empty output file!

Question

empty output file!

marce-sarrias opened this issue 3 years ago · 7 comments

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

Answer 1 · 2021-09-23T01:12:47.000Z

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

Answer 2 · 2021-09-28T05:33:02.000Z

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

Answer 3 · 2021-09-28T07:47:34.000Z

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

Answer 4 · 2021-09-28T10:44:53.000Z

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

Answer 5 · 2021-09-28T10:45:38.000Z

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

Answer 6 · 2021-09-29T02:12:22.000Z

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

Answer 7 · 2021-09-29T06:11:17.000Z

Hi Robert!

It worked! Thanks!!

Marcela