No rule to make target

[stLFR]

Hello All,

I'm attempting to scaffold some contigs using physlr. Here is the full error:

make: *** No rule to make target '../ssb_interleaved.fq.gz.k40-w32.n100-5000.c2-x.physlr.overlap.m85.mol.mol2-bcs.backbone.path', needed by '../ssb_interleaved.fq.gz.physlr.physical-map.path'.  Stop.

And here's the command being run:

physlr-make scaffolds lr=../ssb_interleaved.fq.gz \
    draft=LinkedReads.contig_0.fasta \
    ref=hg38_no_alt_analysis_set.fa \
    protocol=stlfr

I'm not too adept with makefiles, so any help would be appreciated. Sorry for the trouble

[jwcodee]

physlr-make scaffolds lr=../ssb_interleaved \
    draft=LinkedReads.contig_0 \
    ref=hg38_no_alt_analysis_set \
    protocol=stlfr

Try this

[lcoombe]

@stLFR - I'd also suggest soft-linking the reads file to your current working directory. I've found that using paths in the makefile variables can sometimes cause errors.

[aafshinfard]

Closing due to inactivity