running the program from data on a hardrive

[gene-pool-CY]

Hi there,

I'm currently trying to run the program off a directory on an external hard drive (Crucial P3 PCIe Gen3 NVMe M.2 SSD - 4TB, USB C), as there isn't enough room on our communal lab computer (64 GB RAM, RTX 4090, 2TB drive).

Is this error because I'm not running the data from the Ubuntu directory directly? If so, is there a way to fix this?

I tried it before with a smaller dataset with the directory within Ubuntu, and it worked fine.

Sorry, I'm very much a novice.

[gene-pool-CY]

from the log: Running assembly with canu: perl /home/bih/miniconda3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_canu.pl /mnt/d/Metagenome/Pearse-lakes-metagenome-merged-2 Pearse-lakes-metagenome-merged-2 /mnt/d/Metagenome/Pearse-lakes-metagenome-merged-2/data/raw_fastq/par1.fastq mv: cannot stat '/mnt/d/Metagenome/Pearse-lakes-metagenome-merged-2/data/canu/Pearse-lakes-metagenome-merged-2.contigs.fasta': No such file or directory

[jtamames]

Hello My bet is that the assembly did not produce any contigs. You can try running canu using the command in the screen log to check it. Best, J

[gene-pool-CY]

So, it shouldn't matter if the directory is on an external drive? and more likely to be an issue with canu?

[jtamames]

You can check if the external drive is the reason for the failure by running the other dataset, the one you are sure is working, also on the external drive. If it works, then canu is likely to blame. If not, the external drive is. Best, J

[gene-pool-CY]

ok! that's a great idea!

[fpusan]

Closing due to lack of activity, feel free to reopen!