fasta_merge problem

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fasta_merge problem

Maria Jose Gomez Hughes
Hi!

I have been using maker to annotate an eukaryote genome. Since the genome was big (~3Gb), I divided it into 10 chunks with fasta_utils and run maker on each separately. After that, I used gff3_merge and fasta_merge to produce output for each of the chunks. Then I tried using these same tools for merging the different outputs into one, and while gff3_merge ran as expected, fasta_merge did not. I used the following command:

fasta_merge -o maker.all.proteins.fasta -i maker.chunk-00.proteins.fasta maker.chunk-01.proteins.fasta  maker.chunk-02.proteins.fasta  maker.chunk-03.proteins.fasta  maker.chunk-04.proteins.fasta maker.chunk-05.proteins.fasta  maker.chunk-06.proteins.fasta  maker.chunk-07.proteins.fasta maker.chunk-08.proteins.fasta  maker.chunk-09.proteins.fasta

But instead of running it just showed me the help page. I tried just running two of them, but that didn’t help either.

Any help will be much appreciated!

Maria Jose Gomez


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Re: fasta_merge problem

Carson Holt-2
The main function of fasta_merge is to use the datastore index file to find and concatenate fasta files spread throughout the datastore.  If you wish to merge a handful of fasta files into one because you made 10 chunks, you can simply merge the files you want using the Linux ‘cat’ command.

Example 1: ‘cat file1 file2 file3 file4 > merge.fasta'

Example 2: ‘cat *output/*.maker.proteins.fasta > merge.maker.proteins.fasta'

—Carson


On Aug 26, 2020, at 10:35 PM, Maria Jose Gomez Hughes <[hidden email]> wrote:

Hi!

I have been using maker to annotate an eukaryote genome. Since the genome was big (~3Gb), I divided it into 10 chunks with fasta_utils and run maker on each separately. After that, I used gff3_merge and fasta_merge to produce output for each of the chunks. Then I tried using these same tools for merging the different outputs into one, and while gff3_merge ran as expected, fasta_merge did not. I used the following command:

fasta_merge -o maker.all.proteins.fasta -i maker.chunk-00.proteins.fasta maker.chunk-01.proteins.fasta  maker.chunk-02.proteins.fasta  maker.chunk-03.proteins.fasta  maker.chunk-04.proteins.fasta maker.chunk-05.proteins.fasta  maker.chunk-06.proteins.fasta  maker.chunk-07.proteins.fasta maker.chunk-08.proteins.fasta  maker.chunk-09.proteins.fasta

But instead of running it just showed me the help page. I tried just running two of them, but that didn’t help either.

Any help will be much appreciated!

Maria Jose Gomez

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org