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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
272 stars 49 forks source link

empty output file! #198

Closed marce-sarrias closed 3 years ago

marce-sarrias commented 3 years ago

Hello,

I'm running racon but for some reason I get an empty output file.

This is my code:

SBATCH -m 100G

SBATCH -c 100

racon -m 8 -x -6 -g -8 -w 500 -t 32 ./all.trimmed.fastq.gz ./mapped_reads.paf ./assembly.fasta > ./assembly.racon.fasta

size of my input files: 17G all.trimmed.fastq.gz 637M assembly.fasta 246M mapped_reads.paf

and this is what I get in the standard error file: [racon::Polisher::initialize] loaded target sequences 2.601033 s [racon::Polisher::initialize] loaded sequences 293.831238 s [racon::Polisher::initialize] loaded overlaps 3.346442 s [racon::Polisher::initialize] aligning overlaps [====================] 1257.327412 s [racon::Polisher::initialize] transformed data into windows 37.817850 s

Any idea of what the problem is?

Thank you!!

Marcela

rvaser commented 3 years ago

Hi Marcela, is there any error code reported by slurm? Is it still running? Do you have a time constraint on the server?

Best regards, Robert

marce-sarrias commented 3 years ago

Hi Robert,

Sorry for my late response. I do not get any error, I only get something like this (see below):

[racon::Polisher::initialize] loaded target sequences 2.601033 s [racon::Polisher::initialize] loaded sequences 293.831238 s [racon::Polisher::initialize] loaded overlaps 3.346442 s [racon::Polisher::initialize] aligning overlaps [====================] 1257.327412 s [racon::Polisher::initialize] transformed data into windows 37.817850 s

I can use up to 500 cores and 2000G total memory for 14 days. In this case racon run for about 20 min. I tried running it using the test data and I have the same problem (no errors and empty output file).

Marcela

rvaser commented 3 years ago

Weird. Which version are you using? Did you compile from source or are you using the conda executable?

marce-sarrias commented 3 years ago

Hi,

I just did this:

git clone --recursive https://github.com/lbcb-sci/racon.git racon cd racon mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release .. make

marce-sarrias commented 3 years ago

I also tried using a sam file instead of paf and still have the same issue.

rvaser commented 3 years ago

Try running cmake -Dspoa_optimize_for_portability=ON -DCMAKE_BUILD_TYPE=Release .. and make (from racon/build).

marce-sarrias commented 3 years ago

Hi Robert!

It worked! Thanks!!

Marcela