search

mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
Other
149 stars 27 forks source link

Ragout with HAL input #21

Closed stephenrdoyle closed 7 years ago

stephenrdoyle commented 7 years ago

Hi,

Just wondering if you have any example datasets / recipe files available for which you used a HAL file as input? Just trying to troubleshoot.

Best Steve

mikolmogorov commented 7 years ago

Sure, here is an example. hal_example.tar.gz

Let me know if you have more questions - you can write directly to fenderglass@gmail.com

jennomics commented 6 years ago

Hi! Thanks for providing the example files. I'm unable to get ragout to run using them.

I am running this, from within the hal_example directory:

/home/ubuntu/software/ragout-2.0-linux-x86_64/ragout.py cholerae.rcp -o example_out --refine --overwrite --threads 60

here's the error message:

[20:54:55] INFO: Starting Ragout v2.0 [20:54:55] ERROR: An error occured while running Ragout: [20:54:55] ERROR: Could not open target FASTA file or it is not specified

I am able to run halStats on the alignment, so I know HAL tools are working.

I'm running this on an AWS ubuntu instance, r4.16xlarge.

I appreciate your help in troubleshooting this!

mikolmogorov commented 6 years ago

You need to add '-s hal' option.

jennomics commented 6 years ago

thank you - it's working now. I figured I was overlooking something like that. appreciate the help!