The bioBakery help forum

Phylophlan_metagenomic crashed

Microbial community profiling PhyloPhlAn
#1

Hi,

We tried to run phylophlan_metagenomic on the tutorial data (PhyloPhlAn 3.0: Example 03: Metagenomic application · biobakery/biobakery Wiki · GitHub)

But we always get the following error:

[e] [Errno 121] Remote I/O error

[e] error while disting
    ['output_metagenomic_sketches/output_metagenomic_paste_1.msh']
    phylophlan_databases/SGB.Jan19/1669.msh
    output_metagenomic_dists/1669.tsv
    True

[e] [Errno 121] Remote I/O error

[e] disting crashed

Thanks in advance
Sabry

#2

Hi @Sabry,

thanks for reporting this, however, I believe the error you’re getting it is probably not due to phylophlan_metagenomic but it is probably more related to the machine.

I just re-run the example without any problems on my server.

Many thanks,
Francesco

#3

Hi

I had the same problem

[Errno 121] Remote I/O error

I guess this error is related to my use of parallel file systems (beegfs), so, I have a few questions for you:

(1) What is your file system, whether to run directly on native or parallel file systems
(2) Would it be convenient for you to find a beeGFS environment and test it to see if you get the same error we did
(3) Whether other parallel file systems are supported

Thanks in advance

#4

Hi @XiaogangBai and thanks for these details.
I’m not sure I’ll be able to test soon this as I’m not sure I’ll be able to set up an environment using beegfs.
Our computational infrastructure uses NFS to mount the storage on our machines and cluster nodes, but I’m not sure about what file system is implemented in our storage.

Thank you for your feedback!