Starting /dee2/code/volunteer_pipeline.sh ERR3450091 current disk space = 1542671519744 free memory = 1597505516 ERR3450091 SRAfilesize c341332045fe611e387d444d3ae8372a ERR3450091.sra ERR3450091.sra file validated ERR3450091 is paired end ERR3450091 is conventional basespace ERR3450091 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450091_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.01475 37.0 37.0 37.0 37.0 37.0 2 36.285 37.0 37.0 37.0 37.0 37.0 3 36.3825 37.0 37.0 37.0 37.0 37.0 4 36.521 37.0 37.0 37.0 37.0 37.0 5 36.473 37.0 37.0 37.0 37.0 37.0 6 36.468 37.0 37.0 37.0 37.0 37.0 7 36.4285 37.0 37.0 37.0 37.0 37.0 8 36.5025 37.0 37.0 37.0 37.0 37.0 9 36.4945 37.0 37.0 37.0 37.0 37.0 10-11 36.46625 37.0 37.0 37.0 37.0 37.0 12-13 36.52525 37.0 37.0 37.0 37.0 37.0 14-15 36.43075 37.0 37.0 37.0 37.0 37.0 16-17 36.42725 37.0 37.0 37.0 37.0 37.0 18-19 36.468 37.0 37.0 37.0 37.0 37.0 20-21 36.431 37.0 37.0 37.0 37.0 37.0 22-23 36.46425 37.0 37.0 37.0 37.0 37.0 24-25 36.40875 37.0 37.0 37.0 37.0 37.0 26-27 36.382000000000005 37.0 37.0 37.0 37.0 37.0 28-29 36.3155 37.0 37.0 37.0 37.0 37.0 30-31 36.3185 37.0 37.0 37.0 37.0 37.0 32-33 36.26325 37.0 37.0 37.0 37.0 37.0 34-35 36.2505 37.0 37.0 37.0 37.0 37.0 36-37 36.30925 37.0 37.0 37.0 37.0 37.0 38-39 36.278 37.0 37.0 37.0 37.0 37.0 40-41 36.27075 37.0 37.0 37.0 37.0 37.0 42-43 36.16075 37.0 37.0 37.0 37.0 37.0 44-45 36.19925 37.0 37.0 37.0 37.0 37.0 46-47 36.1655 37.0 37.0 37.0 37.0 37.0 48-49 36.08825 37.0 37.0 37.0 37.0 37.0 50-51 36.12425 37.0 37.0 37.0 37.0 37.0 52-53 36.046499999999995 37.0 37.0 37.0 37.0 37.0 54-55 36.096000000000004 37.0 37.0 37.0 37.0 37.0 56-57 36.087 37.0 37.0 37.0 37.0 37.0 58-59 36.11575 37.0 37.0 37.0 37.0 37.0 60-61 36.01375 37.0 37.0 37.0 37.0 37.0 62-63 36.046 37.0 37.0 37.0 37.0 37.0 64-65 35.887249999999995 37.0 37.0 37.0 37.0 37.0 66-67 35.877750000000006 37.0 37.0 37.0 37.0 37.0 68-69 36.00175 37.0 37.0 37.0 37.0 37.0 70-71 35.908 37.0 37.0 37.0 37.0 37.0 72-73 35.937 37.0 37.0 37.0 37.0 37.0 74-75 36.05875 37.0 37.0 37.0 37.0 37.0 76-77 35.963750000000005 37.0 37.0 37.0 37.0 37.0 78-79 35.978750000000005 37.0 37.0 37.0 37.0 37.0 80-81 35.925 37.0 37.0 37.0 37.0 37.0 82-83 35.94225 37.0 37.0 37.0 37.0 37.0 84-85 35.919 37.0 37.0 37.0 37.0 37.0 86-87 35.817499999999995 37.0 37.0 37.0 37.0 37.0 88-89 35.78425 37.0 37.0 37.0 37.0 37.0 90-91 35.76775 37.0 37.0 37.0 37.0 37.0 92-93 35.751000000000005 37.0 37.0 37.0 37.0 37.0 94-95 35.694 37.0 37.0 37.0 37.0 37.0 96-97 35.80475 37.0 37.0 37.0 37.0 37.0 98-99 35.80475 37.0 37.0 37.0 37.0 37.0 100-101 35.704 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 3.0 22 1.0 23 3.0 24 9.0 25 9.0 26 19.0 27 21.0 28 21.0 29 35.0 30 42.0 31 51.0 32 69.0 33 96.0 34 121.0 35 199.0 36 1718.0 37 1581.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.257121250315095 11.26796067557348 10.688177464078649 37.78674061003277 2 21.925 13.850000000000001 29.45 34.775 3 21.725 17.525 25.1 35.65 4 28.425 23.400000000000002 18.25 29.925 5 27.474999999999998 26.825 22.3 23.400000000000002 6 23.7 30.575000000000003 25.05 20.674999999999997 7 20.275000000000002 22.775000000000002 36.925000000000004 20.025000000000002 8 20.875 22.35 30.325000000000003 26.450000000000003 9 22.650000000000002 21.224999999999998 31.474999999999998 24.65 10-11 23.6625 28.499999999999996 22.787499999999998 25.05 12-13 25.224999999999998 23.200000000000003 23.875 27.700000000000003 14-15 23.7125 24.462500000000002 25.974999999999998 25.85 16-17 23.3375 24.6625 25.224999999999998 26.775 18-19 24.325 24.15 25.7125 25.8125 20-21 23.1625 24.462500000000002 25.137500000000003 27.237499999999997 22-23 24.474999999999998 24.087500000000002 24.2875 27.150000000000002 24-25 24.712500000000002 24.45 24.425 26.4125 26-27 23.8375 24.375 24.425 27.3625 28-29 24.3875 23.799999999999997 23.9875 27.825 30-31 24.2375 23.8875 23.775 28.1 32-33 24.5125 23.6125 24.375 27.500000000000004 34-35 24.9125 24.087500000000002 24.175 26.825 36-37 25.174999999999997 23.75 23.2375 27.8375 38-39 24.775 24.125 24.675 26.424999999999997 40-41 24.625 23.775 24.4 27.200000000000003 42-43 25.662499999999998 24.3625 23.9375 26.0375 44-45 23.575 23.9375 25.9625 26.525 46-47 25.4875 23.150000000000002 24.275 27.0875 48-49 24.65 24.7 24.1875 26.4625 50-51 24.474999999999998 24.075 23.875 27.575 52-53 25.4625 24.0375 23.3125 27.187499999999996 54-55 24.525 25.0625 24.05 26.3625 56-57 25.2375 23.075000000000003 25.0625 26.625 58-59 23.9875 24.5375 24.6875 26.787499999999998 60-61 25.2 22.925 24.65 27.224999999999998 62-63 25.374999999999996 24.0 24.3125 26.3125 64-65 25.412499999999998 23.7625 24.275 26.55 66-67 25.55 23.8625 24.2875 26.3 68-69 25.174999999999997 23.0625 24.75 27.0125 70-71 24.575 24.587500000000002 24.95 25.887500000000003 72-73 25.1 22.900000000000002 24.712500000000002 27.287499999999998 74-75 24.925 24.637500000000003 23.1625 27.275 76-77 26.237500000000004 24.575 23.05 26.137500000000003 78-79 25.112499999999997 24.125 24.0 26.7625 80-81 24.4 24.1375 24.0 27.462500000000002 82-83 26.387500000000003 24.0 22.675 26.937499999999996 84-85 25.662499999999998 23.6875 22.825 27.825 86-87 24.349999999999998 24.474999999999998 24.175 27.0 88-89 25.674999999999997 22.975 24.025 27.325 90-91 25.112499999999997 23.4375 24.275 27.175 92-93 25.575 23.875 25.0625 25.4875 94-95 24.337500000000002 25.424999999999997 23.175 27.0625 96-97 25.0625 23.7375 24.2375 26.9625 98-99 24.474999999999998 24.5625 24.4375 26.525 100-101 24.625 24.6125 23.575 27.187499999999996 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 10.0 1 5.5 2 1.5 3 1.5 4 1.0 5 1.5 6 1.5 7 1.0 8 1.5 9 1.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 0.5 21 1.0 22 2.0 23 1.0 24 2.0 25 3.0 26 1.0 27 0.5 28 2.0 29 2.5 30 2.5 31 5.0 32 6.5 33 7.5 34 11.0 35 16.5 36 34.5 37 43.5 38 48.5 39 56.5 40 71.5 41 91.5 42 121.0 43 154.0 44 160.0 45 166.0 46 174.5 47 179.5 48 180.5 49 181.5 50 172.5 51 154.5 52 145.5 53 136.0 54 132.0 55 136.0 56 131.0 57 113.5 58 99.0 59 90.0 60 84.5 61 79.0 62 72.0 63 75.5 64 80.0 65 70.5 66 59.5 67 53.5 68 52.5 69 58.0 70 48.5 71 37.5 72 35.5 73 31.5 74 22.5 75 14.5 76 12.5 77 11.5 78 13.0 79 9.0 80 6.0 81 5.5 82 2.5 83 1.0 84 0.5 85 1.0 86 0.5 87 0.0 88 0.5 89 0.5 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 0.8250000000000001 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 85.8 #Duplication Level Percentage of deduplicated Percentage of total 1 87.12121212121212 74.75 2 10.431235431235432 17.9 3 1.7482517482517483 4.5 4 0.49533799533799533 1.7000000000000002 5 0.05827505827505827 0.25 6 0.08741258741258741 0.44999999999999996 7 0.029137529137529136 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.029137529137529136 0.27499999999999997 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 7 0.17500000000000002 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 6 0.15 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 6 0.15 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 6 0.15 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 5 0.125 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.037500000000000006 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.1875 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.225 0.0 0.0 0.0 0.0 46-47 0.225 0.0 0.0 0.0 0.0 48-49 0.2625 0.0 0.0 0.0 0.0 50-51 0.2875 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.42500000000000004 0.0 0.0 0.0 0.0 56-57 0.575 0.0 0.0 0.0 0.0 58-59 0.675 0.0 0.0 0.0 0.0 60-61 0.875 0.0 0.0 0.0 0.0 62-63 1.1375000000000002 0.0 0.0 0.0 0.0 64-65 1.3125 0.0 0.0 0.0 0.0 66-67 1.4625 0.0 0.0 0.0 0.0 68-69 1.5875 0.0 0.0 0.0 0.0 70-71 1.875 0.0 0.0 0.0 0.0 72-73 2.0125 0.0 0.0 0.0 0.0 74-75 2.3625 0.0 0.0 0.0 0.0 76-77 2.8125 0.0 0.0 0.0 0.0 78-79 3.2125 0.0 0.0 0.0 0.0 80-81 3.4000000000000004 0.0 0.0 0.0 0.0 82-83 3.7125 0.0 0.0 0.0 0.0 84-85 4.2375 0.0 0.0 0.0 0.0 86-87 4.824999999999999 0.0 0.0 0.0 0.0 88-89 5.262499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450091 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450091_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 35.99 37.0 37.0 37.0 37.0 37.0 2 35.915 37.0 37.0 37.0 37.0 37.0 3 35.8885 37.0 37.0 37.0 37.0 37.0 4 36.0495 37.0 37.0 37.0 37.0 37.0 5 36.0575 37.0 37.0 37.0 37.0 37.0 6 36.1765 37.0 37.0 37.0 37.0 37.0 7 36.058 37.0 37.0 37.0 37.0 37.0 8 36.118 37.0 37.0 37.0 37.0 37.0 9 36.256 37.0 37.0 37.0 37.0 37.0 10-11 36.1185 37.0 37.0 37.0 37.0 37.0 12-13 36.14675 37.0 37.0 37.0 37.0 37.0 14-15 36.057500000000005 37.0 37.0 37.0 37.0 37.0 16-17 36.1945 37.0 37.0 37.0 37.0 37.0 18-19 36.156499999999994 37.0 37.0 37.0 37.0 37.0 20-21 36.1435 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 36.1385 37.0 37.0 37.0 37.0 37.0 26-27 36.1345 37.0 37.0 37.0 37.0 37.0 28-29 36.069 37.0 37.0 37.0 37.0 37.0 30-31 36.08525 37.0 37.0 37.0 37.0 37.0 32-33 36.0445 37.0 37.0 37.0 37.0 37.0 34-35 35.9695 37.0 37.0 37.0 37.0 37.0 36-37 36.021 37.0 37.0 37.0 37.0 37.0 38-39 35.941500000000005 37.0 37.0 37.0 37.0 37.0 40-41 35.922 37.0 37.0 37.0 37.0 37.0 42-43 35.986000000000004 37.0 37.0 37.0 37.0 37.0 44-45 35.9865 37.0 37.0 37.0 37.0 37.0 46-47 35.90375 37.0 37.0 37.0 37.0 37.0 48-49 35.9195 37.0 37.0 37.0 37.0 37.0 50-51 35.94175 37.0 37.0 37.0 37.0 37.0 52-53 35.9975 37.0 37.0 37.0 37.0 37.0 54-55 35.98025 37.0 37.0 37.0 37.0 37.0 56-57 36.0285 37.0 37.0 37.0 37.0 37.0 58-59 35.949 37.0 37.0 37.0 37.0 37.0 60-61 35.973749999999995 37.0 37.0 37.0 37.0 37.0 62-63 36.0095 37.0 37.0 37.0 37.0 37.0 64-65 35.922250000000005 37.0 37.0 37.0 37.0 37.0 66-67 35.90325 37.0 37.0 37.0 37.0 37.0 68-69 35.90425 37.0 37.0 37.0 37.0 37.0 70-71 35.83975 37.0 37.0 37.0 37.0 37.0 72-73 35.87675 37.0 37.0 37.0 37.0 37.0 74-75 35.852500000000006 37.0 37.0 37.0 37.0 37.0 76-77 35.707 37.0 37.0 37.0 37.0 37.0 78-79 35.701 37.0 37.0 37.0 37.0 37.0 80-81 35.751000000000005 37.0 37.0 37.0 37.0 37.0 82-83 35.820499999999996 37.0 37.0 37.0 37.0 37.0 84-85 35.77575 37.0 37.0 37.0 37.0 37.0 86-87 35.782 37.0 37.0 37.0 37.0 37.0 88-89 35.73950000000001 37.0 37.0 37.0 37.0 37.0 90-91 35.77325 37.0 37.0 37.0 37.0 37.0 92-93 35.804 37.0 37.0 37.0 37.0 37.0 94-95 35.73025 37.0 37.0 37.0 37.0 37.0 96-97 35.744249999999994 37.0 37.0 37.0 37.0 37.0 98-99 35.62325 37.0 37.0 37.0 37.0 37.0 100-101 35.69475 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 1.0 15 4.0 16 2.0 17 1.0 18 4.0 19 8.0 20 7.0 21 8.0 22 11.0 23 14.0 24 20.0 25 17.0 26 23.0 27 14.0 28 14.0 29 23.0 30 28.0 31 40.0 32 59.0 33 78.0 34 94.0 35 218.0 36 2050.0 37 1261.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.675000000000004 16.825000000000003 11.0 30.5 2 26.400000000000002 23.724999999999998 25.825 24.05 3 25.275 22.775000000000002 26.474999999999998 25.474999999999998 4 30.4 27.675 16.575 25.35 5 28.249999999999996 30.95 18.875 21.925 6 22.05 33.95 21.825 22.175 7 23.9 19.85 31.55 24.7 8 25.775 21.0 24.099999999999998 29.125 9 26.85 21.75 24.625 26.775 10-11 27.55 27.037499999999998 20.3 25.112499999999997 12-13 27.4125 22.6 22.7125 27.275 14-15 26.900000000000002 24.2375 24.125 24.7375 16-17 27.5875 25.412499999999998 22.787499999999998 24.212500000000002 18-19 28.199999999999996 24.3 22.025 25.474999999999998 20-21 26.875 24.962500000000002 23.75 24.4125 22-23 26.875 24.712500000000002 22.9875 25.424999999999997 24-25 26.825 24.4875 23.875 24.8125 26-27 26.950000000000003 25.674999999999997 22.85 24.525 28-29 27.250000000000004 24.762500000000003 22.625 25.362499999999997 30-31 27.35 24.962500000000002 22.925 24.762500000000003 32-33 27.250000000000004 24.725 23.0 25.025 34-35 28.0625 24.887500000000003 22.400000000000002 24.65 36-37 26.6 25.424999999999997 22.537499999999998 25.4375 38-39 26.187500000000004 25.275 23.0375 25.5 40-41 27.6 24.15 23.275000000000002 24.975 42-43 26.737499999999997 23.9375 22.662499999999998 26.6625 44-45 26.6625 24.5125 23.9375 24.887500000000003 46-47 26.887499999999996 25.362499999999997 22.0 25.75 48-49 27.6375 24.224999999999998 22.95 25.1875 50-51 26.174999999999997 25.4875 22.6 25.7375 52-53 27.437499999999996 25.45 21.4125 25.7 54-55 26.887499999999996 23.775 23.8375 25.5 56-57 26.900000000000002 24.425 23.7125 24.962500000000002 58-59 27.775 25.2375 22.3 24.6875 60-61 29.025000000000002 23.974999999999998 21.762500000000003 25.2375 62-63 28.225 24.3875 22.8875 24.5 64-65 28.525 24.5125 22.3125 24.65 66-67 28.0875 25.412499999999998 22.112499999999997 24.3875 68-69 28.15 25.7 21.987499999999997 24.1625 70-71 29.0875 24.3875 22.725 23.799999999999997 72-73 26.887499999999996 24.349999999999998 22.9625 25.8 74-75 26.5125 25.650000000000002 22.6375 25.2 76-77 27.462500000000002 25.2 22.7 24.637500000000003 78-79 27.3375 24.1625 23.6375 24.8625 80-81 27.825 24.1625 23.9 24.1125 82-83 28.349999999999998 25.25 22.4375 23.962500000000002 84-85 28.775000000000002 24.125 22.2 24.9 86-87 27.1625 24.65 23.200000000000003 24.9875 88-89 29.062500000000004 24.6875 21.975 24.275 90-91 28.325 25.6 22.0625 24.0125 92-93 28.9 24.887500000000003 22.0625 24.15 94-95 28.000000000000004 26.3125 21.8125 23.875 96-97 29.362500000000004 24.575 22.225 23.8375 98-99 28.249999999999996 25.0125 22.6 24.1375 100-101 28.712500000000002 25.6125 21.6625 24.0125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 1.0 4 1.5 5 1.0 6 1.5 7 2.0 8 1.0 9 0.5 10 0.5 11 1.5 12 2.0 13 2.0 14 4.5 15 3.5 16 1.0 17 1.0 18 1.5 19 2.5 20 1.5 21 0.5 22 1.0 23 1.5 24 2.5 25 2.5 26 2.0 27 2.5 28 3.0 29 2.0 30 0.5 31 3.0 32 5.0 33 6.5 34 14.5 35 19.5 36 27.5 37 37.5 38 45.0 39 64.5 40 78.0 41 96.5 42 122.0 43 133.0 44 137.0 45 149.0 46 166.5 47 168.5 48 167.5 49 163.0 50 155.0 51 158.0 52 153.0 53 147.5 54 146.0 55 121.0 56 105.5 57 115.5 58 118.0 59 106.0 60 87.0 61 75.0 62 68.0 63 68.5 64 77.0 65 66.5 66 59.5 67 58.0 68 58.0 69 65.5 70 59.5 71 50.0 72 46.5 73 40.0 74 24.0 75 22.5 76 24.0 77 15.0 78 10.5 79 7.0 80 4.0 81 5.0 82 6.0 83 3.5 84 1.5 85 0.5 86 0.0 87 0.0 88 0.5 89 0.5 90 0.5 91 0.5 92 0.5 93 1.5 94 1.0 95 0.5 96 1.0 97 2.0 98 3.0 99 1.5 100 3.5 >>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 86.52499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 87.05576422999133 75.325 2 10.97948569777521 19.0 3 1.5024559375902917 3.9 4 0.34672060098237506 1.2 5 0.08668015024559377 0.375 6 0.0 0.0 7 0.0 0.0 8 0.028893383415197923 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 5 0.125 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 5 0.125 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.037500000000000006 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.1375 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.175 0.0 0.0 0.0 0.0 48-49 0.21250000000000002 0.0 0.0 0.0 0.0 50-51 0.2375 0.0 0.0 0.0 0.0 52-53 0.3375 0.0 0.0 0.0 0.0 54-55 0.375 0.0 0.0 0.0 0.0 56-57 0.5249999999999999 0.0 0.0 0.0 0.0 58-59 0.625 0.0 0.0 0.0 0.0 60-61 0.825 0.0 0.0 0.0 0.0 62-63 1.0875 0.0 0.0 0.0 0.0 64-65 1.2625000000000002 0.0 0.0 0.0 0.0 66-67 1.4125 0.0 0.0 0.0 0.0 68-69 1.5375 0.0 0.0 0.0 0.0 70-71 1.8250000000000002 0.0 0.0 0.0 0.0 72-73 1.9625 0.0 0.0 0.0 0.0 74-75 2.2875 0.0 0.0 0.0 0.0 76-77 2.7625 0.0 0.0 0.0 0.0 78-79 3.1625 0.0 0.0 0.0 0.0 80-81 3.3499999999999996 0.0 0.0 0.0 0.0 82-83 3.6625 0.0 0.0 0.0 0.0 84-85 4.1875 0.0 0.0 0.0 0.0 86-87 4.775 0.0 0.0 0.0 0.0 88-89 5.1875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326333 spots for ERR3450091.sra Written 2326333 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra Read 2326328 spots for ERR3450091.sra Written 2326328 spots for ERR3450091.sra SRR ids: ['ERR3450091.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd___1i3lh6 ERR3450091.sra spots: 46526565 blocks: [[1, 2326328], [2326329, 4652656], [4652657, 6978984], [6978985, 9305312], [9305313, 11631640], [11631641, 13957968], [13957969, 16284296], [16284297, 18610624], [18610625, 20936952], [20936953, 23263280], [23263281, 25589608], [25589609, 27915936], [27915937, 30242264], [30242265, 32568592], [32568593, 34894920], [34894921, 37221248], [37221249, 39547576], [39547577, 41873904], [41873905, 44200232], [44200233, 46526565]] ERR3450091 file size 11201015 ERR3450091 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 ERR3450091 ERR3450091_1.fastq ERR3450091_2.fastq Input file: ERR3450091_1.fastq Paired file: ERR3450091_2.fastq trimmed: ERR3450091-trimmed-pair1.fastq, ERR3450091-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 15:08:16 2024 >> started Sat Dec 7 15:09:25 2024 >> done (69.286s) 46526565 read pairs processed; of these: 387 ( 0.00%) short read pairs filtered out after trimming by size control 89011 ( 0.19%) empty read pairs filtered out after trimming by size control 46437167 (99.81%) read pairs available; of these: 4540859 ( 9.78%) trimmed read pairs available after processing 41896308 (90.22%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 98 0.00% 20 330 0.00% 21 851 0.00% 22 1045 0.00% 23 540 0.00% 24 532 0.00% 25 735 0.00% 26 993 0.00% 27 1565 0.00% 28 2113 0.00% 29 2832 0.01% 30 3265 0.01% 31 4120 0.01% 32 4132 0.01% 33 3924 0.01% 34 4198 0.01% 35 4199 0.01% 36 4681 0.01% 37 5213 0.01% 38 5878 0.01% 39 7018 0.02% 40 8228 0.02% 41 9646 0.02% 42 10995 0.02% 43 11381 0.02% 44 10162 0.02% 45 10140 0.02% 46 10857 0.02% 47 11766 0.03% 48 12961 0.03% 49 14322 0.03% 50 15653 0.03% 51 17718 0.04% 52 19146 0.04% 53 20529 0.04% 54 21555 0.05% 55 22512 0.05% 56 23295 0.05% 57 24738 0.05% 58 27255 0.06% 59 29724 0.06% 60 31843 0.07% 61 34913 0.08% 62 37962 0.08% 63 41404 0.09% 64 42816 0.09% 65 44698 0.10% 66 46516 0.10% 67 49060 0.11% 68 51789 0.11% 69 53783 0.12% 70 57949 0.12% 71 62050 0.13% 72 66940 0.14% 73 70322 0.15% 74 73798 0.16% 75 76871 0.17% 76 79712 0.17% 77 82585 0.18% 78 85671 0.18% 79 90187 0.19% 80 93256 0.20% 81 97325 0.21% 82 103743 0.22% 83 107456 0.23% 84 112289 0.24% 85 116523 0.25% 86 119676 0.26% 87 124896 0.27% 88 128865 0.28% 89 133899 0.29% 90 137962 0.30% 91 144937 0.31% 92 151625 0.33% 93 155316 0.33% 94 161319 0.35% 95 166370 0.36% 96 169449 0.36% 97 175698 0.38% 98 178140 0.38% 99 181776 0.39% 100 208590 0.45% 101 41896308 90.22% 46437167 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=30 prefix-density=0.34 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.10 sequence-density-rank=20 fanout-score=51.01 fanout-score-rank=1 prefix-density=1.15 prefix-fanout=4.4 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACGTTCTCCGGCCGTCCTCCCCACGTCTTCAGGCACGTGTTCTGCAGCGCCCTCGCGTATGAGAAGGACACGTGCCACGGGTTCGGCGACTGGTTCATCGCGTTCAGGTTCAGCGTTGCCTCCACCTCTGACTGCCCGCCCGACAGGAACATGATGCCGGGGACGGAAGGAGGGATCCTCCTCTGGAGGAGCTTGAGGG criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=27 prefix-density=0.21 prefix-fanout=2.0 sequence=AGCCAGAGGAAA criterion=fanout-score sequence-density=0.09 sequence-density-rank=22 fanout-score=205.31 fanout-score-rank=1 prefix-density=0.79 prefix-fanout=22.2 sequence=CGGCGGCGGCGA ERR3450091 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:10:00 Started mapping on | Dec 07 15:10:00 Finished on | Dec 07 15:13:29 Mapping speed, Million of reads per hour | 799.87 Number of input reads | 46437167 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 34775294 Uniquely mapped reads % | 74.89% Average mapped length | 197.92 Number of splices: Total | 21369314 Number of splices: Annotated (sjdb) | 20269042 Number of splices: GT/AG | 21086254 Number of splices: GC/AG | 246435 Number of splices: AT/AC | 11336 Number of splices: Non-canonical | 25289 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2848499 % of reads mapped to multiple loci | 6.13% Number of reads mapped to too many loci | 1449196 % of reads mapped to too many loci | 3.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.09% % of reads unmapped: other | 12.77% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8813374 8813374 8813374 N_multimapping 2848499 2848499 2848499 N_noFeature 1157856 33401332 1989174 N_ambiguous 673997 5307 138979 UnstrandedReadsAssigned:32943441 PositiveStrandReadsAssigned:1368655 NegativeStrandReadsAssigned:32647141 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450091 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: ERR3450091-trimmed-pair1.fastq ERR3450091-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 46,437,167 reads, 34,877,116 reads pseudoaligned [quant] estimated average fragment length: 183.714 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,310 rounds 52973 ERR3450091.ke.tsv 35125 ERR3450091.se.tsv 88098 total ==> ERR3450091.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 753.498 0 0 PNS24247 1044 861.286 68.7203 3.41457 PNS24249 1928 1745.29 314.433 7.71009 PNS24246 1044 861.286 68.7203 3.41457 PNS24248 1044 861.286 68.7203 3.41457 PNS24244 1471 1288.29 93.4063 3.10286 PNS24243 293 130.028 0 0 KQK14069 1603 1420.29 17043.1 513.536 KQK14071 474 294.696 756.046 109.792 ==> ERR3450091.se.tsv <== BRADI_1g14170v3 18297 BRADI_1g53295v3 83 BRADI_1g59795v3 367 BRADI_1g07683v3 0 BRADI_1g00485v3 44 BRADI_1g20270v3 3218 BRADI_1g74790v3 441 BRADI_1g09890v3 19 BRADI_1g77505v3 447 BRADI_1g48960v3 1 ERR3450091 completed mapping pipeline successfully