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morispi / HG-CoLoR

Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads
GNU Affero General Public License v3.0
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Run fails and only prints 'Correcting the short reads' #19

Closed JuliaLopezDelgado closed 3 years ago

JuliaLopezDelgado commented 3 years ago

Hello,

I'm running HgColor (installed from the github repo) to correct Nanopore reads (~30x) using Illumina reads (~150x): /home/bin/HG_CoLoR/HG_CoLoR --longreads ONT_filtered.fasta --shortreads short.fastq --tmpdir ./tmp --out ONT_HgColor --solid 2 --bestn 30 --nproc 48 -K 101

However, it only runs for one second and stops, and prints the message: Correcting the short reads. The output directory doesn't contain any corrected reads.

What could be causing this issue?

Thanks, Julia

morispi commented 3 years ago

Hello,

This seems to indicate there's an issue with QuorUM. Do you have it installed and available through your PATH? If not, I advise you to follow the "Requirements" section of HG-CoLoR's README, all requirements and where to dowload them are provided here.

Please do contact me again if you encounter further issues.

Best, Pierre

JuliaLopezDelgado commented 3 years ago

Hello,

I specified the path and it works fine now! Thanks for your help.

Best wishes, Julia