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skoren / bacValidation

BAC-based validation of assemblies
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Error in read.table("file_bacs.fasta.R") : no lines available in input #1

Open AG-Run opened 4 years ago

AG-Run commented 4 years ago

Dear Skoren:

Cordial greeting. Im running your script and I got the following error

Error in read.table("filegenome_bacs.fasta.R") : no lines available in input

Where filegenome was my input genome. The script once I parsed and compiled everything was

./getStats.sh filegenome.fasta bacs.fasta > test.txt

And bacs.fasta was the list of my bacs. I have the .fai files for both data,

what am I doing wrong?

Thanks

skoren commented 4 years ago

I think the issue is your command. The pipeline only takes one parameter, not two. The bacs.fasta file is assumed to exist, see the docs:

This pipeline assumes you have a file named bacs.fasta in the folder where you are running from your genome to validate. 

...

There is a single shell script, getStats.sh which takes one argument, a fasta file for your assembly.

The second parameter gets passed to minimap2 so I presume that broke the mappings resulting in nothing to read.