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Dmitry-Antipov / viralFlye

viralFlye pipeline
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prodigal run failed #2

Open khoojj opened 1 year ago

khoojj commented 1 year ago

Hi, I'm trying the viralFlye pipeline for the first time today, starting with the directory from metaFlye output and the reads. My input command is the following:

~/tools/viralFlye/viralFlye.py --dir b1_flye/ --hmm /pub59/jingk/tools/pfam/Pfam-A.hmm.gz --reads /pub59/jingk/08_sispa_tickcellline/01_221115_sequencing/01_fas/b1.filt.fastq.gz --outdir b1_viralflye &> b1_viralflye_log.txt

From the log (attached), I see that "Prodigal run failed" keep turning up from the viralVerify step. b1_viralflye_log.txt

Is there a reason why the prodigal runs failed? Was it because there were no complete virus sequence?

iek commented 1 year ago

I am also having this issue!

Dmitry-Antipov commented 1 year ago

Hi. It's hard to suggest anything, prodigal's error message is not really informative...

Can you run prodigal on the viralFlye internal contigs, i.e. vv_circulars/circulars.fasta and vv_linears/linears.fasta ? Does it finish correctly?

mwylerCH commented 11 months ago

I have the same problem, however I guess it's because prodigal is running on empty/no files. However, I noticed, that viral Flye only selected the two longest contigs from my assembly, both low complexity contigs that will not be compatible with the pipeline (i.e. prodigal's error). Has viralFlye a length threshold?

concscid commented 4 months ago

Hi

I'm having the same issue on a sample from which I got a complete viral sequence running a hybrid metaviralSPAdes assembly. I can't find the internal contigs to run a test, any thoughts on how to overcome this issue?

Thank you.