no output?

[hstern2]

Hi, we are trying to run raven 1.6.0 on x86_64, RHEL 7.9
we are not seeing any output with the following:

raven all_subreads.fq.gz interleaved.fq.gz

see attached, also log file..

Thanks for any suggestions!

all_subreads.fq.gz
interleaved.fq.gz

a.log

[rvaser]

Hello,
in Raven's GFA output there are two short non-circular sequences, ~8kbp and ~2kbp long, consisting of 3 connected reads each. Due to the small length, small amount of reads and non-circularity, Raven does not know what to do with them and does not polish/output them. You can get them with option --graphical-fragment-assembly raven.gfa and running awk '/^S/{print ">"$2;print $3}' raven.gfa > raven.fa. What is the expected output of your dataset (i.e. what did you sequence)?

Best regards,
Robert

[antoine4ucsd]

hello
just a quick follow up on this. I am new with raven. running on NP SIV data. I just tried

raven myfastq.gz

but only got a raven.cereal output. I was hoping to get fasta ouput that I could remap to my reference.

also I noticed you recommended to use rebaler if one is interested in mapping to ref and get a consenus. what would be the added value of a de novo assembly prior to rebaler. do you have any specific settings you'd recommend??

thank you!

[antoine4ucsd]

Hello
I just tried the following based on a closed issue:

raven -p 3 -t 30 input.fastq.gz > assembly.fa

but my output is empty. the only output I was able to get is the raven..cereal file.
How can I get a fasta output?
thank you +++

[rvaser]

Hi Antoine,
can you please tell me what NP SIV stands for?

Best regards,
Robert

P.s. Sorry for my late reply!

[antoine4ucsd]

sorry. nanopore simian immunodeficiency virus (~9kb)

[rvaser]

Raven has a cutoff on contig length at 10kbp. You can use option --graphical-fragment-assembly out.gfa and check if anything is inside.

On the other hand, does your data set even need assembly? Either 3rd gen sequencing technology could read the virus in whole and you can do some kind of multiple sequence alignment to get the consensus (not sure what your end goal is).

[antoine4ucsd]

thank you. I will give it a try.

[Lionward]

Raven has a cutoff on contig length at 10kbp. You can use option --graphical-fragment-assembly out.gfa and check if anything is inside.

On the other hand, does your data set even need assembly? Either 3rd gen sequencing technology could read the virus in whole and you can do some kind of multiple sequence alignment to get the consensus (not sure what your end goal is).
Hi,
I am facing a similar Problem, but while running raven in Python,
how can I use this command when I use ravenpy library?