Valentine Murigneux

Yes it is very likely to have insufficient memory. I have 31G and around 43G of compressed of human data. I am trying to run Ra on a larger memory...

Thanks Rhys, yes that is our concern as well. Actually we only used aviary recover so far as the assembly/polishing was already done outside of Aviary.

Hello, I encountered a similar issue when using the Pore-C-Snakemake pipeline within a conda environment, can you help Thank you Valentine

Hi Paul, This is a Flye error that seems to be linked to a high read coverage (1017) which could confuse Flye, it is similar to this issue: https://github.com/fenderglass/Flye/issues/128 Here...

@maddne No the assembly.fasta is an output file of the Flye step. The error is here: OSError: [Errno 30] Read-only file system Work dir: /home/bio/micropipe/micropipe/work/36/fa4934df1db68825ea7799ce4a2f88 Tip: you can try to...

@maddne have you checked that you have permission to write in the output folder? Did the previous steps of the pipeline generated expected output (trimming, filtering)? Can you send the...

@maddne can you post the nextflow.config file line 3 please? would you please be able to post the .command.run inside the work dir /home/bio/micropipe/micropipe/work/36/fa4934df1db68825ea7799ce4a2f88

Hi @bebatut, here is an example to illustrate what seems to be missing from the Metaphlan wrapper: This is the command human_join2 is doing for merge the HUMAN2 tables: the...