Starting /dee2/code/volunteer_pipeline.sh ERR3450069 current disk space = 1542999937024 free memory = 1602298312 ERR3450069 SRAfilesize 66e86ad27e5875bd755aa015b4e74410 ERR3450069.sra ERR3450069.sra file validated ERR3450069 is paired end ERR3450069 is conventional basespace ERR3450069 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450069_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.153 37.0 37.0 37.0 37.0 37.0 2 36.419 37.0 37.0 37.0 37.0 37.0 3 36.489 37.0 37.0 37.0 37.0 37.0 4 36.4485 37.0 37.0 37.0 37.0 37.0 5 36.5675 37.0 37.0 37.0 37.0 37.0 6 36.5555 37.0 37.0 37.0 37.0 37.0 7 36.545 37.0 37.0 37.0 37.0 37.0 8 36.5405 37.0 37.0 37.0 37.0 37.0 9 36.605 37.0 37.0 37.0 37.0 37.0 10-11 36.571 37.0 37.0 37.0 37.0 37.0 12-13 36.49325 37.0 37.0 37.0 37.0 37.0 14-15 36.583 37.0 37.0 37.0 37.0 37.0 16-17 36.597750000000005 37.0 37.0 37.0 37.0 37.0 18-19 36.55025 37.0 37.0 37.0 37.0 37.0 20-21 36.569 37.0 37.0 37.0 37.0 37.0 22-23 36.489000000000004 37.0 37.0 37.0 37.0 37.0 24-25 36.52775 37.0 37.0 37.0 37.0 37.0 26-27 36.423 37.0 37.0 37.0 37.0 37.0 28-29 36.5075 37.0 37.0 37.0 37.0 37.0 30-31 36.449250000000006 37.0 37.0 37.0 37.0 37.0 32-33 36.3485 37.0 37.0 37.0 37.0 37.0 34-35 36.331 37.0 37.0 37.0 37.0 37.0 36-37 36.3665 37.0 37.0 37.0 37.0 37.0 38-39 36.388000000000005 37.0 37.0 37.0 37.0 37.0 40-41 36.318 37.0 37.0 37.0 37.0 37.0 42-43 36.30275 37.0 37.0 37.0 37.0 37.0 44-45 36.279250000000005 37.0 37.0 37.0 37.0 37.0 46-47 36.176500000000004 37.0 37.0 37.0 37.0 37.0 48-49 36.15375 37.0 37.0 37.0 37.0 37.0 50-51 36.194 37.0 37.0 37.0 37.0 37.0 52-53 36.141 37.0 37.0 37.0 37.0 37.0 54-55 36.10925 37.0 37.0 37.0 37.0 37.0 56-57 36.04225 37.0 37.0 37.0 37.0 37.0 58-59 36.03225 37.0 37.0 37.0 37.0 37.0 60-61 35.98925 37.0 37.0 37.0 37.0 37.0 62-63 36.066500000000005 37.0 37.0 37.0 37.0 37.0 64-65 35.994 37.0 37.0 37.0 37.0 37.0 66-67 36.01175 37.0 37.0 37.0 37.0 37.0 68-69 36.0775 37.0 37.0 37.0 37.0 37.0 70-71 35.88775 37.0 37.0 37.0 37.0 37.0 72-73 35.79975 37.0 37.0 37.0 37.0 37.0 74-75 36.17975 37.0 37.0 37.0 37.0 37.0 76-77 36.1435 37.0 37.0 37.0 37.0 37.0 78-79 36.16075 37.0 37.0 37.0 37.0 37.0 80-81 36.11425 37.0 37.0 37.0 37.0 37.0 82-83 36.0775 37.0 37.0 37.0 37.0 37.0 84-85 36.041 37.0 37.0 37.0 37.0 37.0 86-87 35.987750000000005 37.0 37.0 37.0 37.0 37.0 88-89 35.976749999999996 37.0 37.0 37.0 37.0 37.0 90-91 36.0115 37.0 37.0 37.0 37.0 37.0 92-93 35.99875 37.0 37.0 37.0 37.0 37.0 94-95 35.89375 37.0 37.0 37.0 37.0 37.0 96-97 35.8845 37.0 37.0 37.0 37.0 37.0 98-99 35.93475 37.0 37.0 37.0 37.0 37.0 100-101 35.866749999999996 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 3.0 23 6.0 24 2.0 25 6.0 26 15.0 27 13.0 28 20.0 29 32.0 30 42.0 31 67.0 32 63.0 33 69.0 34 94.0 35 174.0 36 1704.0 37 1687.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.21084337349398 8.509036144578314 10.667670682730924 40.61244979919679 2 22.95 13.375 30.025000000000002 33.650000000000006 3 21.25 16.950000000000003 25.95 35.85 4 28.325 21.2 18.85 31.624999999999996 5 27.575 27.05 21.625 23.75 6 24.75 30.725 23.125 21.4 7 21.349999999999998 22.05 36.0 20.599999999999998 8 22.3 21.0 28.599999999999998 28.1 9 23.9 20.775 31.825 23.5 10-11 24.712500000000002 28.1375 21.712500000000002 25.4375 12-13 24.325 21.9 25.137500000000003 28.6375 14-15 23.8875 24.0125 25.2125 26.887499999999996 16-17 24.887500000000003 23.825 24.45 26.8375 18-19 24.8625 24.887500000000003 24.825 25.424999999999997 20-21 25.7125 23.7 24.637500000000003 25.95 22-23 24.7375 24.2625 23.575 27.425 24-25 25.275 24.099999999999998 23.4125 27.212500000000002 26-27 24.8125 23.3875 24.2 27.6 28-29 24.887500000000003 24.125 23.575 27.4125 30-31 24.375 23.7125 23.674999999999997 28.237499999999997 32-33 24.8125 23.200000000000003 24.349999999999998 27.6375 34-35 25.374999999999996 23.9125 23.974999999999998 26.737499999999997 36-37 25.687500000000004 23.200000000000003 23.724999999999998 27.3875 38-39 24.725 24.6625 23.7 26.9125 40-41 25.687500000000004 23.875 24.1875 26.25 42-43 25.0375 23.849999999999998 23.9125 27.200000000000003 44-45 24.425 22.5125 24.3125 28.749999999999996 46-47 25.137500000000003 23.825 23.8875 27.150000000000002 48-49 26.025 23.275000000000002 23.5625 27.1375 50-51 24.7875 23.2875 24.474999999999998 27.450000000000003 52-53 26.075 23.075000000000003 23.6625 27.187499999999996 54-55 25.775 22.662499999999998 23.5 28.0625 56-57 25.4 23.6125 24.2 26.787499999999998 58-59 25.95 23.925 22.575 27.55 60-61 25.5625 22.7625 24.7 26.974999999999998 62-63 25.587500000000002 23.1375 23.7375 27.537499999999998 64-65 25.6 23.0125 24.6875 26.700000000000003 66-67 24.75 24.8625 22.825 27.5625 68-69 25.1 24.0375 24.5 26.3625 70-71 25.45 23.9875 23.1125 27.450000000000003 72-73 26.700000000000003 24.25 22.7 26.35 74-75 26.85 23.799999999999997 22.7625 26.5875 76-77 26.775 23.4125 22.0625 27.750000000000004 78-79 25.75 24.425 22.575 27.250000000000004 80-81 26.450000000000003 23.425 22.15 27.975 82-83 27.800000000000004 23.9125 22.237499999999997 26.05 84-85 26.9125 23.3375 22.3625 27.3875 86-87 25.775 24.1125 23.3375 26.775 88-89 27.0125 24.725 23.025000000000002 25.2375 90-91 25.55 23.575 23.425 27.450000000000003 92-93 25.9875 23.8875 23.5625 26.5625 94-95 26.737499999999997 24.425 23.150000000000002 25.687500000000004 96-97 24.762500000000003 24.5125 22.787499999999998 27.9375 98-99 25.7375 23.7375 23.2375 27.287499999999998 100-101 26.187500000000004 23.7875 22.875 27.150000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 5.0 1 4.0 2 1.5 3 0.0 4 1.5 5 2.0 6 0.5 7 0.0 8 0.0 9 1.0 10 1.0 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 0.5 20 1.5 21 1.5 22 1.0 23 1.0 24 1.5 25 2.0 26 1.0 27 0.0 28 0.0 29 1.0 30 4.5 31 5.5 32 5.5 33 6.5 34 10.0 35 17.5 36 27.5 37 36.0 38 48.5 39 50.0 40 51.0 41 79.5 42 101.0 43 119.0 44 132.0 45 136.0 46 145.5 47 172.0 48 180.0 49 163.0 50 164.0 51 183.5 52 184.0 53 166.0 54 151.5 55 141.0 56 146.5 57 127.0 58 105.0 59 112.0 60 103.5 61 74.0 62 68.5 63 73.5 64 68.0 65 72.5 66 80.0 67 69.0 68 57.5 69 61.5 70 56.0 71 48.0 72 38.0 73 28.5 74 26.0 75 18.5 76 12.5 77 10.5 78 7.0 79 4.0 80 5.0 81 5.0 82 4.0 83 3.5 84 3.5 85 2.0 86 0.5 87 2.0 88 1.5 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 0.4 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.4 #Duplication Level Percentage of deduplicated Percentage of total 1 89.8741418764302 78.55 2 7.866132723112128 13.750000000000002 3 1.4016018306636155 3.675 4 0.3718535469107552 1.3 5 0.2574370709382151 1.125 6 0.08581235697940504 0.44999999999999996 7 0.028604118993135013 0.17500000000000002 8 0.057208237986270026 0.4 9 0.0 0.0 >10 0.057208237986270026 0.575 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGCTATGATCTCGTAT 13 0.325 TruSeq Adapter, Index 7 (97% over 36bp) CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 10 0.25 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGCTATGATCTCGTTT 8 0.2 TruSeq Adapter, Index 7 (97% over 36bp) GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 8 0.2 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7 0.17500000000000002 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 6 0.15 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 6 0.15 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 6 0.15 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 5 0.125 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 5 0.125 No Hit GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 5 0.125 No Hit GCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATT 5 0.125 No Hit TCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATAT 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 5 0.125 No Hit CCCCTATCCTACCATCGAAAGTTGATAGGGCAGAAATTTGAATGATGCGT 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 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.1125 0.0 0.0 0.0 0.0 32-33 0.21250000000000002 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.3 0.0 0.0 0.0 0.0 38-39 0.375 0.0 0.0 0.0 0.0 40-41 0.45 0.0 0.0 0.0 0.0 42-43 0.575 0.0 0.0 0.0 0.0 44-45 0.675 0.0 0.0 0.0 0.0 46-47 0.8125 0.0 0.0 0.0 0.0 48-49 0.8374999999999999 0.0 0.0 0.0 0.0 50-51 0.8875 0.0 0.0 0.0 0.0 52-53 1.075 0.0 0.0 0.0 0.0 54-55 1.275 0.0 0.0 0.0 0.0 56-57 1.4 0.0 0.0 0.0 0.0 58-59 1.675 0.0 0.0 0.0 0.0 60-61 1.8375 0.0 0.0 0.0 0.0 62-63 2.075 0.0 0.0 0.0 0.0 64-65 2.3125 0.0 0.0 0.0 0.0 66-67 2.5875 0.0 0.0 0.0 0.0 68-69 2.925 0.0 0.0 0.0 0.0 70-71 3.4124999999999996 0.0 0.0 0.0 0.0 72-73 3.75 0.0 0.0 0.0 0.0 74-75 4.1625 0.0 0.0 0.0 0.0 76-77 4.5625 0.0 0.0 0.0 0.0 78-79 5.175000000000001 0.0 0.0 0.0 0.0 80-81 5.949999999999999 0.0 0.0 0.0 0.0 82-83 6.525 0.0 0.0 0.0 0.0 84-85 7.25 0.0 0.0 0.0 0.0 86-87 7.7125 0.0 0.0 0.0 0.0 88-89 8.5125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450069 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450069_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1155 37.0 37.0 37.0 37.0 37.0 2 35.9665 37.0 37.0 37.0 37.0 37.0 3 36.1015 37.0 37.0 37.0 37.0 37.0 4 36.0845 37.0 37.0 37.0 37.0 37.0 5 36.2015 37.0 37.0 37.0 37.0 37.0 6 36.236 37.0 37.0 37.0 37.0 37.0 7 36.14 37.0 37.0 37.0 37.0 37.0 8 36.0645 37.0 37.0 37.0 37.0 37.0 9 36.192 37.0 37.0 37.0 37.0 37.0 10-11 36.0095 37.0 37.0 37.0 37.0 37.0 12-13 36.07875 37.0 37.0 37.0 37.0 37.0 14-15 36.1115 37.0 37.0 37.0 37.0 37.0 16-17 35.957 37.0 37.0 37.0 37.0 37.0 18-19 36.051500000000004 37.0 37.0 37.0 37.0 37.0 20-21 35.99575 37.0 37.0 37.0 37.0 37.0 22-23 36.01875 37.0 37.0 37.0 37.0 37.0 24-25 35.936 37.0 37.0 37.0 37.0 37.0 26-27 35.832499999999996 37.0 37.0 37.0 37.0 37.0 28-29 35.773250000000004 37.0 37.0 37.0 37.0 37.0 30-31 35.7385 37.0 37.0 37.0 37.0 37.0 32-33 35.718 37.0 37.0 37.0 37.0 37.0 34-35 35.69175 37.0 37.0 37.0 37.0 37.0 36-37 35.6285 37.0 37.0 37.0 37.0 37.0 38-39 35.5055 37.0 37.0 37.0 37.0 37.0 40-41 35.6015 37.0 37.0 37.0 37.0 37.0 42-43 35.59825 37.0 37.0 37.0 37.0 37.0 44-45 35.59075 37.0 37.0 37.0 37.0 37.0 46-47 35.692 37.0 37.0 37.0 37.0 37.0 48-49 35.61024999999999 37.0 37.0 37.0 37.0 37.0 50-51 35.69825 37.0 37.0 37.0 37.0 37.0 52-53 35.71025 37.0 37.0 37.0 37.0 37.0 54-55 35.679500000000004 37.0 37.0 37.0 37.0 37.0 56-57 35.6235 37.0 37.0 37.0 37.0 37.0 58-59 35.76275 37.0 37.0 37.0 37.0 37.0 60-61 35.77325 37.0 37.0 37.0 37.0 37.0 62-63 35.91 37.0 37.0 37.0 37.0 37.0 64-65 35.7965 37.0 37.0 37.0 37.0 37.0 66-67 35.7635 37.0 37.0 37.0 37.0 37.0 68-69 35.723 37.0 37.0 37.0 37.0 37.0 70-71 35.59425 37.0 37.0 37.0 37.0 37.0 72-73 35.45825 37.0 37.0 37.0 37.0 37.0 74-75 35.46625 37.0 37.0 37.0 37.0 37.0 76-77 35.4735 37.0 37.0 37.0 37.0 37.0 78-79 35.488 37.0 37.0 37.0 37.0 37.0 80-81 35.39875 37.0 37.0 37.0 37.0 37.0 82-83 35.4065 37.0 37.0 37.0 37.0 37.0 84-85 35.57 37.0 37.0 37.0 37.0 37.0 86-87 35.56325 37.0 37.0 37.0 37.0 37.0 88-89 35.539249999999996 37.0 37.0 37.0 37.0 37.0 90-91 35.477500000000006 37.0 37.0 37.0 37.0 37.0 92-93 35.53225 37.0 37.0 37.0 37.0 37.0 94-95 35.5165 37.0 37.0 37.0 37.0 37.0 96-97 35.48125 37.0 37.0 37.0 37.0 37.0 98-99 35.43 37.0 37.0 37.0 37.0 37.0 100-101 35.364000000000004 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 0.0 16 2.0 17 7.0 18 4.0 19 9.0 20 6.0 21 11.0 22 11.0 23 14.0 24 13.0 25 20.0 26 14.0 27 18.0 28 22.0 29 43.0 30 32.0 31 42.0 32 66.0 33 84.0 34 132.0 35 436.0 36 2282.0 37 731.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.9 16.825000000000003 11.899999999999999 30.375000000000004 2 26.75 21.25 26.625 25.374999999999996 3 27.425 23.1 25.35 24.125 4 31.7 26.525 16.825000000000003 24.95 5 30.0 30.275000000000002 17.974999999999998 21.75 6 25.025 32.65 19.7 22.625 7 26.424999999999997 19.3 28.849999999999998 25.424999999999997 8 25.900000000000002 20.45 24.2 29.45 9 27.125 20.974999999999998 24.8 27.1 10-11 29.375 26.35 18.8 25.474999999999998 12-13 29.3375 21.55 22.6 26.5125 14-15 27.975 24.0625 23.150000000000002 24.8125 16-17 28.225 25.337500000000002 21.9625 24.474999999999998 18-19 28.5875 24.349999999999998 22.162499999999998 24.9 20-21 28.9875 23.5875 22.1 25.324999999999996 22-23 27.8375 24.349999999999998 22.05 25.7625 24-25 27.725 23.674999999999997 23.5 25.1 26-27 28.199999999999996 24.375 22.5625 24.8625 28-29 28.762500000000003 24.0 21.637500000000003 25.6 30-31 27.800000000000004 24.3625 22.475 25.362499999999997 32-33 28.4125 24.1875 21.8625 25.5375 34-35 28.8875 23.775 22.3 25.0375 36-37 28.787499999999998 23.45 22.5625 25.2 38-39 28.299999999999997 24.4875 22.075 25.137500000000003 40-41 28.325 23.375 21.7875 26.5125 42-43 28.249999999999996 24.1375 22.075 25.5375 44-45 28.275 23.8875 22.037499999999998 25.8 46-47 28.5875 23.799999999999997 21.462500000000002 26.150000000000002 48-49 28.712500000000002 23.4625 21.8875 25.937500000000004 50-51 28.15 24.5 22.25 25.1 52-53 28.299999999999997 23.6875 22.287499999999998 25.724999999999998 54-55 28.675 22.787499999999998 22.287499999999998 26.25 56-57 28.262500000000003 24.3875 22.237499999999997 25.112499999999997 58-59 28.4 23.7875 22.8375 24.975 60-61 29.6625 22.400000000000002 22.237499999999997 25.7 62-63 29.2 23.9125 22.0625 24.825 64-65 28.575 24.2 21.912499999999998 25.3125 66-67 28.775000000000002 24.2875 22.2 24.7375 68-69 28.4 24.2625 22.112499999999997 25.224999999999998 70-71 29.912499999999998 23.4125 22.575 24.099999999999998 72-73 29.912499999999998 24.0 21.987499999999997 24.099999999999998 74-75 29.1125 24.15 22.662499999999998 24.075 76-77 29.075 23.65 22.75 24.525 78-79 28.212500000000002 23.5375 22.6 25.650000000000002 80-81 29.7125 25.0 21.8125 23.474999999999998 82-83 29.1125 24.1375 22.35 24.4 84-85 29.7125 22.8 22.912499999999998 24.575 86-87 30.1875 23.6625 22.375 23.775 88-89 29.725 23.625 21.775 24.875 90-91 29.4375 24.25 21.45 24.8625 92-93 29.725 24.175 22.2 23.9 94-95 30.099999999999998 24.7 21.1375 24.0625 96-97 30.375000000000004 24.712500000000002 21.8875 23.025000000000002 98-99 29.849999999999998 24.85 21.9375 23.3625 100-101 30.65 24.025 21.224999999999998 24.099999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.5 6 1.0 7 0.5 8 0.5 9 0.5 10 0.5 11 1.0 12 1.0 13 0.5 14 0.0 15 0.5 16 1.0 17 1.0 18 0.5 19 1.0 20 2.0 21 3.5 22 3.0 23 0.5 24 1.0 25 1.0 26 1.5 27 2.5 28 1.5 29 1.5 30 1.0 31 2.5 32 3.0 33 3.0 34 5.5 35 15.5 36 25.5 37 31.0 38 38.0 39 50.0 40 63.5 41 84.0 42 108.0 43 122.0 44 123.5 45 124.5 46 139.0 47 150.5 48 157.0 49 164.5 50 164.5 51 166.0 52 154.5 53 154.0 54 164.0 55 157.0 56 137.5 57 107.0 58 104.5 59 107.5 60 92.5 61 83.0 62 79.5 63 81.0 64 80.0 65 65.5 66 69.5 67 73.5 68 64.5 69 59.5 70 59.5 71 56.0 72 44.0 73 37.0 74 32.0 75 28.5 76 23.5 77 15.5 78 10.5 79 8.5 80 6.0 81 5.0 82 3.0 83 1.5 84 3.0 85 3.0 86 2.5 87 2.0 88 1.5 89 1.0 90 2.0 91 3.5 92 2.5 93 2.0 94 1.0 95 0.5 96 2.0 97 1.5 98 3.0 99 5.5 100 15.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.75 #Duplication Level Percentage of deduplicated Percentage of total 1 90.64788732394366 80.45 2 7.605633802816901 13.5 3 1.211267605633803 3.225 4 0.3380281690140845 1.2 5 0.08450704225352113 0.375 6 0.028169014084507043 0.15 7 0.0 0.0 8 0.028169014084507043 0.2 9 0.028169014084507043 0.22499999999999998 >10 0.028169014084507043 0.675 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 27 0.675 No Hit GCGGGCTTTGCTCGCTGATCCGATGATTCATGATAACTCGACGGATCGCA 9 0.22499999999999998 No Hit CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGGGGCCTACCATGG 8 0.2 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTG 5 0.125 No Hit ATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCC 5 0.125 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 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 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.1125 0.0 0.0 0.0 0.0 32-33 0.21250000000000002 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.3 0.0 0.0 0.0 0.0 38-39 0.4 0.0 0.0 0.0 0.0 40-41 0.475 0.0 0.0 0.0 0.0 42-43 0.6000000000000001 0.0 0.0 0.0 0.0 44-45 0.7 0.0 0.0 0.0 0.0 46-47 0.8374999999999999 0.0 0.0 0.0 0.0 48-49 0.8625 0.0 0.0 0.0 0.0 50-51 0.9375 0.0 0.0 0.0 0.0 52-53 1.125 0.0 0.0 0.0 0.0 54-55 1.3250000000000002 0.0 0.0 0.0 0.0 56-57 1.45 0.0 0.0 0.0 0.0 58-59 1.725 0.0 0.0 0.0 0.0 60-61 1.8875000000000002 0.0 0.0 0.0 0.0 62-63 2.125 0.0 0.0 0.0 0.0 64-65 2.3625 0.0 0.0 0.0 0.0 66-67 2.6375 0.0 0.0 0.0 0.0 68-69 2.975 0.0 0.0 0.0 0.0 70-71 3.4375 0.0 0.0 0.0 0.0 72-73 3.825 0.0 0.0 0.0 0.0 74-75 4.237500000000001 0.0 0.0 0.0 0.0 76-77 4.637499999999999 0.0 0.0 0.0 0.0 78-79 5.2375 0.0 0.0 0.0 0.0 80-81 6.0 0.0 0.0 0.0 0.0 82-83 6.574999999999999 0.0 0.0 0.0 0.0 84-85 7.3 0.0 0.0 0.0 0.0 86-87 7.762499999999999 0.0 0.0 0.0 0.0 88-89 8.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805815 spots for ERR3450069.sra Written 1805815 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra Read 1805810 spots for ERR3450069.sra Written 1805810 spots for ERR3450069.sra SRR ids: ['ERR3450069.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_upgkxrn5 ERR3450069.sra spots: 36116205 blocks: [[1, 1805810], [1805811, 3611620], [3611621, 5417430], [5417431, 7223240], [7223241, 9029050], [9029051, 10834860], [10834861, 12640670], [12640671, 14446480], [14446481, 16252290], [16252291, 18058100], [18058101, 19863910], [19863911, 21669720], [21669721, 23475530], [23475531, 25281340], [25281341, 27087150], [27087151, 28892960], [28892961, 30698770], [30698771, 32504580], [32504581, 34310390], [34310391, 36116205]] ERR3450069 file size 8689923 ERR3450069 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 ERR3450069 ERR3450069_1.fastq ERR3450069_2.fastq Input file: ERR3450069_1.fastq Paired file: ERR3450069_2.fastq trimmed: ERR3450069-trimmed-pair1.fastq, ERR3450069-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 14:33:14 2024 >> started Sat Dec 7 14:33:47 2024 >> done (33.447s) 36116205 read pairs processed; of these: 454 ( 0.00%) short read pairs filtered out after trimming by size control 186695 ( 0.52%) empty read pairs filtered out after trimming by size control 35929056 (99.48%) read pairs available; of these: 5423077 (15.09%) trimmed read pairs available after processing 30505979 (84.91%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 121 0.00% 19 247 0.00% 20 992 0.00% 21 2586 0.01% 22 2543 0.01% 23 1170 0.00% 24 894 0.00% 25 1339 0.00% 26 1810 0.01% 27 2583 0.01% 28 3635 0.01% 29 4628 0.01% 30 5649 0.02% 31 6981 0.02% 32 7337 0.02% 33 6960 0.02% 34 6983 0.02% 35 6867 0.02% 36 7661 0.02% 37 8376 0.02% 38 10053 0.03% 39 11510 0.03% 40 13553 0.04% 41 15722 0.04% 42 17980 0.05% 43 18875 0.05% 44 17154 0.05% 45 16819 0.05% 46 17777 0.05% 47 19732 0.05% 48 21731 0.06% 49 23893 0.07% 50 26196 0.07% 51 29516 0.08% 52 31867 0.09% 53 33136 0.09% 54 34897 0.10% 55 35624 0.10% 56 36868 0.10% 57 38580 0.11% 58 41869 0.12% 59 45744 0.13% 60 48069 0.13% 61 52829 0.15% 62 58095 0.16% 63 60832 0.17% 64 63004 0.18% 65 65246 0.18% 66 67507 0.19% 67 70371 0.20% 68 72928 0.20% 69 75012 0.21% 70 78876 0.22% 71 84719 0.24% 72 90279 0.25% 73 94442 0.26% 74 97060 0.27% 75 98687 0.27% 76 101113 0.28% 77 102776 0.29% 78 106447 0.30% 79 111237 0.31% 80 113482 0.32% 81 116897 0.33% 82 122556 0.34% 83 126716 0.35% 84 129033 0.36% 85 134297 0.37% 86 136139 0.38% 87 139314 0.39% 88 141743 0.39% 89 147385 0.41% 90 149192 0.42% 91 157424 0.44% 92 162313 0.45% 93 164842 0.46% 94 169576 0.47% 95 171360 0.48% 96 173900 0.48% 97 178303 0.50% 98 178366 0.50% 99 177976 0.50% 100 194276 0.54% 101 30505979 84.91% 35929056 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=33 prefix-density=0.38 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=161.77 fanout-score-rank=1 prefix-density=0.62 prefix-fanout=20.9 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=27 prefix-density=0.24 prefix-fanout=2.0 sequence=AGCCAGAGGAAA criterion=fanout-score sequence-density=0.08 sequence-density-rank=25 fanout-score=217.46 fanout-score-rank=1 prefix-density=0.77 prefix-fanout=22.4 sequence=CGGCGGCGGCGC ERR3450069 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:34:30 Started mapping on | Dec 07 14:34:30 Finished on | Dec 07 14:37:18 Mapping speed, Million of reads per hour | 769.91 Number of input reads | 35929056 Average input read length | 195 UNIQUE READS: Uniquely mapped reads number | 25326535 Uniquely mapped reads % | 70.49% Average mapped length | 195.39 Number of splices: Total | 15494614 Number of splices: Annotated (sjdb) | 14692874 Number of splices: GT/AG | 15294037 Number of splices: GC/AG | 173880 Number of splices: AT/AC | 9475 Number of splices: Non-canonical | 17222 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.15 Insertion rate per base | 0.01% Insertion average length | 1.97 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1835976 % of reads mapped to multiple loci | 5.11% Number of reads mapped to too many loci | 1684624 % of reads mapped to too many loci | 4.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.13% % of reads unmapped: other | 16.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8766545 8766545 8766545 N_multimapping 1835976 1835976 1835976 N_noFeature 764432 24246273 1482711 N_ambiguous 435965 3656 76953 UnstrandedReadsAssigned:24126138 PositiveStrandReadsAssigned:1076606 NegativeStrandReadsAssigned:23766871 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450069 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: ERR3450069-trimmed-pair1.fastq ERR3450069-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,929,056 reads, 25,076,815 reads pseudoaligned [quant] estimated average fragment length: 174.533 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,273 rounds 52973 ERR3450069.ke.tsv 35125 ERR3450069.se.tsv 88098 total ==> ERR3450069.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 762.665 21.6224 1.67418 PNS24247 1044 870.467 37.3682 2.53501 PNS24249 1928 1754.47 226.717 7.63079 PNS24246 1044 870.467 37.3682 2.53501 PNS24248 1044 870.467 37.3682 2.53501 PNS24244 1471 1297.47 43.5563 1.98237 PNS24243 293 138.64 0 0 KQK14069 1603 1429.47 6487.4 267.996 KQK14071 474 303.968 173.98 33.7989 ==> ERR3450069.se.tsv <== BRADI_1g14170v3 6687 BRADI_1g53295v3 10 BRADI_1g59795v3 142 BRADI_1g07683v3 0 BRADI_1g00485v3 70 BRADI_1g20270v3 3515 BRADI_1g74790v3 233 BRADI_1g09890v3 32 BRADI_1g77505v3 336 BRADI_1g48960v3 0 ERR3450069 completed mapping pipeline successfully