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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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Braker runtime #131

Closed kazuaki0816 closed 2 years ago

kazuaki0816 commented 4 years ago

I am running the following command. $ braker.pl --species=yourSpecies --cores 8 --genome=/home/Braker/genome.fasta.masked --prot_seq=/home/Braker/Protein_hints.fasta --prg=gth --bam=/home/Braker/RNAseq_hints.sorted.bam --softmasking --UTR=off --makehub --gff3 --AUGUSTUS_ab_initio --email=hoge@co.jp

The Braker run has not finished and the gth process has been in progress for about a month. I created Protein_hints.fasta by selecting and translating closely related transcripts assembly sequences using Transdecoder. The number of sequences is 853,133. Is the gth process protracted due to the number of protein sequences?

By the way, the genome assembly sequence includes scaffold sequences of 10 kb or less, and shows the following stats. Number of scaffolds: 67,748 Total assembly size: 2,871,809,165 Minimum length: 500 Average length: 42,389.6 Maximum length: 187,018,787

baizixiansheng commented 4 years ago

For the running time, I have kill the task, but the data is still uploaded. I wonder know how to stop the data being uploaded. There is my condition: -rw-r--r-- 1 chens customer 17G Feb 5 19:15 prot_addstop.fasta

KatharinaHoff commented 4 years ago

I am not sure what you mean. BRAKER should not upload data to any server.