Unused argument

[jiadong324]

Dear author,

Thanks for developing this interesting tool! I've successfully tested on the demo data, but I got issues running the following command on my own assemblies.

I first tried the following command, but it gives me the unused arguments error.

nahrwhals(ref_fa='./T2T-CHM13v2.fasta',alt_fa='./HG00733.vkk.hap1.fasta',outdir='res',threads=10)

Then I found in your source code, the parameter is asm_fa instead of alt_fa as you used in README.md. Thus, I changed my code as below:

nahrwhals(ref_fa='./T2T-CHM13v2.fasta',asm_fa='./HG00733.vkk.hap1.fasta',outdir='res',threads=10)

However, I still got the unused arguments error.

Looking forward to your reply! Thanks!

[WHops]

Hi Jiadong,

Thx for your patience! I refactored bits and pieces of the code and made a new release. Could I ask you to install the latest version 1.4 and try again? Things should hopefully work now.

best Wolfy

[jiadong324]

Hi Wolfy,

I got another error

[1] "No region or regionfile provided. Running whole genome discovery mode." 
[1] "No minimap2 index \".mmi\" file of one of the fastas found. Creating one now (takes around 1 minute for a whole human genome assembly.)"
[1] "No minimap2 index \".mmi\" file of one of the fastas found. Creating one now (takes around 1 minute for a whole human genome assembly.)"  
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
 line 1 did not have 2 elements
In addition: Warning messages:
1: In read.table(fasta_awk_tmp_file, stringsAsFactors = FALSE) :
 line 2 appears to contain embedded nulls
2: In read.table(fasta_awk_tmp_file, stringsAsFactors = FALSE) :
 line 3 appears to contain embedded nulls
3: In read.table(fasta_awk_tmp_file, stringsAsFactors = FALSE) :
 line 4 appears to contain embedded nulls 

Here are the outputs under outdir

drwxrwsr-x 2 jdlin eichlerlab 4096 Apr 16 08:48 minimap_idxs
drwxrwsr-x 3 jdlin eichlerlab 4096 Apr 16 08:49 whole-genome-windows

[WHops]

Hi Jiadong,

I haven't seen this error before, and have not managed to reproduce it. One thing I did notice is that the program is allergic to tabs or spaces in the contignames. Can that explain your error? Otherwise, which OS are you using?

What I would suggest to debug:

• can you try if the error persists with another fasta? E.g., throwing hg38 in?
• do you get a tmpinfodeleteme[number].bed after your error? If so, could you share it?
• could you try if nahrwhals::get_fasta_info('./HG00733.vkk.hap1.fasta', 'out.txt') produces an out.txt file?
• can you try if the 'targeted' mode is working, by giving e.g. one random 1mbp reference region as input?

Thanks for sticking by! Anything that can help reproduce the error on my end would help a lot!

cheers Wolfy

[jiadong324]

Hi,

I used both hg38 and CHM13 with targeted mode. It works and I feel that this is more like a targeted caller.

FYI

I do have a binary output file from get_fasta_info('./HG00733.vkk.hap1.fasta', 'out.txt')

It would be great if this can be applied genome wide.

[jiadong324]

It is strange when I change to another regions, I get new errors:

[1] "Coordinates provided. Genotyping that region." 
[1] "Step 1: Identifying homologous regions in the y assembly" 
[1] "Step 2: Computing detailed pairwise alignment"
[1] "Step 3: Segmenting pairwise alignment"
[1] "Step 4: BFS search for mutation chains." 
ERROR: LoadError: ArgumentError: Package ArgParse not found in current path.
Run `import Pkg; Pkg.add("ArgParse")` to install the ArgParse package. 
Error in count.fields(juliares_path, sep = "\t") : 
cannot open the connection