populations - vcf output file empty, all others fine

[Melanie LaCava]

I have run the following sequence with Stacks:

1. process_radtags
   
2. denovo_map
3. rxstacks
4. cstacks
5. sstacks
6. populations

Up until running populations, everything seemed ok. When running populations, I used the following script:

populations -P [path] -M [path] -b 1 -k -r 0.6 -f p_value -t 8 --structure --genepop --vcf --write_random_snp

Populations ran fine and the structure and genepop output look great, but the vcf file is completely empty. I ran 11 iterations through all of the programs listed (varying parameters in denovo_map) and only 2 / 11 produced vcf files with data in them. The other nine are all blank.

Here are the iterations of parameters I ran in denovo_map (with the two that produced .vcf files in bold):

Test	-m	-M	-n	-X
denovo-test-a	3	2	2	ustacks:--max_locus_stacks 3
denovo-test-b	5	2	2	ustacks:--max_locus_stacks 3
denovo-test-c	7	2	2	ustacks:--max_locus_stacks 3
denovo-test-d	3	3	2	ustacks:--max_locus_stacks 3
denovo-test-e	3	4	2	ustacks:--max_locus_stacks 3
denovo-test-f	3	5	2	ustacks:--max_locus_stacks 3
denovo-test-g	3	2	3	ustacks:--max_locus_stacks 3
denovo-test-h	3	2	4	ustacks:--max_locus_stacks 3
denovo-test-i	3	2	5	ustacks:--max_locus_stacks 3
denovo-test-j	3	2	2	ustacks:--max_locus_stacks 4
denovo-test-k	3	2	2	ustacks:--max_locus_stacks 5

Any thoughts on why only the vcf output would not work, and why it would work for some parameter combinations and not others?

Thanks for any help,

Melanie

[Melanie LaCava]

FYI we solved this problem by matching 1) the number of tasks per node in our sbatch code to the cluster we are using, and 2) -t in the populations command. In all previous steps of the Stacks pipeline these numbers did not match and everything worked fine, but for some reason this solved out problem in populations. Odd fix, but it worked for us.