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Dmitry-Antipov / viralFlye

viralFlye pipeline
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Flye assembly directory not found #1

Open emmannaemeka opened 2 years ago

emmannaemeka commented 2 years ago

Hello, I ran this command

viralFlye.py --dir /Users/emmannaemeka/Documents/bioiformatics_program/viralFlye --hmm ~Pfam-A.hmm --reads ~ myfile_6.fq.gz --outdir ~viral_flye_pam_6

It returned the error Flye assembly directory not found: /Users/emmannaemeka/Documents/bioiformatics_program/viralFlye

Electrocyte commented 1 year ago

I have been having a similar issue, did you find a solution?

Dmitry-Antipov commented 1 year ago

Hi, Sorry, skipped the original message. Can you share the full log of the run?

Electrocyte commented 1 year ago

I realised my error: I needed to build the flye assembly first. I have a related question regarding that: do I use the original fasta file that I intend to use with viralflye, or would I be using a reference genome?

Dmitry-Antipov commented 1 year ago

Not sure that I get your question, but viralFlye does not use reference genomes.

Electrocyte commented 1 year ago

One of the requirements for viralflye is the --dir assembly generated using flye with --meta flag. When building the assembly in flye, what is the recommended input file - is it your sample fastq or a reference genome?

After generating the assembly, you then point viral flye at the assembly folder and then input your sample fastq/a

Is this correct?

SoSongzhi commented 3 months ago

I got the same question. what does --dir mean? thanks.