Output directory MEGAHIT already exists, please change the parameter -o to another value to avoid overwriting.
s-junguy opened this issue · comments
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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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
I use v2.3.2. How can I update the latest version? I installed nextflow via the typical installation (not conda).
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
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.
I deleted the directory /home/user/.nextflow/assets/nf-core/mag and then executed nextflow pull. It worked. Thank you!
Glad you hear!