arks-make error : no rule to make target

[lebarsarthur]

Hello arks team,

I am trying to run arks+LINKS on my draft assembly, but I get the following error when running the pipeline "$ arks-make arks reads=xxx draft=xxx":

make: *** No rule to make target `/xx/xx/xx/xx/GENOME_ASSEMBLY/10x/ARKS/data/SN_all_pseudohap_arks.fasta.fa', needed by `/xx/xx/xx/xx/GENOME_ASSEMBLY/10x/ARKS/data/SN_all_pseudohap_arks.fasta.renamed.fa'.  Stop.

This error isn't very clear to me: I ran longranger basic on my fastq files, and supernova run + mkoutput from this data to generate my scaffolds, with success. "arks/Examples/arks-make" and binaries are also in PATH.

This is on CentOS 7. Also prior to running arks I activate a conda environment holding LINKS, sparsehash and time binaries. This is not human data if that makes any difference.

Any idea about what do I do wrong ?

Thank you

[lcoombe]

Hi @Mada2,
It looks like you are providing absolute paths to your arks-make command? Try making soft links (ln -s) to the reads and assemblies file in your working directory prior to running the makefile.
Also, make sure that your command is in this form (If you draft assembly is assembly.fa, and your post-longranger basic reads are lr.fq.gz):

arks-make arks reads=lr draft=assembly

Hope that helps!
Lauren

[lebarsarthur]

I was indeed giving the full path to my files to the arks-make arks command (I was already using symlinks as arguments)...

The problem is now fixed, thank you @lcoombe !

[lcoombe]

Glad to hear you got it working!