No output file?

[desmodus1984]

Hi, I ran raven with the following commands and I got nothing out of it.

!/bin/bash

SBATCH --time=120:00:00

SBATCH --mem=170G

SBATCH --ntasks=48

SBATCH --job-name=Raven_ONTq-set1-1K

SBATCH --account=PHS0338

module load python && source activate assembly-Y raven ONTq-set1-1K.fa -t 48

Is there a way to get the output as a file - Fasta?

There are just a file called raven.cereal, and that's it.

I don't even know the final assemble size or anything... to check for completeness or else.

[rvaser]

Hello, the assembly is sent to stdout, so you have to redirect it to a file with > asm.fa. You do not have to rerun it from the beginning, just submit a resume run with raven ONTq-set1-1K.fa -t 48 --resume > asm.fa.

Best regards, Robert

[ardy20]

Hi Robert Thanks for this. It would be great if you add this into the main page.

[rvaser]

Hi, this information is written in the usage section of the README and when you run raven --help.

Best regards, Robert

[wanyuac]

Hi, this information is written in the usage section of the README and when you run raven --help.

Best regards, Robert

Sorry, but I could not find such information in the usage section or the output of raven --help (v2.8.1-b1676) as of today. In fact, I had the same issue just now, until I figured it out that raven writes outputs to stdin.

[rvaser]

Raven's latest version is 1.5.0, not sure what is with the version in brackets. If you run raven --help you get the following (I added an arrow to emphasize the output to stdout part):

usage: raven [options ...] <sequences>

  # default output is to stdout in FASTA format  <----------------------------------
  <sequences>
    input file in FASTA/FASTQ format (can be compressed with gzip)

  options:
    --weaken
      use larger (k, w) when assembling highly accurate sequences
    -p, --polishing-rounds <int>
      default: 2
      number of times racon is invoked
    -m, --match <int>
      default: 3
      score for matching bases
    -n, --mismatch <int>
      default: -5
      score for mismatching bases
    -g, --gap <int>
      default: -4
      gap penalty (must be negative)
    --graphical-fragment-assembly <string>
      prints the assembly graph in GFA format
    --resume
      resume previous run from last checkpoint
    --disable-checkpoints
      disable checkpoint file creation
    -t, --threads <int>
      default: 1
      number of threads
    --version
      prints the version number
    -h, --help
      prints the usage

[jpinus]

I used the "--resume" command, because "raven input.fa --resume > output.fa" always just generated a FASTA-file which was empty. But since today I experience an error when using the "--resume"-command: $ raven unmapped.fastq.gz --resume > test.fa [raven::] loaded previous run 4.904889s [raven::] loaded 2223978 sequences 216.895768s Illegal instruction

I also tried it with data that worked before but I get the same error.

any idea what can cause this?

[wanyuac]

My issue has been solved and raven works for me.