Starting /dee2/code/volunteer_pipeline.sh ERR3450072 current disk space = 1543021219840 free memory = 1603104728 ERR3450072 SRAfilesize 1155b4cf924e6e2efa8b1d3c813c6707 ERR3450072.sra ERR3450072.sra file validated ERR3450072 is paired end ERR3450072 is conventional basespace ERR3450072 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450072_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 36.09825 37.0 37.0 37.0 37.0 37.0 2 36.355 37.0 37.0 37.0 37.0 37.0 3 36.3915 37.0 37.0 37.0 37.0 37.0 4 36.5355 37.0 37.0 37.0 37.0 37.0 5 36.502 37.0 37.0 37.0 37.0 37.0 6 36.5465 37.0 37.0 37.0 37.0 37.0 7 36.4765 37.0 37.0 37.0 37.0 37.0 8 36.561 37.0 37.0 37.0 37.0 37.0 9 36.5125 37.0 37.0 37.0 37.0 37.0 10-11 36.50275 37.0 37.0 37.0 37.0 37.0 12-13 36.49225 37.0 37.0 37.0 37.0 37.0 14-15 36.5505 37.0 37.0 37.0 37.0 37.0 16-17 36.48175 37.0 37.0 37.0 37.0 37.0 18-19 36.52525 37.0 37.0 37.0 37.0 37.0 20-21 36.45275 37.0 37.0 37.0 37.0 37.0 22-23 36.48725 37.0 37.0 37.0 37.0 37.0 24-25 36.4535 37.0 37.0 37.0 37.0 37.0 26-27 36.44075 37.0 37.0 37.0 37.0 37.0 28-29 36.44875 37.0 37.0 37.0 37.0 37.0 30-31 36.453 37.0 37.0 37.0 37.0 37.0 32-33 36.3865 37.0 37.0 37.0 37.0 37.0 34-35 36.457 37.0 37.0 37.0 37.0 37.0 36-37 36.403499999999994 37.0 37.0 37.0 37.0 37.0 38-39 36.38575 37.0 37.0 37.0 37.0 37.0 40-41 36.36375 37.0 37.0 37.0 37.0 37.0 42-43 36.3735 37.0 37.0 37.0 37.0 37.0 44-45 36.286500000000004 37.0 37.0 37.0 37.0 37.0 46-47 36.30675 37.0 37.0 37.0 37.0 37.0 48-49 36.26875 37.0 37.0 37.0 37.0 37.0 50-51 36.289500000000004 37.0 37.0 37.0 37.0 37.0 52-53 36.20525000000001 37.0 37.0 37.0 37.0 37.0 54-55 36.2185 37.0 37.0 37.0 37.0 37.0 56-57 36.298500000000004 37.0 37.0 37.0 37.0 37.0 58-59 36.206999999999994 37.0 37.0 37.0 37.0 37.0 60-61 36.153000000000006 37.0 37.0 37.0 37.0 37.0 62-63 36.167500000000004 37.0 37.0 37.0 37.0 37.0 64-65 36.0715 37.0 37.0 37.0 37.0 37.0 66-67 36.170500000000004 37.0 37.0 37.0 37.0 37.0 68-69 36.23225 37.0 37.0 37.0 37.0 37.0 70-71 36.24125 37.0 37.0 37.0 37.0 37.0 72-73 36.189750000000004 37.0 37.0 37.0 37.0 37.0 74-75 36.159499999999994 37.0 37.0 37.0 37.0 37.0 76-77 36.185500000000005 37.0 37.0 37.0 37.0 37.0 78-79 36.18325 37.0 37.0 37.0 37.0 37.0 80-81 36.25175 37.0 37.0 37.0 37.0 37.0 82-83 36.127250000000004 37.0 37.0 37.0 37.0 37.0 84-85 36.152249999999995 37.0 37.0 37.0 37.0 37.0 86-87 36.18725 37.0 37.0 37.0 37.0 37.0 88-89 36.12075 37.0 37.0 37.0 37.0 37.0 90-91 36.11125 37.0 37.0 37.0 37.0 37.0 92-93 36.118 37.0 37.0 37.0 37.0 37.0 94-95 36.05175 37.0 37.0 37.0 37.0 37.0 96-97 36.06225 37.0 37.0 37.0 37.0 37.0 98-99 35.92825 37.0 37.0 37.0 37.0 37.0 100-101 35.97275 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 4.0 25 7.0 26 9.0 27 18.0 28 25.0 29 22.0 30 44.0 31 57.0 32 61.0 33 69.0 34 87.0 35 188.0 36 1650.0 37 1757.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.76387842250691 9.319266515950767 10.7008289374529 40.216026124089424 2 21.224999999999998 12.65 29.775000000000002 36.35 3 22.525000000000002 17.775 24.75 34.949999999999996 4 28.599999999999998 22.75 17.775 30.875000000000004 5 28.325 26.025 20.875 24.775 6 23.1 31.125000000000004 23.625 22.15 7 20.349999999999998 21.325 37.925 20.4 8 20.424999999999997 20.974999999999998 29.75 28.849999999999998 9 22.15 21.175 31.4 25.275 10-11 24.375 27.900000000000002 22.1 25.624999999999996 12-13 24.087500000000002 21.6875 26.687499999999996 27.537499999999998 14-15 23.1375 24.625 25.937500000000004 26.3 16-17 24.3875 23.4125 25.7125 26.487500000000004 18-19 23.875 24.975 24.962500000000002 26.187500000000004 20-21 23.9375 24.5375 24.9125 26.6125 22-23 24.825 24.55 24.825 25.8 24-25 24.962500000000002 23.8125 25.137500000000003 26.087500000000002 26-27 24.2625 23.5 24.6 27.6375 28-29 25.3 22.825 23.674999999999997 28.199999999999996 30-31 23.95 23.3 24.0375 28.712500000000002 32-33 23.6375 23.8875 25.937500000000004 26.5375 34-35 24.6625 23.4625 24.6125 27.2625 36-37 23.962500000000002 24.2 24.275 27.5625 38-39 24.1375 23.5625 23.95 28.349999999999998 40-41 24.7375 23.2375 23.2125 28.812500000000004 42-43 25.1 23.8875 24.3125 26.700000000000003 44-45 24.825 24.4375 24.425 26.3125 46-47 25.637500000000003 24.125 23.5625 26.674999999999997 48-49 24.462500000000002 23.25 24.4875 27.800000000000004 50-51 23.7625 24.1375 24.825 27.275 52-53 25.7375 23.724999999999998 24.0375 26.5 54-55 24.2875 23.6375 24.625 27.450000000000003 56-57 25.2125 23.5 24.3625 26.924999999999997 58-59 25.4625 24.6625 23.2875 26.5875 60-61 25.4 23.925 23.425 27.250000000000004 62-63 24.7875 23.9125 23.9 27.400000000000002 64-65 24.5 23.775 25.0625 26.6625 66-67 23.9125 24.637500000000003 23.45 28.000000000000004 68-69 24.887500000000003 24.025 24.3875 26.700000000000003 70-71 24.7875 24.3625 23.7125 27.1375 72-73 25.474999999999998 23.825 23.4625 27.237499999999997 74-75 24.85 24.6625 24.125 26.3625 76-77 25.7875 23.849999999999998 23.45 26.9125 78-79 25.112499999999997 23.799999999999997 24.05 27.037499999999998 80-81 25.624999999999996 22.787499999999998 23.8625 27.725 82-83 25.25 23.75 23.8125 27.187499999999996 84-85 26.487500000000004 23.3 23.3 26.9125 86-87 25.0 24.3625 23.05 27.5875 88-89 25.7875 24.05 23.175 26.987499999999997 90-91 25.724999999999998 24.474999999999998 22.4875 27.3125 92-93 25.4375 25.0125 23.4125 26.137500000000003 94-95 24.6125 24.2875 23.35 27.750000000000004 96-97 24.6875 24.337500000000002 23.35 27.625 98-99 26.224999999999998 23.125 23.625 27.025 100-101 25.587500000000002 24.2 22.675 27.537499999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 5.0 1 3.5 2 1.5 3 0.5 4 0.5 5 0.5 6 1.0 7 2.5 8 2.0 9 1.5 10 2.0 11 2.0 12 1.5 13 1.0 14 2.0 15 1.5 16 0.5 17 1.0 18 0.5 19 0.0 20 0.0 21 0.5 22 0.5 23 0.5 24 0.5 25 0.5 26 1.0 27 0.5 28 0.0 29 0.0 30 3.5 31 6.0 32 7.5 33 10.0 34 10.5 35 17.0 36 33.0 37 39.5 38 48.5 39 56.5 40 66.0 41 85.5 42 114.0 43 135.5 44 150.0 45 156.5 46 154.5 47 167.0 48 174.0 49 174.0 50 170.5 51 174.5 52 166.5 53 155.5 54 139.0 55 138.5 56 144.5 57 127.0 58 118.0 59 101.5 60 79.5 61 76.0 62 73.5 63 66.0 64 65.0 65 64.0 66 58.0 67 53.0 68 50.0 69 48.5 70 49.5 71 45.5 72 45.0 73 35.0 74 24.5 75 22.0 76 17.5 77 14.5 78 11.0 79 6.5 80 4.0 81 4.5 82 5.0 83 3.5 84 1.0 85 0.0 86 0.0 87 0.5 88 0.5 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 0.475 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 87.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 89.81745579007416 78.725 2 7.815173987450086 13.700000000000001 3 1.4831717056474614 3.9 4 0.513405590416429 1.7999999999999998 5 0.19965772960638906 0.8750000000000001 6 0.11409013120365087 0.6 7 0.028522532800912718 0.17500000000000002 8 0.0 0.0 9 0.028522532800912718 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 TCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATAT 9 0.22499999999999998 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 7 0.17500000000000002 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6 0.15 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 6 0.15 No Hit GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 6 0.15 No Hit TACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGAC 6 0.15 No Hit CCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCT 5 0.125 No Hit CTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATC 5 0.125 No Hit CCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTA 5 0.125 No Hit CCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGG 5 0.125 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 5 0.125 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 5 0.125 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 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 0.025 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.0625 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.1375 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 0.23750000000000002 0.0 0.0 0.0 0.0 44-45 0.2875 0.0 0.0 0.0 0.0 46-47 0.3 0.0 0.0 0.0 0.0 48-49 0.32499999999999996 0.0 0.0 0.0 0.0 50-51 0.375 0.0 0.0 0.0 0.0 52-53 0.4375 0.0 0.0 0.0 0.0 54-55 0.45 0.0 0.0 0.0 0.0 56-57 0.475 0.0 0.0 0.0 0.0 58-59 0.525 0.0 0.0 0.0 0.0 60-61 0.6499999999999999 0.0 0.0 0.0 0.0 62-63 0.825 0.0 0.0 0.0 0.0 64-65 1.0875 0.0 0.0 0.0 0.0 66-67 1.2125 0.0 0.0 0.0 0.0 68-69 1.4375 0.0 0.0 0.0 0.0 70-71 1.8375 0.0 0.0 0.0 0.0 72-73 2.075 0.0 0.0 0.0 0.0 74-75 2.375 0.0 0.0 0.0 0.0 76-77 2.8125 0.0 0.0 0.0 0.0 78-79 3.1500000000000004 0.0 0.0 0.0 0.0 80-81 3.45 0.0 0.0 0.0 0.0 82-83 3.7625 0.0 0.0 0.0 0.0 84-85 4.2875 0.0 0.0 0.0 0.0 86-87 4.825 0.0 0.0 0.0 0.0 88-89 5.4125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCACAA 15 0.009957196 47.5 12-13 AGCCGAC 15 0.009957196 47.5 30-31 >>END_MODULE ERR3450072 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450072_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.7635 37.0 37.0 37.0 37.0 37.0 2 35.7795 37.0 37.0 37.0 37.0 37.0 3 35.7005 37.0 37.0 37.0 37.0 37.0 4 35.962 37.0 37.0 37.0 37.0 37.0 5 36.1225 37.0 37.0 37.0 37.0 37.0 6 36.101 37.0 37.0 37.0 37.0 37.0 7 36.1755 37.0 37.0 37.0 37.0 37.0 8 36.1085 37.0 37.0 37.0 37.0 37.0 9 36.045 37.0 37.0 37.0 37.0 37.0 10-11 36.1045 37.0 37.0 37.0 37.0 37.0 12-13 36.091499999999996 37.0 37.0 37.0 37.0 37.0 14-15 36.06975 37.0 37.0 37.0 37.0 37.0 16-17 36.04325 37.0 37.0 37.0 37.0 37.0 18-19 36.03175 37.0 37.0 37.0 37.0 37.0 20-21 35.963750000000005 37.0 37.0 37.0 37.0 37.0 22-23 36.05275 37.0 37.0 37.0 37.0 37.0 24-25 35.980000000000004 37.0 37.0 37.0 37.0 37.0 26-27 35.963499999999996 37.0 37.0 37.0 37.0 37.0 28-29 35.889250000000004 37.0 37.0 37.0 37.0 37.0 30-31 35.8865 37.0 37.0 37.0 37.0 37.0 32-33 35.853750000000005 37.0 37.0 37.0 37.0 37.0 34-35 35.91825 37.0 37.0 37.0 37.0 37.0 36-37 35.902 37.0 37.0 37.0 37.0 37.0 38-39 35.758250000000004 37.0 37.0 37.0 37.0 37.0 40-41 35.78425 37.0 37.0 37.0 37.0 37.0 42-43 35.811 37.0 37.0 37.0 37.0 37.0 44-45 35.8055 37.0 37.0 37.0 37.0 37.0 46-47 35.7815 37.0 37.0 37.0 37.0 37.0 48-49 35.72 37.0 37.0 37.0 37.0 37.0 50-51 35.722 37.0 37.0 37.0 37.0 37.0 52-53 35.831999999999994 37.0 37.0 37.0 37.0 37.0 54-55 35.69825 37.0 37.0 37.0 37.0 37.0 56-57 35.67425 37.0 37.0 37.0 37.0 37.0 58-59 35.724 37.0 37.0 37.0 37.0 37.0 60-61 35.6185 37.0 37.0 37.0 37.0 37.0 62-63 35.65725 37.0 37.0 37.0 37.0 37.0 64-65 35.61875 37.0 37.0 37.0 37.0 37.0 66-67 35.67400000000001 37.0 37.0 37.0 37.0 37.0 68-69 35.5805 37.0 37.0 37.0 37.0 37.0 70-71 35.65975 37.0 37.0 37.0 37.0 37.0 72-73 35.6155 37.0 37.0 37.0 37.0 37.0 74-75 35.614999999999995 37.0 37.0 37.0 37.0 37.0 76-77 35.729749999999996 37.0 37.0 37.0 37.0 37.0 78-79 35.53775 37.0 37.0 37.0 37.0 37.0 80-81 35.6245 37.0 37.0 37.0 37.0 37.0 82-83 35.53725 37.0 37.0 37.0 37.0 37.0 84-85 35.6455 37.0 37.0 37.0 37.0 37.0 86-87 35.70275 37.0 37.0 37.0 37.0 37.0 88-89 35.643249999999995 37.0 37.0 37.0 37.0 37.0 90-91 35.665 37.0 37.0 37.0 37.0 37.0 92-93 35.68725 37.0 37.0 37.0 37.0 37.0 94-95 35.68725 37.0 37.0 37.0 37.0 37.0 96-97 35.685 37.0 37.0 37.0 37.0 37.0 98-99 35.7635 37.0 37.0 37.0 37.0 37.0 100-101 35.55575 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 3.0 16 2.0 17 8.0 18 9.0 19 4.0 20 8.0 21 10.0 22 11.0 23 14.0 24 8.0 25 23.0 26 11.0 27 17.0 28 26.0 29 34.0 30 49.0 31 54.0 32 55.0 33 71.0 34 111.0 35 297.0 36 2267.0 37 908.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.099999999999994 15.25 11.325000000000001 32.324999999999996 2 28.1 22.025 25.575 24.3 3 25.424999999999997 24.175 26.150000000000002 24.25 4 30.099999999999998 27.55 17.25 25.1 5 30.2 30.225 18.275 21.3 6 25.174999999999997 32.5 19.775000000000002 22.55 7 24.0 19.825 31.85 24.325 8 25.575 19.25 23.474999999999998 31.7 9 26.150000000000002 22.25 23.9 27.700000000000003 10-11 27.487499999999997 27.400000000000002 18.95 26.1625 12-13 28.325 21.675 23.1375 26.8625 14-15 27.175 25.0 23.0875 24.7375 16-17 28.262500000000003 24.474999999999998 21.675 25.587500000000002 18-19 27.287499999999998 25.45 22.3625 24.9 20-21 26.487500000000004 25.5625 22.4625 25.4875 22-23 28.549999999999997 23.7 22.8375 24.9125 24-25 27.750000000000004 24.6 22.625 25.025 26-27 27.2625 24.9375 22.7375 25.0625 28-29 28.425 24.887500000000003 21.525 25.162499999999998 30-31 26.950000000000003 25.362499999999997 22.0875 25.6 32-33 27.400000000000002 24.637500000000003 22.425 25.5375 34-35 27.487499999999997 24.55 22.275 25.687500000000004 36-37 28.000000000000004 25.35 21.9625 24.6875 38-39 26.6 25.7125 22.287499999999998 25.4 40-41 27.0875 24.15 22.8 25.9625 42-43 26.825 24.9 22.525000000000002 25.75 44-45 27.500000000000004 25.0 22.875 24.625 46-47 26.5375 24.075 23.25 26.137500000000003 48-49 26.450000000000003 25.2625 22.8375 25.45 50-51 27.8125 25.4625 22.025 24.7 52-53 27.212500000000002 25.45 22.912499999999998 24.425 54-55 27.900000000000002 23.9 23.2125 24.9875 56-57 26.4125 25.162499999999998 23.724999999999998 24.7 58-59 27.237499999999997 24.275 22.912499999999998 25.575 60-61 27.1375 24.5125 23.9 24.45 62-63 27.437499999999996 24.175 23.6875 24.7 64-65 27.025 23.3875 23.1125 26.474999999999998 66-67 28.1375 24.975 22.1 24.7875 68-69 27.0125 25.162499999999998 22.325 25.5 70-71 28.1 24.125 23.375 24.4 72-73 27.025 24.625 23.1625 25.1875 74-75 27.4125 23.7625 22.575 26.25 76-77 27.6 24.325 23.8625 24.212500000000002 78-79 26.75 24.125 23.849999999999998 25.275 80-81 27.5125 24.05 23.8625 24.575 82-83 27.625 23.575 23.0875 25.7125 84-85 28.125 24.0125 23.625 24.2375 86-87 28.1875 24.45 23.225 24.1375 88-89 29.012500000000003 24.725 21.0625 25.2 90-91 28.4125 24.375 22.675 24.5375 92-93 28.725 25.35 21.9375 23.9875 94-95 30.175 24.65 21.3 23.875 96-97 28.5625 25.687500000000004 21.9 23.849999999999998 98-99 28.7375 25.474999999999998 22.6 23.1875 100-101 29.062500000000004 25.087500000000002 22.0125 23.8375 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.5 5 1.0 6 1.5 7 2.0 8 1.5 9 0.5 10 0.0 11 0.5 12 2.0 13 2.0 14 1.0 15 0.5 16 0.0 17 1.0 18 2.0 19 2.5 20 2.0 21 1.0 22 1.5 23 1.5 24 1.5 25 2.5 26 2.0 27 0.5 28 3.0 29 4.0 30 4.0 31 3.5 32 1.0 33 4.5 34 11.5 35 16.5 36 27.5 37 40.5 38 44.5 39 50.5 40 67.5 41 86.0 42 113.0 43 129.0 44 142.5 45 159.5 46 153.5 47 159.0 48 168.0 49 168.5 50 162.0 51 152.0 52 150.0 53 155.0 54 148.0 55 135.0 56 133.5 57 132.0 58 118.0 59 94.0 60 79.5 61 69.5 62 71.0 63 77.0 64 69.0 65 63.0 66 73.5 67 73.0 68 63.0 69 54.5 70 53.5 71 52.5 72 44.0 73 40.5 74 30.0 75 25.5 76 26.0 77 17.0 78 13.0 79 11.5 80 7.5 81 5.5 82 1.5 83 1.0 84 1.0 85 0.5 86 0.5 87 0.0 88 0.0 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 1.0 99 1.0 100 2.0 >>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 89.275 #Duplication Level Percentage of deduplicated Percentage of total 1 91.094931391767 81.325 2 7.056846821618594 12.6 3 1.288154578549426 3.45 4 0.2800336040324839 1.0 5 0.11201344161299356 0.5 6 0.05600672080649678 0.3 7 0.02800336040324839 0.17500000000000002 8 0.05600672080649678 0.4 9 0.0 0.0 >10 0.02800336040324839 0.25 >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 CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 10 0.25 No Hit GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 8 0.2 No Hit GGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCAC 8 0.2 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 7 0.17500000000000002 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 6 0.15 No Hit GTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACG 6 0.15 No Hit CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGGGGCCTACCATGG 5 0.125 No Hit AGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAA 5 0.125 No Hit GGCCGGTCCGCCTCACGGCGAGCACCGACCTACTCGACCCTTCAGCCGGC 5 0.125 No Hit GCGGGCTTTGCTCGCTGATCCGATGATTCATGATAACTCGACGGATCGCA 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 0.025 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.0625 0.0 0.0 0.0 0.0 34-35 0.0875 0.0 0.0 0.0 0.0 36-37 0.1125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.1875 0.0 0.0 0.0 0.0 44-45 0.2375 0.0 0.0 0.0 0.0 46-47 0.25 0.0 0.0 0.0 0.0 48-49 0.275 0.0 0.0 0.0 0.0 50-51 0.32499999999999996 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.4 0.0 0.0 0.0 0.0 56-57 0.42500000000000004 0.0 0.0 0.0 0.0 58-59 0.475 0.0 0.0 0.0 0.0 60-61 0.6000000000000001 0.0 0.0 0.0 0.0 62-63 0.7625 0.0 0.0 0.0 0.0 64-65 1.0125 0.0 0.0 0.0 0.0 66-67 1.1375000000000002 0.0 0.0 0.0 0.0 68-69 1.3625 0.0 0.0 0.0 0.0 70-71 1.7625000000000002 0.0 0.0 0.0 0.0 72-73 2.0 0.0 0.0 0.0 0.0 74-75 2.3 0.0 0.0 0.0 0.0 76-77 2.7375 0.0 0.0 0.0 0.0 78-79 3.075 0.0 0.0 0.0 0.0 80-81 3.375 0.0 0.0 0.0 0.0 82-83 3.6875 0.0 0.0 0.0 0.0 84-85 4.2125 0.0 0.0 0.0 0.0 86-87 4.737500000000001 0.0 0.0 0.0 0.0 88-89 5.3125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCTAGAG 15 0.009957196 47.5 44-45 CGCCATC 15 0.009957196 47.5 24-25 TCTTCGG 15 0.009957196 47.5 30-31 >>END_MODULE Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125222 spots for ERR3450072.sra Written 2125222 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra Read 2125207 spots for ERR3450072.sra Written 2125207 spots for ERR3450072.sra SRR ids: ['ERR3450072.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jmxhgapn ERR3450072.sra spots: 42504155 blocks: [[1, 2125207], [2125208, 4250414], [4250415, 6375621], [6375622, 8500828], [8500829, 10626035], [10626036, 12751242], [12751243, 14876449], [14876450, 17001656], [17001657, 19126863], [19126864, 21252070], [21252071, 23377277], [23377278, 25502484], [25502485, 27627691], [27627692, 29752898], [29752899, 31878105], [31878106, 34003312], [34003313, 36128519], [36128520, 38253726], [38253727, 40378933], [40378934, 42504155]] ERR3450072 file size 10230766 ERR3450072 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 ERR3450072 ERR3450072_1.fastq ERR3450072_2.fastq Input file: ERR3450072_1.fastq Paired file: ERR3450072_2.fastq trimmed: ERR3450072-trimmed-pair1.fastq, ERR3450072-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 14:36:20 2024 >> started Sat Dec 7 14:37:08 2024 >> done (47.880s) 42504155 read pairs processed; of these: 217 ( 0.00%) short read pairs filtered out after trimming by size control 22014 ( 0.05%) empty read pairs filtered out after trimming by size control 42481924 (99.95%) read pairs available; of these: 3565842 ( 8.39%) trimmed read pairs available after processing 38916082 (91.61%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 54 0.00% 20 183 0.00% 21 461 0.00% 22 593 0.00% 23 254 0.00% 24 309 0.00% 25 385 0.00% 26 532 0.00% 27 798 0.00% 28 1228 0.00% 29 1512 0.00% 30 1882 0.00% 31 2335 0.01% 32 2488 0.01% 33 2329 0.01% 34 2349 0.01% 35 2299 0.01% 36 2678 0.01% 37 3085 0.01% 38 3594 0.01% 39 4244 0.01% 40 4907 0.01% 41 5899 0.01% 42 6588 0.02% 43 6825 0.02% 44 6337 0.01% 45 6295 0.01% 46 6809 0.02% 47 7949 0.02% 48 8666 0.02% 49 9533 0.02% 50 10785 0.03% 51 12136 0.03% 52 13221 0.03% 53 14066 0.03% 54 15096 0.04% 55 15940 0.04% 56 16548 0.04% 57 17145 0.04% 58 18991 0.04% 59 20958 0.05% 60 22388 0.05% 61 24948 0.06% 62 27813 0.07% 63 29822 0.07% 64 31297 0.07% 65 32344 0.08% 66 34292 0.08% 67 36585 0.09% 68 37961 0.09% 69 39790 0.09% 70 43059 0.10% 71 45831 0.11% 72 49721 0.12% 73 52914 0.12% 74 55789 0.13% 75 58625 0.14% 76 60487 0.14% 77 62882 0.15% 78 66225 0.16% 79 69578 0.16% 80 71940 0.17% 81 76145 0.18% 82 80960 0.19% 83 84693 0.20% 84 87784 0.21% 85 92646 0.22% 86 95434 0.22% 87 99884 0.24% 88 103090 0.24% 89 108916 0.26% 90 111539 0.26% 91 118537 0.28% 92 124755 0.29% 93 128291 0.30% 94 133245 0.31% 95 139665 0.33% 96 140533 0.33% 97 147594 0.35% 98 150539 0.35% 99 152545 0.36% 100 176435 0.42% 101 38916082 91.61% 42481924 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=2.48 fanout-score-rank=30 prefix-density=0.22 prefix-fanout=2.5 sequence=GTCAAATTAAGCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATAAGCAACATCCGCCGATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAGCGCATCGCCGGCTGAAGGGTCGAGTA criterion=fanout-score sequence-density=0.07 sequence-density-rank=28 fanout-score=176.95 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=21.1 sequence=CCGCCGCCGCCG criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=27 prefix-density=0.22 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=201.46 fanout-score-rank=1 prefix-density=0.69 prefix-fanout=22.9 sequence=CGGCGGCGGCGC ERR3450072 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:38:10 Started mapping on | Dec 07 14:38:11 Finished on | Dec 07 14:41:45 Mapping speed, Million of reads per hour | 714.65 Number of input reads | 42481924 Average input read length | 199 UNIQUE READS: Uniquely mapped reads number | 30494989 Uniquely mapped reads % | 71.78% Average mapped length | 198.56 Number of splices: Total | 19554386 Number of splices: Annotated (sjdb) | 18576784 Number of splices: GT/AG | 19294914 Number of splices: GC/AG | 223248 Number of splices: AT/AC | 12644 Number of splices: Non-canonical | 23580 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.17 Insertion rate per base | 0.01% Insertion average length | 1.89 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1811156 % of reads mapped to multiple loci | 4.26% Number of reads mapped to too many loci | 1732388 % of reads mapped to too many loci | 4.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.98% % of reads unmapped: other | 16.90% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10175779 10175779 10175779 N_multimapping 1811156 1811156 1811156 N_noFeature 896254 29478402 1464479 N_ambiguous 544527 4320 101939 UnstrandedReadsAssigned:29054208 PositiveStrandReadsAssigned:1012267 NegativeStrandReadsAssigned:28928571 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450072 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: ERR3450072-trimmed-pair1.fastq ERR3450072-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 42,481,924 reads, 30,405,147 reads pseudoaligned [quant] estimated average fragment length: 189.606 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,198 rounds 52973 ERR3450072.ke.tsv 35125 ERR3450072.se.tsv 88098 total ==> ERR3450072.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 747.601 0 0 PNS24247 1044 855.394 42.6061 2.4032 PNS24249 1928 1739.39 332.049 9.2106 PNS24246 1044 855.394 42.6061 2.4032 PNS24248 1044 855.394 42.6061 2.4032 PNS24244 1471 1282.39 46.133 1.7357 PNS24243 293 127.39 1 0.378748 KQK14069 1603 1414.39 1619.66 55.2508 KQK14071 474 289.65 65.1105 10.8458 ==> ERR3450072.se.tsv <== BRADI_1g14170v3 1709 BRADI_1g53295v3 23 BRADI_1g59795v3 309 BRADI_1g07683v3 0 BRADI_1g00485v3 95 BRADI_1g20270v3 8118 BRADI_1g74790v3 286 BRADI_1g09890v3 29 BRADI_1g77505v3 449 BRADI_1g48960v3 1 ERR3450072 completed mapping pipeline successfully