Starting /dee2/code/volunteer_pipeline.sh ERR6133331 current disk space = 1548192960512 free memory = 1604508152 ERR6133331 SRAfilesize 770fbfefbf4194a3b7c9e72c1a50a1d3 ERR6133331.sra ERR6133331.sra file validated ERR6133331 is single end ERR6133331 is conventional basespace ERR6133331 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133331_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.03375 37.0 37.0 37.0 33.0 37.0 2 36.561 37.0 37.0 37.0 37.0 37.0 3 36.59575 37.0 37.0 37.0 37.0 37.0 4 36.446 37.0 37.0 37.0 37.0 37.0 5 36.4635 37.0 37.0 37.0 37.0 37.0 6 36.5795 37.0 37.0 37.0 37.0 37.0 7 38.80025 40.0 37.0 40.0 37.0 40.0 8 38.88175 40.0 37.0 40.0 37.0 40.0 9 38.87975 40.0 37.0 40.0 37.0 40.0 10-11 38.833125 40.0 37.0 40.0 37.0 40.0 12-13 38.835750000000004 40.0 37.0 40.0 37.0 40.0 14-15 38.826750000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.7785 40.0 37.0 40.0 37.0 40.0 18-19 38.733625 40.0 37.0 40.0 37.0 40.0 20-21 38.69125 40.0 37.0 40.0 37.0 40.0 22-23 38.63825 40.0 37.0 40.0 37.0 40.0 24-25 38.5035 40.0 37.0 40.0 37.0 40.0 26-27 38.491875 40.0 37.0 40.0 37.0 40.0 28-29 38.568625 40.0 37.0 40.0 37.0 40.0 30-31 38.523875 40.0 37.0 40.0 37.0 40.0 32-33 38.44225 40.0 37.0 40.0 37.0 40.0 34-35 38.260625 40.0 37.0 40.0 37.0 40.0 36-37 38.215625 40.0 37.0 40.0 37.0 40.0 38-39 38.148875000000004 40.0 37.0 40.0 37.0 40.0 40-41 38.082750000000004 40.0 37.0 40.0 37.0 40.0 42-43 37.97225 40.0 37.0 40.0 37.0 40.0 44-45 37.842125 37.0 37.0 40.0 37.0 40.0 46-47 37.66575 37.0 37.0 40.0 37.0 40.0 48-49 37.518125 37.0 37.0 40.0 35.0 40.0 50-51 37.310500000000005 37.0 37.0 40.0 33.0 40.0 52-53 37.099000000000004 37.0 37.0 40.0 33.0 40.0 54-55 36.920500000000004 37.0 37.0 38.5 33.0 40.0 56-57 36.84925 37.0 37.0 37.0 33.0 40.0 58-59 36.643 37.0 37.0 37.0 33.0 40.0 60-61 36.500875 37.0 37.0 37.0 33.0 40.0 62-63 36.37025 37.0 37.0 37.0 33.0 37.0 64-65 36.20075 37.0 37.0 37.0 33.0 37.0 66-67 36.027125 37.0 37.0 37.0 33.0 37.0 68-69 35.195499999999996 35.0 35.0 37.0 33.0 37.0 70-71 35.39707786471479 37.0 35.0 37.0 33.0 37.0 72-73 35.78886515949735 37.0 37.0 37.0 33.0 37.0 74-75 35.72634404639049 37.0 37.0 37.0 33.0 37.0 76-77 35.81596726451754 37.0 37.0 37.0 33.0 37.0 78-79 35.802552435802816 37.0 37.0 37.0 33.0 37.0 80-81 35.717584868631405 37.0 37.0 37.0 33.0 37.0 82-83 35.59386190075014 37.0 37.0 37.0 33.0 37.0 84-85 35.612352106279815 37.0 37.0 37.0 33.0 37.0 86-87 35.5237556561086 37.0 33.0 37.0 33.0 37.0 88-89 35.508766968325794 37.0 35.0 37.0 33.0 37.0 90-91 35.440186651583716 37.0 33.0 37.0 33.0 37.0 92-93 35.37980769230769 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 4.0 23 2.0 24 6.0 25 11.0 26 4.0 27 13.0 28 16.0 29 18.0 30 24.0 31 37.0 32 37.0 33 59.0 34 97.0 35 199.0 36 668.0 37 1152.0 38 1560.0 39 91.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 63.66591647911978 9.977494373593398 8.927231807951989 17.429357339334832 2 46.025 27.3 15.425 11.25 3 30.099999999999998 37.65 18.25 14.000000000000002 4 30.175 26.3 22.6 20.925 5 26.5 25.575 27.375 20.549999999999997 6 22.0 31.3 28.375 18.325 7 31.525 27.224999999999998 23.95 17.299999999999997 8 27.450000000000003 28.575 27.675 16.3 9 26.6 25.3 29.825000000000003 18.275 10-11 24.9 27.5125 27.5125 20.075000000000003 12-13 24.6875 27.6875 28.875 18.75 14-15 21.2625 27.3125 31.5125 19.9125 16-17 24.4875 29.5 25.650000000000002 20.3625 18-19 24.637500000000003 25.4625 29.875 20.025000000000002 20-21 26.174999999999997 26.487500000000004 26.687499999999996 20.65 22-23 27.5625 24.2 26.025 22.2125 24-25 25.15 26.6 28.175 20.075000000000003 26-27 25.5 25.587500000000002 28.4375 20.474999999999998 28-29 24.9375 27.85 26.9125 20.3 30-31 23.974999999999998 27.6375 28.549999999999997 19.8375 32-33 24.5625 25.662499999999998 29.75 20.025000000000002 34-35 23.95 28.237499999999997 27.9375 19.875 36-37 23.2875 27.8625 25.912499999999998 22.9375 38-39 23.674999999999997 26.5125 28.5875 21.224999999999998 40-41 26.1 25.974999999999998 27.237499999999997 20.6875 42-43 25.4375 27.950000000000003 27.037499999999998 19.575 44-45 22.15 27.6 29.2375 21.0125 46-47 24.825 27.537499999999998 27.5875 20.05 48-49 23.625 26.700000000000003 28.7 20.974999999999998 50-51 22.912499999999998 27.462500000000002 30.6875 18.9375 52-53 24.625 27.725 28.787499999999998 18.862499999999997 54-55 24.6625 28.875 28.449999999999996 18.0125 56-57 23.8125 28.0875 28.762500000000003 19.3375 58-59 24.224999999999998 27.6125 28.6875 19.475 60-61 25.825 27.987499999999997 26.7625 19.425 62-63 22.1375 30.099999999999998 29.5 18.2625 64-65 23.090386298287285 29.87873484185523 28.478559819977495 18.552319039879986 66-67 24.212500000000002 29.312500000000004 27.150000000000002 19.325 68-69 22.925 29.062500000000004 27.6375 20.375 70-71 25.006279829188642 27.857322280833962 27.0032655111781 20.133132378799296 72-73 24.70963624760689 28.615188257817486 27.874920229738354 18.80025526483727 74-75 23.68182407047545 28.60474154683249 28.319730535043398 19.39370384764866 76-77 24.182319716274794 27.912780769735978 27.833968212268488 20.07093130172074 78-79 24.42015462543322 26.59290855771794 29.898693681684886 19.088243135163957 80-81 23.424156161041072 29.754642808729837 27.35529347973431 19.465907550494784 82-83 21.399063618837786 29.867805012393276 27.774717708620216 20.958413660148718 84-85 22.67678897792774 27.02094756080416 29.55152537607198 20.75073808519612 86-87 22.355769230769234 29.298642533936654 28.407805429864254 19.937782805429865 88-89 22.016402714932127 31.221719457013574 27.276583710407238 19.485294117647058 90-91 22.92138009049774 30.995475113122172 25.466628959276015 20.61651583710407 92-93 21.111425339366516 32.63574660633484 27.446266968325794 18.806561085972852 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 3.0 19 4.0 20 1.5 21 2.5 22 4.5 23 3.5 24 5.5 25 12.5 26 17.0 27 20.5 28 24.0 29 26.0 30 38.5 31 48.5 32 54.0 33 71.5 34 86.0 35 98.0 36 132.0 37 168.0 38 177.5 39 189.5 40 222.0 41 230.5 42 245.0 43 272.5 44 235.0 45 203.5 46 206.5 47 189.0 48 169.5 49 165.0 50 152.5 51 154.0 52 134.5 53 109.0 54 114.5 55 94.5 56 73.5 57 68.0 58 54.5 59 30.0 60 18.0 61 19.0 62 15.0 63 7.0 64 6.5 65 10.0 66 11.0 67 9.0 68 14.5 69 22.5 70 15.5 71 6.0 72 4.5 73 2.0 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 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 0.0125 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 38.0 71 32.0 72 25.0 73 29.0 74 33.0 75 22.0 76 29.0 77 26.0 78 30.0 79 34.0 80 27.0 81 26.0 82 36.0 83 36.0 84 41.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3536.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.625 #Duplication Level Percentage of deduplicated Percentage of total 1 90.70146818923328 69.5 2 4.600326264274062 7.049999999999999 3 1.5660685154975529 3.5999999999999996 4 0.9461663947797716 2.9000000000000004 5 0.7177814029363785 2.75 6 0.1957585644371941 0.8999999999999999 7 0.13050570962479607 0.7000000000000001 8 0.1631321370309951 1.0 9 0.13050570962479607 0.8999999999999999 >10 0.8482871125611746 10.7 >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 CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 39 0.975 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 38 0.95 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 29 0.7250000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 26 0.65 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 19 0.475 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 17 0.42500000000000004 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 17 0.42500000000000004 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 17 0.42500000000000004 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 17 0.42500000000000004 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 15 0.375 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 13 0.325 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 12 0.3 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 12 0.3 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 12 0.3 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 12 0.3 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 12 0.3 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 11 0.27499999999999997 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 10 0.25 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 9 0.22499999999999998 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 9 0.22499999999999998 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 8 0.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 8 0.2 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 8 0.2 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 6 0.15 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGA 6 0.15 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 6 0.15 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 5 0.125 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGGCGGACGTCTCGCCATGGTCGACGCTCTCACAAGTTGTTGTAATATTG 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 5 0.125 No Hit GCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGA 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GCGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGT 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit ATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAAT 5 0.125 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 5 0.125 No Hit GGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAA 5 0.125 No Hit CGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGG 5 0.125 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 5 0.125 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 5 0.125 No Hit GTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTA 5 0.125 No Hit CGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACT 5 0.125 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 5 0.125 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.0625 0.0 0.0 0.0 0.0 34-35 0.2 0.0 0.0 0.0 0.0 36-37 0.2 0.0 0.0 0.0 0.0 38-39 0.2 0.0 0.0 0.0 0.0 40-41 0.225 0.0 0.0 0.0 0.0 42-43 0.225 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 0.225 0.0 0.0 0.0 0.0 50-51 0.225 0.0 0.0 0.0 0.0 52-53 0.225 0.0 0.0 0.0 0.0 54-55 0.225 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.225 0.0 0.0 0.0 0.0 60-61 0.25 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.25 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.2625 0.0 0.0 0.0 0.0 78-79 0.275 0.0 0.0 0.0 0.0 80-81 0.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33746 READS because READLEN < 1 Read 33746 spots for ERR6133331.sra Written 33746 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra Rejected 33743 READS because READLEN < 1 Read 33743 spots for ERR6133331.sra Written 33743 spots for ERR6133331.sra SRR ids: ['ERR6133331.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_oxipif9x ERR6133331.sra spots: 674863 blocks: [[1, 33743], [33744, 67486], [67487, 101229], [101230, 134972], [134973, 168715], [168716, 202458], [202459, 236201], [236202, 269944], [269945, 303687], [303688, 337430], [337431, 371173], [371174, 404916], [404917, 438659], [438660, 472402], [472403, 506145], [506146, 539888], [539889, 573631], [573632, 607374], [607375, 641117], [641118, 674863]] ERR6133331 file size 146286 ERR6133331 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 ERR6133331 ERR6133331_1.fastq Input file: ERR6133331_1.fastq trimmed: ERR6133331-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 00:53:42 2024 >> started Sat Dec 7 00:53:43 2024 >> done (0.503s) 674863 reads processed; of these: 29 ( 0.00%) short reads filtered out after trimming by size control 2 ( 0.00%) empty reads filtered out after trimming by size control 674832 (100.00%) reads available; of these: 5608 ( 0.83%) trimmed reads available after processing 669224 (99.17%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 4 0.00% 20 3 0.00% 21 2 0.00% 22 4 0.00% 23 1 0.00% 24 2 0.00% 25 1 0.00% 26 5 0.00% 27 6 0.00% 28 23 0.00% 29 346 0.05% 30 2 0.00% 31 4 0.00% 32 10 0.00% 33 1156 0.17% 34 13 0.00% 35 13 0.00% 36 4 0.00% 37 9 0.00% 38 3 0.00% 39 24 0.00% 40 30 0.00% 41 8 0.00% 42 3 0.00% 43 7 0.00% 44 7 0.00% 45 8 0.00% 46 3 0.00% 47 3 0.00% 48 2 0.00% 49 3 0.00% 50 5 0.00% 51 18 0.00% 52 6 0.00% 53 5 0.00% 54 9 0.00% 55 3 0.00% 56 3 0.00% 57 9 0.00% 58 7 0.00% 59 14 0.00% 60 4 0.00% 61 11 0.00% 62 2 0.00% 63 4 0.00% 64 3 0.00% 65 3 0.00% 66 8 0.00% 67 10 0.00% 68 19 0.00% 69 28 0.00% 70 5517 0.82% 71 5055 0.75% 72 5262 0.78% 73 5110 0.76% 74 4986 0.74% 75 4749 0.70% 76 4577 0.68% 77 4848 0.72% 78 4969 0.74% 79 5162 0.76% 80 5083 0.75% 81 5930 0.88% 82 6190 0.92% 83 5634 0.83% 84 6175 0.92% 85 28 0.00% 86 24 0.00% 87 58 0.01% 88 89 0.01% 89 141 0.02% 90 251 0.04% 91 581 0.09% 92 1960 0.29% 93 590568 87.51% 674832 reads passed initial QC criterion=sequence-density sequence-density=3.84 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=22 prefix-density=3.91 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=24 fanout-score=71.83 fanout-score-rank=1 prefix-density=0.91 prefix-fanout=2.1 sequence=TTAAAAGATTTATTAGATAATCGAAAACAGAGGATCTTGAGTACTATTCGAAATTCGGAAGAATTGCGTAGAGGGACCTTTGAGCAGCTCGAAAAAGCTCGGATTCGATTACAGAAAGTCGAACTAGAAGCGGATGAGTATCGAATGAATGGATACTCTGAGATAGAACGAG Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:06:16 Started mapping on | Dec 07 01:06:16 Finished on | Dec 07 01:06:43 Mapping speed, Million of reads per hour | 89.98 Number of input reads | 674832 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 363886 Uniquely mapped reads % | 53.92% Average mapped length | 89.91 Number of splices: Total | 7687 Number of splices: Annotated (sjdb) | 6175 Number of splices: GT/AG | 7213 Number of splices: GC/AG | 185 Number of splices: AT/AC | 12 Number of splices: Non-canonical | 277 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.65 Insertion rate per base | 0.02% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 257384 % of reads mapped to multiple loci | 38.14% Number of reads mapped to too many loci | 33700 % of reads mapped to too many loci | 4.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.69% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 53562 53562 53562 N_multimapping 257384 257384 257384 N_noFeature 27228 30486 348278 N_ambiguous 14202 1857 50 UnstrandedReadsAssigned:322456 PositiveStrandReadsAssigned:331543 NegativeStrandReadsAssigned:15558 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133331 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: ERR6133331-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 674,832 reads, 481,636 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 846 rounds 52973 ERR6133331.ke.tsv 35125 ERR6133331.se.tsv 88098 total ==> ERR6133331.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 4 8.23502 PNS24243 293 194 0 0 KQK14069 1603 1504 6 11.2684 KQK14071 474 375 0 0 ==> ERR6133331.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 1 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 7 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 ERR6133331 completed mapping pipeline successfully