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nf-core / mag

Assembly and binning of metagenomes
https://nf-co.re/mag
MIT License
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Output directory MEGAHIT already exists, please change the parameter -o to another value to avoid overwriting. #560

Closed s-junguy closed 5 months ago

s-junguy commented 5 months ago

Description of the bug

Hi, I use Illumina paired-end reads and got this error message megahit: Output directory MEGAHIT already exists, please change the parameter -o to another value to avoid overwriting.. I do not know where to put the option -o or how to change it.

I submitted nextflow run nf-core/mag --input samples.csv --outdir /home/s-junguy/magall -profile singularity -c ~/.nextflow/config --coassemble_group true -resume.

I also tried nextflow run nf-core/mag --input samples.csv --outdir /home/s-junguy/magall -profile singularity -c ~/.nextflow/config --coassemble_group true -resume --megahit_options="--continue -o out" but then MEGAHIT starts from the beginning even though it had almost finished before.

So my question is... how do I put the option -o in there so that the pipeline starts from where it broke off?

Command used and terminal output

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Relevant files

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System information

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jfy133 commented 5 months ago

Hi @s-junguy

Which version of the pipelinare you running?

We fixed this exact problem recently: https://github.com/nf-core/mag/pull/516/files

s-junguy commented 5 months ago

I use v2.3.2. How can I update the latest version? I installed nextflow via the typical installation (not conda).

jfy133 commented 5 months ago

To update the pipeline just run nextflow pull nf-core/mag -r 2.5.1 (if it doesn't work first time, try without the -r 2.5.1 and then try with it again). 2.5.1 is the current latest of version of the pipeline

If you need to update nextflow too< run nextflow self-update

s-junguy commented 5 months ago

Thanks for your help! I already updated nextflow. If I execute nextflow pull nf-core/mag I get the message: Checking nf-core/mag ... nf-core/mag contains uncommitted changes -- cannot pull from repository.

s-junguy commented 5 months ago

I deleted the directory /home/user/.nextflow/assets/nf-core/mag and then executed nextflow pull. It worked. Thank you!

jfy133 commented 5 months ago

Glad you hear!