCTTTCCAGTTAACTTCTGTCGGAGGCGTA 5 0.125 No Hit GTATTGTCACAGCTGCCACTCATCTCTGCAACGGAATCTCCTATGGAGTA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 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 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.2875 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.425 0.0 0.0 0.0 0.0 88-89 0.425 0.0 0.0 0.0 0.0 90-91 0.44999999999999996 0.0 0.0 0.0 0.0 92-93 0.5125 0.0 0.0 0.0 0.0 94-95 0.525 0.0 0.0 0.0 0.0 96-97 0.5625 0.0 0.0 0.0 0.0 98-99 0.65 0.0 0.0 0.0 0.0 100-101 0.6875 0.0 0.0 0.0 0.0 102-103 0.8125 0.0 0.0 0.0 0.0 104-105 0.975 0.0 0.0 0.0 0.0 106-107 1.05 0.0 0.0 0.0 0.0 108-109 1.2875 0.0 0.0 0.0 0.0 110-111 1.7125 0.0 0.0 0.0 0.0 112-113 1.9749999999999999 0.0 0.0 0.0 0.0 114-115 2.125 0.0 0.0 0.0 0.0 116-117 2.575 0.0 0.0 0.0 0.0 118-119 2.9 0.0 0.0 0.0 0.0 120-121 3.3 0.0 0.0 0.0 0.0 122-123 3.6624999999999996 0.0 0.0 0.0 0.0 124-125 4.0375 0.0 0.0 0.0 0.0 126-127 4.475 0.0 0.0 0.0 0.0 128-129 4.8 0.0 0.0 0.0 0.0 130-131 5.1625 0.0 0.0 0.0 0.0 132-133 5.65 0.0 0.0 0.0 0.0 134-135 6.074999999999999 0.0 0.0 0.0 0.0 136-137 6.4625 0.0 0.0 0.0 0.0 138-139 6.949999999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAATCGA 10 0.006830828 145.0 4 >>END_MODULE SRR13695453 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695453_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.05725 37.0 37.0 37.0 37.0 37.0 2 36.134 37.0 37.0 37.0 37.0 37.0 3 36.0125 37.0 37.0 37.0 37.0 37.0 4 36.232 37.0 37.0 37.0 37.0 37.0 5 36.2395 37.0 37.0 37.0 37.0 37.0 6 36.17 37.0 37.0 37.0 37.0 37.0 7 36.1695 37.0 37.0 37.0 37.0 37.0 8 36.2995 37.0 37.0 37.0 37.0 37.0 9 36.177 37.0 37.0 37.0 37.0 37.0 10-14 36.2414 37.0 37.0 37.0 37.0 37.0 15-19 36.140699999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.1279 37.0 37.0 37.0 37.0 37.0 25-29 36.0257 37.0 37.0 37.0 37.0 37.0 30-34 36.016400000000004 37.0 37.0 37.0 37.0 37.0 35-39 35.9814 37.0 37.0 37.0 37.0 37.0 40-44 36.01369999999999 37.0 37.0 37.0 37.0 37.0 45-49 35.9948 37.0 37.0 37.0 37.0 37.0 50-54 35.91930000000001 37.0 37.0 37.0 37.0 37.0 55-59 35.9305 37.0 37.0 37.0 37.0 37.0 60-64 35.91799999999999 37.0 37.0 37.0 37.0 37.0 65-69 35.8633 37.0 37.0 37.0 37.0 37.0 70-74 35.864999999999995 37.0 37.0 37.0 37.0 37.0 75-79 35.8408 37.0 37.0 37.0 37.0 37.0 80-84 35.8323 37.0 37.0 37.0 37.0 37.0 85-89 35.723699999999994 37.0 37.0 37.0 37.0 37.0 90-94 35.6605 37.0 37.0 37.0 37.0 37.0 95-99 35.7076 37.0 37.0 37.0 37.0 37.0 100-104 35.6682 37.0 37.0 37.0 37.0 37.0 105-109 35.6972 37.0 37.0 37.0 37.0 37.0 110-114 35.6043 37.0 37.0 37.0 37.0 37.0 115-119 35.5563 37.0 37.0 37.0 37.0 37.0 120-124 35.51559999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.5886 37.0 37.0 37.0 37.0 37.0 130-134 35.3626 37.0 37.0 37.0 34.6 37.0 135-139 35.4968 37.0 37.0 37.0 37.0 37.0 140-144 35.3043 37.0 37.0 37.0 34.6 37.0 145-149 35.3597 37.0 37.0 37.0 34.6 37.0 150-151 35.0965 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 4.0 14 7.0 15 2.0 16 3.0 17 3.0 18 0.0 19 2.0 20 2.0 21 3.0 22 1.0 23 5.0 24 9.0 25 7.0 26 9.0 27 13.0 28 11.0 29 22.0 30 22.0 31 40.0 32 61.0 33 110.0 34 223.0 35 563.0 36 2651.0 37 225.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.80762478053674 21.8209179834462 12.064208678204164 25.30724855781289 2 27.525 24.8 32.95 14.725 3 20.724999999999998 27.700000000000003 31.374999999999996 20.200000000000003 4 24.3 33.475 23.95 18.275 5 24.975 36.3 23.375 15.35 6 20.075000000000003 40.525 21.725 17.675 7 19.950000000000003 22.85 37.974999999999994 19.225 8 21.375 26.6 28.025 24.0 9 21.5 24.95 31.4 22.15 10-14 23.34 30.159999999999997 26.68 19.82 15-19 23.005 28.92 27.47 20.605 20-24 23.150000000000002 28.63 27.985 20.235 25-29 22.895 28.575 28.345 20.185 30-34 22.869999999999997 28.37 28.355000000000004 20.405 35-39 22.615 28.985 28.21 20.19 40-44 22.27 28.854999999999997 28.804999999999996 20.07 45-49 23.185 27.875 28.744999999999997 20.195 50-54 22.605 28.415000000000003 28.07 20.91 55-59 23.544999999999998 27.92 27.97 20.565 60-64 23.13 27.92 28.999999999999996 19.950000000000003 65-69 23.380000000000003 27.73 27.685 21.205 70-74 23.255 28.125 27.279999999999998 21.34 75-79 22.355 27.765 28.555000000000003 21.325 80-84 23.599999999999998 28.65 27.389999999999997 20.36 85-89 23.11 28.51 27.615000000000002 20.765 90-94 22.485 28.715000000000003 28.03 20.77 95-99 22.955000000000002 27.675 28.7 20.669999999999998 100-104 23.325000000000003 28.02 27.500000000000004 21.154999999999998 105-109 23.765 28.105000000000004 28.08 20.05 110-114 23.73 28.875 26.979999999999997 20.415 115-119 23.215 28.939999999999998 27.634999999999998 20.21 120-124 24.240000000000002 28.294999999999998 27.425 20.04 125-129 24.18 28.01 27.33 20.48 130-134 24.55 28.16 27.0 20.29 135-139 24.75 28.7 26.965 19.585 140-144 24.995 28.775000000000002 26.775 19.455 145-149 25.485000000000003 28.845 26.085 19.585 150-151 25.0 29.575000000000003 26.674999999999997 18.75 >>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 1.0 11 1.5 12 0.5 13 0.5 14 0.5 15 0.5 16 1.0 17 0.5 18 1.5 19 1.5 20 1.0 21 2.5 22 2.5 23 8.0 24 8.0 25 5.0 26 6.0 27 8.0 28 15.5 29 21.5 30 29.0 31 26.5 32 25.0 33 40.0 34 61.0 35 80.5 36 100.5 37 135.0 38 155.0 39 168.5 40 211.5 41 240.5 42 248.5 43 253.5 44 261.0 45 279.5 46 264.0 47 223.0 48 179.5 49 154.0 50 146.5 51 127.0 52 104.5 53 82.0 54 71.5 55 60.0 56 41.5 57 30.5 58 22.0 59 17.0 60 18.0 61 15.5 62 10.0 63 6.0 64 2.5 65 0.5 66 1.5 67 2.5 68 1.5 69 1.0 70 1.5 71 4.0 72 3.0 73 0.0 74 0.5 75 1.0 76 0.5 77 0.5 78 0.5 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.5 87 1.0 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 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 0.325 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 0.0 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 70.92500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 72.78815650334862 51.625 2 18.364469510045822 26.05 3 5.569263306309482 11.85 4 2.1854071201973917 6.2 5 0.7402185407120198 2.625 6 0.21149101163200562 0.8999999999999999 7 0.07049700387733521 0.35000000000000003 8 0.07049700387733521 0.4 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 TAAAAACAAACCCTATAAAGCACTCAAAAAAAAATTATAAATCAGTTTTT 8 0.2 No Hit GTTTAACCTATTTTGAGCAAAGGCTGTTCCAAGTAACTTGGTTGACGAAA 8 0.2 No Hit GAAGGACGTTTCAGCATTTTCGAGTGAGTCTGGAGATTCTTTAAGGGCTA 7 0.17500000000000002 No Hit GTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGC 7 0.17500000000000002 No Hit GTTTGAATGTTCCTCAGAGGTTTTTTGAAGGGATGAAAGAAATTGAGGTT 6 0.15 No Hit GGAGATTGTGAAAAAAGAAAGGCAGAAGCAAGTTCAGTAATGGCAGCCTC 6 0.15 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 6 0.15 No Hit GTCTCTTTTAGAACACTTGTTATATCTGATGCCTGGTATCTTCACAGGAT 6 0.15 No Hit AGTCAAGGCAGATGTTTACAGTTACGGAGTAATGCTCTTGGAAATTGTTT 6 0.15 No Hit TATGCTTCTCAAGGTGAAGAGAGGAAGCGCTGAAGAGAAGCTCAAGGTAG 6 0.15 No Hit GTTCAACCTTACCATCCTCACCTGAAGAATTTCTGGTATCCTGTTGCTTT 5 0.125 No Hit CAACAATTCAGTTTGAGGATCTGGGTGTGTGTATCTACTGATTTCAATCT 5 0.125 No Hit GTGTAACGTCAGTTCTTCTATGTCTCTCAACACTGAAAACATGGCTAACA 5 0.125 No Hit GGCCAGTTCCTGGAACACTTATGATTGAACCCACTGAGAGTGAAAGCAAG 5 0.125 No Hit GGAAGGAGAATCTGCCCAGGAATGACCTTTGGTTTGGCTAATGTCGAGTT 5 0.125 No Hit GCAAACCACACGAATGAAGCCTCATCAGTACAGGACAGAAATAATAATAA 5 0.125 No Hit GTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGTCCCTTC 5 0.125 No Hit CATCTATTCAAGAAAGAAACACCAACAATGAGTTTCAGGTTCTTTCTGCC 5 0.125 No Hit ATTACATATGACATGCTGATTGAGGCTCTTGCAAAGAGTGGCAAACCGAG 5 0.125 No Hit CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATC 5 0.125 No Hit AAAAAGTCAGATGAAATAGTCAGGCTAAATGGAATTTACAAGAGGTTACT 5 0.125 No Hit TGGATGTGAAAGGTTACTCTTGTGGAGGGGGGAACTATGAAATGCTCGGG 5 0.125 No Hit GTTGTTCTTAGCTCCATCTGTGGCTCGCTAATAGGTTTTATTGTTGCATC 5 0.125 No Hit GGGGAAGGAGATCTGAATCAAATTCATTTAAGAAGTTAGTTATTCCCAGT 5 0.125 No Hit GGAGTTTTTGTGGATGGCCCTGGTGCTGGGAAACATATTCAAGCTGGTGC 5 0.125 No Hit GCCGTCTGTTTGCCAAGAAAGAAATGCGAATTCTCATGGTGGGTCTTGAC 5 0.125 No Hit GGCCAAGGGTGGCAAAGTGACCAGAGAACCTGGTCCTGTTAAAGGTGGCA 5 0.125 No Hit ATCACCATATTAATAGAGAACATGCGACGAGAAGGATACGAATTCATGGT 5 0.125 No Hit GGGTGCGAGAGAGACTCTGAGATTGCTCATCAGTAGTACAAGCCAAACCA 5 0.125 No Hit GTTGGAGGAATTTTTGGTGCTTGTTGTTGTTGTGCAGTGCTCCATGGAAT 5 0.125 No Hit GAAAGATAAATGCTGCGGAATATTCGTGTCCATTTTGGTTTTCCCCTGGG 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 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 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.2875 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.425 0.0 0.0 0.0 0.0 88-89 0.425 0.0 0.0 0.0 0.0 90-91 0.44999999999999996 0.0 0.0 0.0 0.0 92-93 0.5125 0.0 0.0 0.0 0.0 94-95 0.525 0.0 0.0 0.0 0.0 96-97 0.5625 0.0 0.0 0.0 0.0 98-99 0.65 0.0 0.0 0.0 0.0 100-101 0.7124999999999999 0.0 0.0 0.0 0.0 102-103 0.8375 0.0 0.0 0.0 0.0 104-105 1.0 0.0 0.0 0.0 0.0 106-107 1.075 0.0 0.0 0.0 0.0 108-109 1.2999999999999998 0.0 0.0 0.0 0.0 110-111 1.7125 0.0 0.0 0.0 0.0 112-113 1.9749999999999999 0.0 0.0 0.0 0.0 114-115 2.125 0.0 0.0 0.0 0.0 116-117 2.55 0.0 0.0 0.0 0.0 118-119 2.85 0.0 0.0 0.0 0.0 120-121 3.25 0.0 0.0 0.0 0.0 122-123 3.6125 0.0 0.0 0.0 0.0 124-125 4.0 0.0 0.0 0.0 0.0 126-127 4.4 0.0 0.0 0.0 0.0 128-129 4.7 0.0 0.0 0.0 0.0 130-131 5.0875 0.0 0.0 0.0 0.0 132-133 5.574999999999999 0.0 0.0 0.0 0.0 134-135 6.0 0.0 0.0 0.0 0.0 136-137 6.362500000000001 0.0 0.0 0.0 0.0 138-139 6.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAATGT 10 0.006830828 145.0 9 GATGCAG 10 0.006830828 145.0 7 >>END_MODULE Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041347 spots for SRR13695453.sra Written 1041347 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra Read 1041329 spots for SRR13695453.sra Written 1041329 spots for SRR13695453.sra SRR ids: ['SRR13695453.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_thlb2_aq SRR13695453.sra spots: 20826598 blocks: [[1, 1041329], [1041330, 2082658], [2082659, 3123987], [3123988, 4165316], [4165317, 5206645], [5206646, 6247974], [6247975, 7289303], [7289304, 8330632], [8330633, 9371961], [9371962, 10413290], [10413291, 11454619], [11454620, 12495948], [12495949, 13537277], [13537278, 14578606], [14578607, 15619935], [15619936, 16661264], [16661265, 17702593], [17702594, 18743922], [18743923, 19785251], [19785252, 20826598]] SRR13695453 file size 7056088 SRR13695453 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 SRR13695453 SRR13695453_1.fastq SRR13695453_2.fastq Input file: SRR13695453_1.fastq Paired file: SRR13695453_2.fastq trimmed: SRR13695453-trimmed-pair1.fastq, SRR13695453-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 04:49:15 2025 >> started Wed Feb 12 04:49:38 2025 >> done (22.354s) 20826598 read pairs processed; of these: 133 ( 0.00%) short read pairs filtered out after trimming by size control 2721 ( 0.01%) empty read pairs filtered out after trimming by size control 20823744 (99.99%) read pairs available; of these: 2152408 (10.34%) trimmed read pairs available after processing 18671336 (89.66%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 3 0.00% 20 4 0.00% 21 3 0.00% 22 4 0.00% 23 6 0.00% 24 1 0.00% 25 2 0.00% 26 0 0.00% 27 6 0.00% 28 3 0.00% 29 2 0.00% 30 6 0.00% 31 2 0.00% 32 5 0.00% 33 6 0.00% 34 3 0.00% 35 4 0.00% 36 5 0.00% 37 11 0.00% 38 3 0.00% 39 3 0.00% 40 14 0.00% 41 16 0.00% 42 8 0.00% 43 18 0.00% 44 24 0.00% 45 25 0.00% 46 16 0.00% 47 21 0.00% 48 42 0.00% 49 42 0.00% 50 51 0.00% 51 48 0.00% 52 62 0.00% 53 59 0.00% 54 89 0.00% 55 81 0.00% 56 105 0.00% 57 116 0.00% 58 120 0.00% 59 161 0.00% 60 181 0.00% 61 225 0.00% 62 295 0.00% 63 285 0.00% 64 344 0.00% 65 384 0.00% 66 405 0.00% 67 519 0.00% 68 570 0.00% 69 686 0.00% 70 799 0.00% 71 924 0.00% 72 1121 0.01% 73 1303 0.01% 74 1545 0.01% 75 1691 0.01% 76 1773 0.01% 77 1971 0.01% 78 2340 0.01% 79 2520 0.01% 80 2820 0.01% 81 3239 0.02% 82 3649 0.02% 83 3969 0.02% 84 4665 0.02% 85 5085 0.02% 86 5670 0.03% 87 6089 0.03% 88 6497 0.03% 89 6825 0.03% 90 7492 0.04% 91 8247 0.04% 92 8734 0.04% 93 9665 0.05% 94 10452 0.05% 95 11225 0.05% 96 11691 0.06% 97 12530 0.06% 98 13400 0.06% 99 13622 0.07% 100 14680 0.07% 101 15248 0.07% 102 16203 0.08% 103 17200 0.08% 104 18089 0.09% 105 18912 0.09% 106 19611 0.09% 107 21159 0.10% 108 21414 0.10% 109 22374 0.11% 110 23123 0.11% 111 23726 0.11% 112 24726 0.12% 113 25827 0.12% 114 27141 0.13% 115 28029 0.13% 116 29120 0.14% 117 30222 0.15% 118 31455 0.15% 119 32252 0.15% 120 33191 0.16% 121 34368 0.17% 122 35154 0.17% 123 36146 0.17% 124 37326 0.18% 125 38160 0.18% 126 39954 0.19% 127 40870 0.20% 128 41570 0.20% 129 42594 0.20% 130 44091 0.21% 131 44878 0.22% 132 45939 0.22% 133 46837 0.22% 134 47457 0.23% 135 48575 0.23% 136 49926 0.24% 137 51300 0.25% 138 51877 0.25% 139 53577 0.26% 140 54042 0.26% 141 55435 0.27% 142 56151 0.27% 143 56286 0.27% 144 57834 0.28% 145 58389 0.28% 146 59932 0.29% 147 61921 0.30% 148 62892 0.30% 149 64098 0.31% 150 64476 0.31% 151 18671336 89.66% 20823744 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=25 prefix-density=0.35 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=404.39 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=18.9 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=1.10 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=32 prefix-density=1.09 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.13 sequence-density-rank=26 fanout-score=40.73 fanout-score-rank=1 prefix-density=0.39 prefix-fanout=13.1 sequence=AAAGAAAAGAAAA SRR13695453 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 04:50:19 Started mapping on | Feb 12 04:50:19 Finished on | Feb 12 04:52:33 Mapping speed, Million of reads per hour | 559.44 Number of input reads | 20823744 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 19451158 Uniquely mapped reads % | 93.41% Average mapped length | 295.62 Number of splices: Total | 18978805 Number of splices: Annotated (sjdb) | 18533289 Number of splices: GT/AG | 18585949 Number of splices: GC/AG | 299370 Number of splices: AT/AC | 12018 Number of splices: Non-canonical | 81468 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.78 Insertion rate per base | 0.03% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 508465 % of reads mapped to multiple loci | 2.44% Number of reads mapped to too many loci | 166877 % of reads mapped to too many loci | 0.80% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.15% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 864356 864356 864356 N_multimapping 508465 508465 508465 N_noFeature 901665 18928991 1221024 N_ambiguous 345650 2440 141010 UnstrandedReadsAssigned:18203843 PositiveStrandReadsAssigned:519727 NegativeStrandReadsAssigned:18089124 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13695453 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: SRR13695453-trimmed-pair1.fastq SRR13695453-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,823,744 reads, 18,140,379 reads pseudoaligned [quant] estimated average fragment length: 256.125 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,158 rounds 52401 SRR13695453.ke.tsv 34699 SRR13695453.se.tsv 87100 total ==> SRR13695453.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1762.88 969 27.0867 Potri.005G024800.1.v4.1 1035 779.875 487 30.7722 Potri.004G059700.1.v4.1 961 706.027 0 0 Potri.007G009000.2.v4.1 1416 1160.88 0 0 Potri.003G141000.2.v4.1 2943 2687.88 1284.56 23.5505 Potri.016G087400.1.v4.1 270 83.0517 1144 678.785 Potri.015G069301.1.v4.1 564 319.85 0 0 Potri.010G195200.1.v4.1 1773 1517.88 292.912 9.50946 Potri.012G127500.1.v4.1 977 721.961 132 9.00979 ==> SRR13695453.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 108 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 267 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 30 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 4 SRR13695453 completed mapping pipeline successfully