noporpoise
commented
6 years ago By default make just constructs the McCortex graph. To make VCFs you must request vcfs:
make -f my_job_script.mk CTXDIR=<mccortex_dir> MEM=40G NTHREADS=20 vcfsA reference is a requirement to construct a VCF file.
Apologies for the very delayed response.
Hi
I am trying to use McCortex to find variant between two strains of yeast. I have tried running it both with a reference and without using make-pipeline.pl and then make, but I don't get any output in the vcfs dir.
What I have done is: With reference: make-pipeline.pl -r ref.fa '31,41,51,61,71' output_dir V1vsV4_colour_list.tsv > my_job_script.mk make -f my_job_script.mk CTXDIR= MEM=40G NTHREADS=20
Without reference: make-pipeline.pl '31,41,51,61,71' output_dir V1vsV4_colour_list.tsv > my_job_script.mk make -f my_job_script.mk CTXDIR= MEM=40G NTHREADS=20
The V1vsV4_colour_list.tsv file looks like: V1 ../../trimmed/V1_S66_single.fastq.gz ../../trimmed/V1_S66_R1_paired.fastq.gz:../../trimmed/V1_S66_R2_paired.fastq.gz . V4 ../../trimmed/V4_S69_single.fastq.gz ../../trimmed/V4_S69_R1_paired.fastq.gz:../../trimmed/V4_S69_R2_paired.fastq.gz .
When running with the reference I get output in the bubbles_links, graphs, links and ref directories for each of the kmers. Running without reference I get output in bubbles_links, bubbles_plain, graphs and links. Looking at the log files I don't see any errors. Do you have any idea where I could have gone wrong?
Best, Ida