Nullarbor reference errors

#1

Hi Matt,
| am doing two nullarbor runs using E. coli references I downloaded from GenBank. Both are giving a similar error.
Here’s the first,
Invalid --reference filename
Makefile:33: recipe for target ‘580-2/580-2/snps.tab’ failed
make: *** [580-2/580-2/snps.tab] Error 2

And for the second,

*** No rule to make target ‘/home/ubuntu/efn/concat_reads/trimmed_reads/gff_files_for_good_cov_genomes/E_coli_Sakai_ref.fasta’, needed by ‘ref.fa’. Stop.
make: Leaving directory ‘/home/ubuntu/efn/concat_reads/nullarbor_ST315_20Apr2018’

Are my references the issue please?
Grateful for your kind assistance,
Ebenn

#2

Based on the logs that you’ve provided, it looks like that’s the case, yes.

Check that all of the paths you provided to nullarbor.pl are correct, and also check the reference .fasta files - use less to check that they contain what you think they contain.

#3

You’re right–it had to do with the path. Thx! Sorted now. :muscle:

Cheers,
Ebenn

#4

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