Paul Turner

Many thanks for these replies...unfortunately no joy yet. For the first option (changed template filename to fc_spades.py and updated the .nf file accordingly), spades still fails with error exist status...

Thanks CreatorOfMoon - as far as I can tell that folder and log is not present in the tmp folder. Is it possible that this is part of the problem?...

Hi - thanks for working on this. I'm using singularity v 2.5.2. It seems to be working ok and i can pull containers successfully. ________________________________ From: Inês Mendes Sent: Wednesday,...

Thanks for this - I removed singularity and reinstalled (carefully) to version 3.6.3 following the instructions here: https://sylabs.io/guides/3.6/admin-guide/installation.html#installation-on-linux. There is a comment "By default Singularity will be installed in the...

An update - have just located the singularity.conf file and (I think) confirmed that /tmp is accessible: # MOUNT TMP: [BOOL] # DEFAULT: yes # Should we automatically bind mount...

OK - progress. I changed the pipeline params.config so that the scratch option was false (disableRR_1_2 = false)...this meant the spades files all ended up in the pipeline /work folder....

Thanks - am using Ubuntu 20.04 via WSL2. I wondered about that or whether its all a WSL issue. I've been having trouble with docker too. Am in the process...

Thank - yes, not that helpful. I've upped the memory to 48Gb and also tried with the SPAdes toy data, but no luck. Will try with another installation (virtualbox rather...

Resolution :-) ...thanks for all of your help with this I set up Ubuntu 18.04 using VirtualBox on my Windows machine, installed flowcraft using conda, and my spades pipeline worked...

I have the same issue...running ubuntu 20.04 via WSL2.