Starting /dee2/code/volunteer_pipeline.sh ERR3450061 current disk space = 1543061762048 free memory = 1593712004 ERR3450061 SRAfilesize 03c1d93f464fa2df63b5ca3e2e9899f6 ERR3450061.sra ERR3450061.sra file validated ERR3450061 is paired end ERR3450061 is conventional basespace ERR3450061 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450061_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 36.123 37.0 37.0 37.0 37.0 37.0 2 36.413 37.0 37.0 37.0 37.0 37.0 3 36.3945 37.0 37.0 37.0 37.0 37.0 4 36.4555 37.0 37.0 37.0 37.0 37.0 5 36.56 37.0 37.0 37.0 37.0 37.0 6 36.4925 37.0 37.0 37.0 37.0 37.0 7 36.4155 37.0 37.0 37.0 37.0 37.0 8 36.5045 37.0 37.0 37.0 37.0 37.0 9 36.454 37.0 37.0 37.0 37.0 37.0 10-11 36.50075 37.0 37.0 37.0 37.0 37.0 12-13 36.55175 37.0 37.0 37.0 37.0 37.0 14-15 36.48925 37.0 37.0 37.0 37.0 37.0 16-17 36.484750000000005 37.0 37.0 37.0 37.0 37.0 18-19 36.4735 37.0 37.0 37.0 37.0 37.0 20-21 36.481750000000005 37.0 37.0 37.0 37.0 37.0 22-23 36.46 37.0 37.0 37.0 37.0 37.0 24-25 36.41825 37.0 37.0 37.0 37.0 37.0 26-27 36.3475 37.0 37.0 37.0 37.0 37.0 28-29 36.368750000000006 37.0 37.0 37.0 37.0 37.0 30-31 36.3065 37.0 37.0 37.0 37.0 37.0 32-33 36.3045 37.0 37.0 37.0 37.0 37.0 34-35 36.13675 37.0 37.0 37.0 37.0 37.0 36-37 36.275499999999994 37.0 37.0 37.0 37.0 37.0 38-39 36.35575 37.0 37.0 37.0 37.0 37.0 40-41 36.2455 37.0 37.0 37.0 37.0 37.0 42-43 36.263999999999996 37.0 37.0 37.0 37.0 37.0 44-45 36.111999999999995 37.0 37.0 37.0 37.0 37.0 46-47 35.96875 37.0 37.0 37.0 37.0 37.0 48-49 36.099500000000006 37.0 37.0 37.0 37.0 37.0 50-51 36.0935 37.0 37.0 37.0 37.0 37.0 52-53 36.064750000000004 37.0 37.0 37.0 37.0 37.0 54-55 36.070750000000004 37.0 37.0 37.0 37.0 37.0 56-57 36.06125 37.0 37.0 37.0 37.0 37.0 58-59 35.963499999999996 37.0 37.0 37.0 37.0 37.0 60-61 36.01275 37.0 37.0 37.0 37.0 37.0 62-63 35.98725 37.0 37.0 37.0 37.0 37.0 64-65 35.8985 37.0 37.0 37.0 37.0 37.0 66-67 35.947 37.0 37.0 37.0 37.0 37.0 68-69 35.979 37.0 37.0 37.0 37.0 37.0 70-71 35.936 37.0 37.0 37.0 37.0 37.0 72-73 35.828500000000005 37.0 37.0 37.0 37.0 37.0 74-75 36.093 37.0 37.0 37.0 37.0 37.0 76-77 36.07025 37.0 37.0 37.0 37.0 37.0 78-79 36.03875 37.0 37.0 37.0 37.0 37.0 80-81 36.01075 37.0 37.0 37.0 37.0 37.0 82-83 36.088499999999996 37.0 37.0 37.0 37.0 37.0 84-85 35.9485 37.0 37.0 37.0 37.0 37.0 86-87 35.893249999999995 37.0 37.0 37.0 37.0 37.0 88-89 35.97825 37.0 37.0 37.0 37.0 37.0 90-91 35.98350000000001 37.0 37.0 37.0 37.0 37.0 92-93 35.876999999999995 37.0 37.0 37.0 37.0 37.0 94-95 35.9015 37.0 37.0 37.0 37.0 37.0 96-97 35.83375 37.0 37.0 37.0 37.0 37.0 98-99 35.82525 37.0 37.0 37.0 37.0 37.0 100-101 35.81325 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 1.0 23 3.0 24 9.0 25 12.0 26 10.0 27 15.0 28 26.0 29 45.0 30 45.0 31 57.0 32 62.0 33 83.0 34 115.0 35 191.0 36 1796.0 37 1529.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.10320641282566 9.544088176352705 10.896793587174349 40.4559118236473 2 21.275 13.575000000000001 30.45 34.699999999999996 3 21.3 17.599999999999998 24.65 36.449999999999996 4 28.175 23.150000000000002 17.875 30.8 5 27.0 27.650000000000002 22.075 23.275000000000002 6 24.9 29.525000000000002 22.85 22.725 7 19.3 24.15 36.875 19.675 8 20.65 21.4 31.075000000000003 26.875 9 22.675 21.224999999999998 30.5 25.6 10-11 23.65 28.6125 22.237499999999997 25.5 12-13 23.8625 23.0625 25.2125 27.8625 14-15 23.325000000000003 24.5625 26.6 25.5125 16-17 24.2375 23.5125 25.45 26.8 18-19 23.6375 25.087500000000002 25.25 26.025 20-21 24.775 24.6875 24.55 25.9875 22-23 24.7375 24.125 24.875 26.2625 24-25 25.2 23.3375 23.65 27.8125 26-27 25.2375 24.55 23.3875 26.825 28-29 25.6125 22.925 24.425 27.037499999999998 30-31 24.6875 24.0 23.925 27.3875 32-33 24.4875 23.8375 24.2375 27.437499999999996 34-35 24.175 24.425 24.625 26.775 36-37 24.637500000000003 24.8625 23.95 26.55 38-39 24.5 24.0625 24.175 27.2625 40-41 25.2625 24.5 23.2125 27.025 42-43 24.425 24.1125 24.675 26.787499999999998 44-45 24.5625 23.2375 24.8 27.400000000000002 46-47 24.525 23.8125 24.212500000000002 27.450000000000003 48-49 23.9125 22.900000000000002 24.9875 28.199999999999996 50-51 24.275 23.4125 25.1 27.212500000000002 52-53 25.474999999999998 23.575 24.2375 26.7125 54-55 24.25 24.4375 23.6375 27.675 56-57 24.7 22.662499999999998 25.85 26.787499999999998 58-59 24.4375 23.575 24.275 27.712500000000002 60-61 24.925 24.2375 23.7375 27.1 62-63 25.587500000000002 23.4625 24.0 26.950000000000003 64-65 24.725 23.7375 24.3125 27.224999999999998 66-67 24.4125 23.962500000000002 24.762500000000003 26.8625 68-69 25.85 23.875 23.474999999999998 26.8 70-71 24.9125 24.3875 23.3875 27.3125 72-73 26.0 24.3125 22.55 27.1375 74-75 26.5 24.375 22.287499999999998 26.8375 76-77 25.5125 24.2 22.825 27.462500000000002 78-79 25.912499999999998 24.1625 21.8125 28.1125 80-81 25.275 23.825 23.6125 27.287499999999998 82-83 25.637500000000003 24.325 23.3625 26.674999999999997 84-85 26.2625 23.225 23.925 26.5875 86-87 25.5125 23.7875 23.1875 27.5125 88-89 25.775 24.575 22.8 26.85 90-91 25.662499999999998 25.174999999999997 22.775000000000002 26.387500000000003 92-93 24.762500000000003 25.1 24.474999999999998 25.662499999999998 94-95 25.224999999999998 23.3875 24.05 27.3375 96-97 25.362499999999997 24.1875 23.45 27.0 98-99 25.35 23.962500000000002 23.65 27.037499999999998 100-101 24.4 25.587500000000002 22.412499999999998 27.6 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 6.0 1 3.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 1.5 9 2.5 10 2.0 11 1.0 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 0.5 21 1.5 22 2.0 23 1.0 24 0.0 25 0.0 26 0.5 27 0.5 28 1.0 29 2.0 30 3.5 31 6.0 32 7.0 33 8.0 34 9.0 35 14.5 36 30.0 37 38.5 38 41.0 39 60.0 40 83.0 41 106.0 42 124.0 43 130.5 44 147.0 45 153.5 46 153.5 47 177.5 48 178.0 49 165.5 50 180.0 51 179.0 52 167.0 53 156.5 54 137.0 55 125.5 56 134.5 57 138.5 58 119.5 59 102.0 60 88.5 61 79.0 62 74.0 63 66.5 64 64.5 65 59.0 66 43.5 67 43.0 68 49.5 69 50.5 70 50.0 71 43.0 72 38.5 73 33.5 74 23.5 75 21.5 76 20.0 77 13.0 78 8.0 79 7.5 80 8.5 81 7.0 82 4.5 83 1.0 84 1.0 85 1.5 86 1.0 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 0.2 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 86.725 #Duplication Level Percentage of deduplicated Percentage of total 1 89.27644854424906 77.425 2 8.330931104064572 14.45 3 1.3260305563562986 3.45 4 0.4324012683770539 1.5 5 0.3170942634765062 1.375 6 0.23061400980109542 1.2 7 0.028826751225136928 0.17500000000000002 8 0.028826751225136928 0.2 9 0.028826751225136928 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 GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 9 0.22499999999999998 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit CTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGG 7 0.17500000000000002 No Hit GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 6 0.15 No Hit CGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGATTT 6 0.15 No Hit CTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTC 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTACTCGATCTCGTTT 6 0.15 TruSeq Adapter, Index 27 (97% over 39bp) CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 6 0.15 No Hit GGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGA 6 0.15 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 6 0.15 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 6 0.15 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 5 0.125 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 5 0.125 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 5 0.125 No Hit CTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGAT 5 0.125 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 5 0.125 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCC 5 0.125 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 5 0.125 No Hit GCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAA 5 0.125 No Hit CTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATC 5 0.125 No Hit CTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAG 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 0.05 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.15 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.21250000000000002 0.0 0.0 0.0 0.0 44-45 0.275 0.0 0.0 0.0 0.0 46-47 0.36250000000000004 0.0 0.0 0.0 0.0 48-49 0.5 0.0 0.0 0.0 0.0 50-51 0.6 0.0 0.0 0.0 0.0 52-53 0.6625 0.0 0.0 0.0 0.0 54-55 0.75 0.0 0.0 0.0 0.0 56-57 0.8375 0.0 0.0 0.0 0.0 58-59 0.925 0.0 0.0 0.0 0.0 60-61 1.1 0.0 0.0 0.0 0.0 62-63 1.3625 0.0 0.0 0.0 0.0 64-65 1.6875 0.0 0.0 0.0 0.0 66-67 1.85 0.0 0.0 0.0 0.0 68-69 2.1125 0.0 0.0 0.0 0.0 70-71 2.3875 0.0 0.0 0.0 0.0 72-73 2.6875 0.0 0.0 0.0 0.0 74-75 3.1375 0.0 0.0 0.0 0.0 76-77 3.5250000000000004 0.0 0.0 0.0 0.0 78-79 3.95 0.0 0.0 0.0 0.0 80-81 4.4 0.0 0.0 0.0 0.0 82-83 4.9125 0.0 0.0 0.0 0.0 84-85 5.4375 0.0 0.0 0.0 0.0 86-87 5.95 0.0 0.0 0.0 0.0 88-89 6.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450061 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450061_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 36.158 37.0 37.0 37.0 37.0 37.0 2 35.9885 37.0 37.0 37.0 37.0 37.0 3 35.9765 37.0 37.0 37.0 37.0 37.0 4 36.0835 37.0 37.0 37.0 37.0 37.0 5 36.2175 37.0 37.0 37.0 37.0 37.0 6 36.3255 37.0 37.0 37.0 37.0 37.0 7 36.1725 37.0 37.0 37.0 37.0 37.0 8 36.1195 37.0 37.0 37.0 37.0 37.0 9 36.2225 37.0 37.0 37.0 37.0 37.0 10-11 36.1085 37.0 37.0 37.0 37.0 37.0 12-13 36.055 37.0 37.0 37.0 37.0 37.0 14-15 36.081500000000005 37.0 37.0 37.0 37.0 37.0 16-17 35.998000000000005 37.0 37.0 37.0 37.0 37.0 18-19 35.966499999999996 37.0 37.0 37.0 37.0 37.0 20-21 36.06175 37.0 37.0 37.0 37.0 37.0 22-23 36.1195 37.0 37.0 37.0 37.0 37.0 24-25 35.9525 37.0 37.0 37.0 37.0 37.0 26-27 35.837999999999994 37.0 37.0 37.0 37.0 37.0 28-29 35.8335 37.0 37.0 37.0 37.0 37.0 30-31 35.764250000000004 37.0 37.0 37.0 37.0 37.0 32-33 35.72575 37.0 37.0 37.0 37.0 37.0 34-35 35.64525 37.0 37.0 37.0 37.0 37.0 36-37 35.70075 37.0 37.0 37.0 37.0 37.0 38-39 35.646 37.0 37.0 37.0 37.0 37.0 40-41 35.6665 37.0 37.0 37.0 37.0 37.0 42-43 35.720749999999995 37.0 37.0 37.0 37.0 37.0 44-45 35.69175 37.0 37.0 37.0 37.0 37.0 46-47 35.7 37.0 37.0 37.0 37.0 37.0 48-49 35.74025 37.0 37.0 37.0 37.0 37.0 50-51 35.70225000000001 37.0 37.0 37.0 37.0 37.0 52-53 35.64325 37.0 37.0 37.0 37.0 37.0 54-55 35.7175 37.0 37.0 37.0 37.0 37.0 56-57 35.710499999999996 37.0 37.0 37.0 37.0 37.0 58-59 35.80525 37.0 37.0 37.0 37.0 37.0 60-61 35.83725 37.0 37.0 37.0 37.0 37.0 62-63 35.90825 37.0 37.0 37.0 37.0 37.0 64-65 35.729749999999996 37.0 37.0 37.0 37.0 37.0 66-67 35.702749999999995 37.0 37.0 37.0 37.0 37.0 68-69 35.709 37.0 37.0 37.0 37.0 37.0 70-71 35.6365 37.0 37.0 37.0 37.0 37.0 72-73 35.6665 37.0 37.0 37.0 37.0 37.0 74-75 35.48625 37.0 37.0 37.0 37.0 37.0 76-77 35.555499999999995 37.0 37.0 37.0 37.0 37.0 78-79 35.526250000000005 37.0 37.0 37.0 37.0 37.0 80-81 35.436 37.0 37.0 37.0 37.0 37.0 82-83 35.43575 37.0 37.0 37.0 37.0 37.0 84-85 35.661249999999995 37.0 37.0 37.0 37.0 37.0 86-87 35.667500000000004 37.0 37.0 37.0 37.0 37.0 88-89 35.533500000000004 37.0 37.0 37.0 37.0 37.0 90-91 35.5715 37.0 37.0 37.0 37.0 37.0 92-93 35.54675 37.0 37.0 37.0 37.0 37.0 94-95 35.56725 37.0 37.0 37.0 37.0 37.0 96-97 35.652 37.0 37.0 37.0 37.0 37.0 98-99 35.504000000000005 37.0 37.0 37.0 37.0 37.0 100-101 35.55775 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 2.0 17 4.0 18 6.0 19 12.0 20 6.0 21 8.0 22 14.0 23 11.0 24 19.0 25 11.0 26 11.0 27 19.0 28 23.0 29 19.0 30 33.0 31 52.0 32 74.0 33 76.0 34 162.0 35 358.0 36 2363.0 37 716.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.15 16.0 12.5 30.349999999999998 2 28.000000000000004 22.900000000000002 24.725 24.375 3 26.200000000000003 22.275 25.900000000000002 25.624999999999996 4 30.875000000000004 27.425 17.075000000000003 24.625 5 29.549999999999997 30.325000000000003 19.05 21.075 6 24.875 32.300000000000004 20.5 22.325 7 27.025 19.125 30.85 23.0 8 25.474999999999998 21.175 23.525 29.825000000000003 9 26.5 22.0 24.7 26.8 10-11 29.15 26.325 19.6875 24.837500000000002 12-13 28.4 21.75 22.8125 27.037499999999998 14-15 27.275 25.4375 22.8 24.4875 16-17 26.950000000000003 24.587500000000002 22.6875 25.775 18-19 29.762499999999996 23.974999999999998 22.025 24.2375 20-21 27.725 24.3125 22.537499999999998 25.424999999999997 22-23 28.5625 24.6625 21.8875 24.887500000000003 24-25 27.175 24.5 22.5875 25.7375 26-27 28.225 24.875 21.6125 25.2875 28-29 28.8625 23.7375 22.1875 25.2125 30-31 27.6375 25.2 21.762500000000003 25.4 32-33 27.3125 25.0 22.475 25.2125 34-35 28.0875 24.625 22.2 25.087500000000002 36-37 28.3625 24.337500000000002 22.825 24.474999999999998 38-39 27.950000000000003 24.5 22.7 24.85 40-41 28.199999999999996 24.3625 22.425 25.0125 42-43 28.425 23.7875 22.912499999999998 24.875 44-45 27.900000000000002 23.474999999999998 23.525 25.1 46-47 28.1625 23.65 21.575 26.6125 48-49 27.737499999999997 24.712500000000002 22.4875 25.0625 50-51 27.525 25.074999999999996 22.1375 25.2625 52-53 27.775 24.175 23.075000000000003 24.975 54-55 27.4125 23.825 22.1875 26.575 56-57 26.924999999999997 24.675 22.9375 25.4625 58-59 28.0875 25.224999999999998 22.075 24.6125 60-61 28.1 24.3125 22.400000000000002 25.1875 62-63 28.9 23.3875 22.787499999999998 24.925 64-65 29.575000000000003 23.9 21.212500000000002 25.3125 66-67 28.237499999999997 24.5 22.15 25.112499999999997 68-69 28.762500000000003 23.8625 22.025 25.35 70-71 29.812499999999996 25.124999999999996 21.224999999999998 23.8375 72-73 28.8875 24.2375 22.4625 24.4125 74-75 28.475 23.8875 22.625 25.0125 76-77 28.512500000000003 23.7375 22.3 25.45 78-79 29.3375 23.35 22.5875 24.725 80-81 27.5625 24.962500000000002 22.525000000000002 24.95 82-83 28.449999999999996 24.975 21.825 24.75 84-85 29.2 24.0375 22.35 24.4125 86-87 28.575 25.8125 22.2625 23.35 88-89 28.9875 24.325 21.987499999999997 24.7 90-91 30.55 23.8375 22.237499999999997 23.375 92-93 28.925 25.224999999999998 22.162499999999998 23.6875 94-95 29.25 24.7875 22.5625 23.400000000000002 96-97 30.3 24.7 21.8875 23.1125 98-99 29.225 24.462500000000002 22.7375 23.575 100-101 30.4375 24.525 22.162499999999998 22.875 >>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 1.0 11 1.0 12 0.5 13 0.0 14 0.5 15 1.5 16 1.0 17 0.5 18 1.0 19 2.0 20 2.0 21 1.0 22 2.0 23 2.0 24 1.0 25 1.0 26 0.5 27 0.5 28 1.5 29 1.5 30 1.5 31 2.5 32 4.0 33 6.5 34 7.5 35 14.0 36 27.0 37 36.5 38 45.0 39 61.5 40 82.0 41 92.0 42 106.5 43 129.5 44 131.5 45 125.0 46 139.0 47 174.0 48 196.0 49 190.5 50 168.5 51 142.0 52 135.5 53 147.5 54 140.5 55 139.5 56 143.5 57 114.0 58 101.5 59 92.5 60 77.5 61 83.0 62 80.0 63 71.0 64 67.0 65 65.0 66 64.5 67 57.5 68 51.5 69 58.5 70 59.5 71 55.0 72 58.5 73 50.5 74 36.0 75 22.0 76 19.5 77 19.5 78 14.0 79 11.5 80 6.0 81 3.5 82 3.5 83 2.5 84 1.5 85 1.0 86 1.0 87 1.5 88 1.0 89 0.5 90 0.5 91 1.0 92 1.0 93 1.5 94 2.5 95 1.5 96 1.0 97 1.5 98 2.0 99 4.5 100 11.5 >>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 88.25 #Duplication Level Percentage of deduplicated Percentage of total 1 90.39660056657223 79.77499999999999 2 7.733711048158639 13.65 3 1.246458923512748 3.3000000000000003 4 0.22662889518413595 0.8 5 0.22662889518413595 1.0 6 0.028328611898016994 0.15 7 0.028328611898016994 0.17500000000000002 8 0.08498583569405099 0.6 9 0.0 0.0 >10 0.028328611898016994 0.5499999999999999 >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 22 0.5499999999999999 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTG 8 0.2 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 8 0.2 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 6 0.15 No Hit TACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGA 5 0.125 No Hit TCTAGAGCTAATACGTGCAACAAACCCCGACTTCTGGGAGGGGCGCATTT 5 0.125 No Hit AGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTCTGGGAGGGGC 5 0.125 No Hit GATTAATAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAA 5 0.125 No Hit GGACTTTGGGCCGGGTCGGCCGGTCCGCCTCACGGCGAGCACCGACCTAC 5 0.125 No Hit CGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCA 5 0.125 No Hit GGCGCATTTATTAGATAAAAGGCTGACGCGGGCTTTGCTCGCTGATCCGA 5 0.125 No Hit GTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACG 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 0.025 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.0625 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.16249999999999998 0.0 0.0 0.0 0.0 44-45 0.225 0.0 0.0 0.0 0.0 46-47 0.3125 0.0 0.0 0.0 0.0 48-49 0.44999999999999996 0.0 0.0 0.0 0.0 50-51 0.55 0.0 0.0 0.0 0.0 52-53 0.6125 0.0 0.0 0.0 0.0 54-55 0.725 0.0 0.0 0.0 0.0 56-57 0.8125 0.0 0.0 0.0 0.0 58-59 0.9 0.0 0.0 0.0 0.0 60-61 1.075 0.0 0.0 0.0 0.0 62-63 1.3625 0.0 0.0 0.0 0.0 64-65 1.7125 0.0 0.0 0.0 0.0 66-67 1.875 0.0 0.0 0.0 0.0 68-69 2.1125 0.0 0.0 0.0 0.0 70-71 2.3875 0.0 0.0 0.0 0.0 72-73 2.6875 0.0 0.0 0.0 0.0 74-75 3.1375 0.0 0.0 0.0 0.0 76-77 3.5250000000000004 0.0 0.0 0.0 0.0 78-79 3.9375 0.0 0.0 0.0 0.0 80-81 4.4 0.0 0.0 0.0 0.0 82-83 4.925000000000001 0.0 0.0 0.0 0.0 84-85 5.4375 0.0 0.0 0.0 0.0 86-87 5.95 0.0 0.0 0.0 0.0 88-89 6.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159151 spots for ERR3450061.sra Written 1159151 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra Read 1159149 spots for ERR3450061.sra Written 1159149 spots for ERR3450061.sra SRR ids: ['ERR3450061.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9i1ph87r ERR3450061.sra spots: 23182982 blocks: [[1, 1159149], [1159150, 2318298], [2318299, 3477447], [3477448, 4636596], [4636597, 5795745], [5795746, 6954894], [6954895, 8114043], [8114044, 9273192], [9273193, 10432341], [10432342, 11591490], [11591491, 12750639], [12750640, 13909788], [13909789, 15068937], [15068938, 16228086], [16228087, 17387235], [17387236, 18546384], [18546385, 19705533], [19705534, 20864682], [20864683, 22023831], [22023832, 23182982]] ERR3450061 file size 5570288 ERR3450061 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 ERR3450061 ERR3450061_1.fastq ERR3450061_2.fastq Input file: ERR3450061_1.fastq Paired file: ERR3450061_2.fastq trimmed: ERR3450061-trimmed-pair1.fastq, ERR3450061-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 14:18:35 2024 >> started Sat Dec 7 14:19:01 2024 >> done (25.756s) 23182982 read pairs processed; of these: 186 ( 0.00%) short read pairs filtered out after trimming by size control 89718 ( 0.39%) empty read pairs filtered out after trimming by size control 23093078 (99.61%) read pairs available; of these: 2714696 (11.76%) trimmed read pairs available after processing 20378382 (88.24%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 45 0.00% 19 96 0.00% 20 388 0.00% 21 967 0.00% 22 1013 0.00% 23 453 0.00% 24 454 0.00% 25 558 0.00% 26 793 0.00% 27 1120 0.00% 28 1538 0.01% 29 2047 0.01% 30 2492 0.01% 31 3182 0.01% 32 3236 0.01% 33 3094 0.01% 34 2911 0.01% 35 2963 0.01% 36 3269 0.01% 37 3609 0.02% 38 4244 0.02% 39 4990 0.02% 40 5791 0.03% 41 6654 0.03% 42 7606 0.03% 43 7832 0.03% 44 7162 0.03% 45 7025 0.03% 46 7460 0.03% 47 8325 0.04% 48 9052 0.04% 49 10142 0.04% 50 11281 0.05% 51 12458 0.05% 52 13488 0.06% 53 14365 0.06% 54 14725 0.06% 55 15171 0.07% 56 16212 0.07% 57 16648 0.07% 58 17979 0.08% 59 19962 0.09% 60 21446 0.09% 61 23305 0.10% 62 25614 0.11% 63 27124 0.12% 64 27822 0.12% 65 28967 0.13% 66 30207 0.13% 67 31909 0.14% 68 33350 0.14% 69 34451 0.15% 70 37003 0.16% 71 39701 0.17% 72 42128 0.18% 73 45089 0.20% 74 46169 0.20% 75 47135 0.20% 76 48645 0.21% 77 49341 0.21% 78 51911 0.22% 79 54457 0.24% 80 56460 0.24% 81 58833 0.25% 82 62207 0.27% 83 63910 0.28% 84 66427 0.29% 85 68655 0.30% 86 69692 0.30% 87 72591 0.31% 88 74333 0.32% 89 77196 0.33% 90 79114 0.34% 91 82952 0.36% 92 87251 0.38% 93 87957 0.38% 94 90802 0.39% 95 93257 0.40% 96 95039 0.41% 97 98137 0.42% 98 99297 0.43% 99 100088 0.43% 100 111924 0.48% 101 20378382 88.24% 23093078 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=35 prefix-density=0.35 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.08 sequence-density-rank=13 fanout-score=157.46 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=21.0 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=33 prefix-density=0.20 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.07 sequence-density-rank=25 fanout-score=221.03 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=22.1 sequence=CGGCGGCGGCGC ERR3450061 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:19:31 Started mapping on | Dec 07 14:19:31 Finished on | Dec 07 14:21:19 Mapping speed, Million of reads per hour | 769.77 Number of input reads | 23093078 Average input read length | 197 UNIQUE READS: Uniquely mapped reads number | 16514639 Uniquely mapped reads % | 71.51% Average mapped length | 197.02 Number of splices: Total | 10108834 Number of splices: Annotated (sjdb) | 9565512 Number of splices: GT/AG | 9976244 Number of splices: GC/AG | 113970 Number of splices: AT/AC | 6664 Number of splices: Non-canonical | 11956 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.12 Insertion rate per base | 0.01% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1054863 % of reads mapped to multiple loci | 4.57% Number of reads mapped to too many loci | 957905 % of reads mapped to too many loci | 4.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.40% % of reads unmapped: other | 16.37% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5523576 5523576 5523576 N_multimapping 1054863 1054863 1054863 N_noFeature 554224 15889809 938166 N_ambiguous 292503 2352 54697 UnstrandedReadsAssigned:15667912 PositiveStrandReadsAssigned:622478 NegativeStrandReadsAssigned:15521776 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450061 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: ERR3450061-trimmed-pair1.fastq ERR3450061-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,093,078 reads, 16,320,619 reads pseudoaligned [quant] estimated average fragment length: 180.409 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,309 rounds 52973 ERR3450061.ke.tsv 35125 ERR3450061.se.tsv 88098 total ==> ERR3450061.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 756.924 0 0 PNS24247 1044 864.591 38.8419 4.16961 PNS24249 1928 1748.59 191.667 10.1733 PNS24246 1044 864.591 38.8419 4.16961 PNS24248 1044 864.591 38.8419 4.16961 PNS24244 1471 1291.59 48.8075 3.50725 PNS24243 293 133.346 0 0 KQK14069 1603 1423.59 4373.12 285.109 KQK14071 474 297.928 259.73 80.9124 ==> ERR3450061.se.tsv <== BRADI_1g14170v3 4711 BRADI_1g53295v3 22 BRADI_1g59795v3 164 BRADI_1g07683v3 0 BRADI_1g00485v3 56 BRADI_1g20270v3 2177 BRADI_1g74790v3 146 BRADI_1g09890v3 22 BRADI_1g77505v3 210 BRADI_1g48960v3 0 ERR3450061 completed mapping pipeline successfully