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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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phyloFlash_makedb.pl aborts during clustering: return code 152 #164

Open annettemcgrath opened 2 years ago

annettemcgrath commented 2 years ago

Hi and thanks for creating this tool. It appears to be exactly what I am looking for!

I am however having problems creating the database.

I am using phyloFlash v3.4 and trying to create a database for SILVA 138.1 . I got the following error message while it was running vsearch cluster-fast .

Clustering 72%[12:53:49] FATAL: Tool execution failed!. Error was 'No such file or directory' and return code '152' Aborting.

I also tried with SILVA 132 and received the same error with 33% clustered. Clustering 33%[15:00:26] FATAL: Tool execution failed!. Error was 'No such file or directory' and return code '152' Aborting.

The files for clustering using vsearch eg running subcommand: /apps/vsearch/2.17.1/bin/vsearch --cluster_fast ./132/SILVA_SSU.noLSU.masked.trimmed.fasta --id 0.99 --centroids ./132/SILVA_SSU.noLSU.masked.trimmed.NR99.fasta --notrunclabels --threads 128 exist in the appropriate folder and clustering seems to have started but dies mid-way through.

What does error code 152 mean and how can I fix the problem? Thanks for your help!

HansSCHR commented 2 years ago

Hi annettemcgrath, I have exactly the same issue. Did you find a solution to fix the problem? Thank you

annettemcgrath commented 2 years ago

Hi, unfortunately I didn't find a solution. I am still really interested in this tool. If you do find a solution, I'd love to hear about it! Thanks

kbseah commented 2 years ago

Did you find a solution to this problem? It sounds like it might be a filesystem issue, though.

annettemcgrath commented 2 years ago

Hi, sorry no solution to the problem. What should I check to confirm a filesystem issue? The clustering step starts, and gets quite some way through, before dying. Does the error code (152) shed any light?

kbseah commented 2 years ago

From what you describe it sounds like the job is being killed, not easy to diagnose from our side because we can't replicate the problem. It depends on the system that you're using: do you have a workstation or server that you use exclusively, or are you running the job on a cluster with job manager?

In the latter case, jobs may be killed if they use too much resources. You could check what the defaults are for run time and memory usage, and try increasing the requested resources if necessary. If that's not the case, could check your disk quota.

Sorry I can't offer a more specific solution.