populations fail to open (create) boostrap archive file

[Dennis]

Hello,

I am a long time user of Stacks 2 and I really enjoy it!

But I am having some trouble running populations to create some f-statistics for my project. I am running version 2.68 of stacks 2 and populations on Ubuntu 24.04.4 LTS.

When I run the following command:
$ populations -t 12 --in-vcf ./populations.snps.vcf --out-path ./fstats/east/ --popmap ../popmap_east --fstats --fst-correction --bootstrap-fst --smooth-fstats

I get the following error:
Logging to './fstats/east/populations.snps.p.log'.
Locus/sample distributions will be written to './fstats/east/populations.snps.p.log.distribs'.
populations parameters selected:
  Input mode: VCF
  Percent samples limit per population: 0
  Locus Population limit: 1
  Percent samples overall: 0
  Minor allele frequency cutoff: 0
  Maximum observed heterozygosity cutoff: 1
  Applying Fst correction: P-value correction.
  Pi/Fis kernel smoothing: on
  F-stats kernel smoothing: on
  Bootstrap resampling: on, 100 reptitions per variable site
 

Parsing population map...

[Bunch of text about my 35 populations and 139 samples]

Error: Failed to open the boostrap archive file './fstats/east/populations.snps.p.bsarchive.tsv'.
Aborted.

I have checked that the folder exists:
$ ls fstats/east/
populations.snps.p.log  populations.snps.p.log.distribs

and it returns the two log files of the failed run, so it is there.

I tried to increase my ulimit from the default 4096 open files to 300,000 open files, which I can remember can be a problem:
$ ulimit -n 300000

$ ulimit -Hn
300000 

but it still fails with the same error.

If I try to run it without the '--bootstrap-fst' parameter it runs fine, so it is definitely a problem there.

I am also confused as to why it tries to create a bootstrap archive file when the '--bootstrap-archive' parameter isn't used/activated?

I am thankful for any help, Stacks 2 is a pleasure to use and I rarely have problems, especially in the last few years, but this is really confusing me!

[Angel Rivera-Colón]

Hi Dennis,

Thanks for using Stacks!

Before running --bootstrap-fst, did you run populations with --bootstrap-archive? If not, that should be the problem. Since the release of bootstrap resampling in version 2.60, the procedure takes two steps. First, you need to create an archive of the values to be sampled, running populations with --bootstrap-archive and the statistics of interest (e.g., Fst). Once that completes, you then rerun populations with --bootstrap (or in your case, --bootstrap-fst), which uses the archive generated on the first step to do the resampling. There's some examples of the usage in the populations docs page: https://catchenlab.life.illinois.edu/stacks/comp/populations.php. 

Hope this helps.

Thanks,

Angel

[Dennis]

Hi Angel,

Oh I had no idea that had changed in version 2.60. I have not used the fstats functionality since 2.60 so I had no idea this had changed. I did the archive then the bootstrap and now it works. Thanks!