Question: Problem running QUAST assembly evaluation: quast tries to write to read-only FS
0
gravatar for tospo
25 days ago by
tospo40
United Kingdom
tospo40 wrote:

I am trying to run QUAST to evaluate a spades assembly. Most of the analysis works and several plots are being created but then the tool crashes because it seems to be trying to write to the folder where the software is installed:

Running Contig analyzer...
Compiling Minimap2 (details are in /XXX/quast-5.0.2/quast_libs/minimap2/make.log and make.err)

[Errno 30] Read-only file system: '/XXX/quast-5.0.2/quast_libs/minimap2/make.log'

which is where the software is installed:

$ which quast.py
/XXX/quast-5.0.2/quast.py

I have to install the software on a read-only file system to use it on our cluster. Is there any way to tell quast to write those files somewhere else? I can't find anything in the manuals. Thanks!

quast spades • 112 views
ADD COMMENTlink modified 24 days ago • written 25 days ago by tospo40

It seems to be compiling minimap2, which seems strange for it to do at run time.

Do you already have minimap available within your $PATH? If Quast can find it automatically, it might circumvent the need to do that step at all (just a guess at this stage though).

ADD REPLYlink written 25 days ago by Joe16k

According to the manual QUAST needs following. Don't see minimap2 mentioned unless they include it in the source. In that case OP has not installed the software properly.

Its default pipeline requires:

Python2 (2.5 or higher) or Python3 (3.3 or higher)
GCC 4.7 or higher
Perl 5.6.0 or higher
GNU make and ar
zlib development files
In addition, QUAST submodules require:

Time::HiRes perl module for GeneMark-ES (gene prediction in eukaryotes)
Java 1.8 or later for GRIDSS (SV detection)
R for GRIDSS (SV detection)
ADD REPLYlink modified 25 days ago • written 25 days ago by genomax78k

I guess quast script is looking for create_minimap_output_dir function. But then this function is imported from quast_libs.ca_utils.misc (from https://github.com/ablab/quast/blob/master/quast_libs/contigs_analyzer.py).

ADD REPLYlink modified 25 days ago • written 25 days ago by cpad011212k
  1. QUAST default pipeline utilizes Minimap2.
  2. Functional elements prediction modules use GeneMarkS, GeneMark-ES, GlimmerHMM, Barrnap, and BUSCO.
  3. QUAST module for finding structural variations applies BWA, Sambamba, and GRIDSS.
  4. Bedtools for calculating raw and physical read coverage.
  5. Icarus also can use Circos if it is installed in PATH.
  6. QUAST-LG introduced modules requiring KMC and Red.
  7. MetaQUAST uses MetaGeneMark, Krona tools, BLAST, and SILVA 16S rRNA database.

(from: http://cab.spbu.ru/files/quast/latest-docs/manual.html)

However, Almost all tools listed above are built in into the QUAST package (copy/pasted). If those are not installed by any chance, install them and run quast.

ADD REPLYlink modified 25 days ago • written 25 days ago by cpad011212k

I can't find anything in the manuals

And yet: http://quast.sourceforge.net/docs/manual.html#sec2.3

-o <output_dir> Output directory. The default value is quast_results/results_<date_time>. Also, quast_results/latest symlink
is created.

Note: QUAST reuses existing alignments if run repeatedly with the same
output directory. Thus, you can efficiently reuse already computed
results when running QUAST with different parameters, or adding more
assemblies to the existing comparison.
ADD REPLYlink modified 25 days ago • written 25 days ago by WouterDeCoster42k

thanks but that is not the problem. I have provided a data output directory and the plots etc are being written to it. The problem is that quast is also trying to write some make files to a subdir of the directory where it is installed.

ADD REPLYlink written 25 days ago by tospo40

Try installing minimap first..then run quast. Mention the code and output directory in OP.

ADD REPLYlink modified 25 days ago • written 25 days ago by cpad011212k

ah, ok, yes, that might be the solution. Sorry, I didn't know minimap was a separate piece of software and didn't see it mentioned in the installation manual. I will look for it now. Thanks!

ADD REPLYlink written 25 days ago by tospo40

That was a guess from the log you posted...it may not be the solution. Try also having look at the tools listed here: https://github.com/ablab/quast/tree/master/quast_libs and check if they are installed on your system @ tospo

ADD REPLYlink modified 25 days ago • written 25 days ago by cpad011212k

As several people have pointed out, it appears that my quast installation (which is simply the extracted tar archive downloaded from the website with all the binaries) is trying to install another tool called "minimap". I am not familiar with this tool. Does anybody know whether this is the correct one: https://github.com/lh3/minimap2

ADD REPLYlink modified 25 days ago • written 25 days ago by tospo40

That is indeed the tool yes.

I would advise getting it installed properly and available through the PATH variable as I mentioned. I'm not sure what symlink/program name Quast will be expecting (likely minimap2 or minimap) so it should be available in PATH as somethign to that effect.

ADD REPLYlink written 25 days ago by Joe16k
1
gravatar for tospo
24 days ago by
tospo40
United Kingdom
tospo40 wrote:

Thanks for all the comments, it works now!

The solution was indeed to install minimap2 which I got here: https://github.com/lh3/minimap2, as suggested by several people in the comments.

ADD COMMENTlink written 24 days ago by tospo40
0
gravatar for genomax
25 days ago by
genomax78k
United States
genomax78k wrote:

Have you tried to specify a directory where you are able to write the results.

-o <output_dir>
Output directory. The default value is quast_results/results_<date_time>.
Also, quast_results/latest symlink is created.
ADD COMMENTlink written 25 days ago by genomax78k

I have indeed provided an output directory and that is not the problem. the problem is quast trying to write something to the directory where it is installed.

ADD REPLYlink written 25 days ago by tospo40
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