search

cpouchon / REFMAKER

Make your own nuclear references from genomic assemblies of shotgun libraries.
4 stars 0 forks source link

Question in sample file #2

Closed lishuhanin closed 1 year ago

lishuhanin commented 1 year ago

Hello charles, I'm interesting in your soft REFMAKER.It can get the nuclear loci from low-coverage libraries.I want share it in my group meeting. But i try it in assemble step,I find i don't know how to correctly make Sample file.I made a samples.txt,like this image then ran ./refmaker -m assembly -o sample -p parameter.txt,appeared next situation

[INFO]: spades assembly run -2 --cov-cutoff auto -o res_refmaker/assembly/spades/Ajuga_decumbens_167911_AJ19 -t 4 -m 10 -k 55 SPAdes genome assembler v3.15.5

Usage: spades.py [options] -o spades.py: error: argument -2: expected 1 argument -2 --cov-cutoff auto -o res_refmaker/assembly/spades//mnt2/Lish/second_uncomplement_AJ/Ajuga_decumbens_167911/Ajuga_decumbens_167911_AJ19_1.fq.gz -t 4 -m 10 -k 55 SPAdes genome assembler v3.15.5

Usage: spades.py [options] -o spades.py: error: argument -2: expected 1 argument [INFO]: time ellapsed for assembly step: 0:0:1 (hh:mm:ss)

I don't know why appear this question.Could you tell me how to solution this question?I'm looking forward to your reply.

Thank you for your time,

Li shuhan

lishuhanin commented 1 year ago

I have modify the sample.txt,like this image Remenber choose Linux in the top tool! Now it is working. Thank you for your REFMAKER,i wish you will get more achievement in future. Best wishes

cpouchon commented 1 year ago

Hi Li, thank your for comment, I had also some issues about the format between Mac/Linux. Let me know if it is running properly. Best regards, Charles