What is inside intermediate folder after qc and what can be removed to save space on device?

[bioinfogini]

Hello there,

I am posting this issue beacuse after running atlas qc on my samples, I find a new folder called Intermediate, that contains qc, which in turn contains decontamination. Inside decontamintation, I find a folder for each of my samples, containing fastq.gz files named PhiX and Host (as I was trying to ddecontaminate also for my host organism).

I would like to make sure about what this fastq.gz are.
Are they the sequences of Phix and host that were in my sequenced and in my sample?
Why do they get saved? Shall I remove them to save same space on my computer?

Thanks in advance.

[SilasK]

So they are the few? reads that map to host and phix for each sample.

If you want you can delete them.

[bioinfogini]

Got it, thanks!

[bioinfogini]

Actually @SilasK could you please tell me if there are any other folders I can remove?
I am trying to run the assembly and Atlas get stuck because there is no more space on the device.
Are there some not fundamental/temporary files I can remove? Or are there flags I can use to remove temporary files during assembly instead of when it completes?
Thanks in advance :)