Issue using realSFS with conda install

[shannonekj]

Hi all,

I've been having an issue using realSFS where I've installed angsd via conda. (Version 0.931)

I use the following commands (with a sorted rf file):

angsd -bam random20.global_path.bamlist -out random20 -ref reference_genome.fa -anc reference_genome.fa -rf random20.loci -GL 2 -doSaf 1 -minMapQ 10 -minQ 20
realSFS random20.saf.idx -fold 1 -maxIter 100 > random20.folded.sfs

And I get the following error:

...
        -> Region lookup 375/376
[shared.cpp.changeChr():281] refid:44
Charnge chr:44
        -> Region lookup 376/376
[shared.cpp.changeChr():281] refid:45
Charnge chr:45

        -> Done reading data waiting for calculations to finish
        -> Done waiting for threads
        -> Output filenames:
                ->"random20.arg"
                ->"random20.saf.gz"
                ->"random20.saf.pos.gz"
                ->"random20.saf.idx"
        -> Sat May  1 10:52:14 2021
        -> Arguments and parameters for all analysis are located in .arg file
        -> Total number of sites analyzed: 16860739
        -> Number of sites retained after filtering: 16667329
        [ALL done] cpu-time used =  403.87 sec
        [ALL done] walltime used =  405.00 sec
realSFS random20.saf.idx -fold 1 -maxIter 100
        -> Version of fname:random20.saf.idx is:2
Problem with chr: , key already exists, saffile needs to be sorted. (sort your -rf that you used for input)

Curiously, when I run angsd from a module load angsd on another system, the exact same commands work perfectly. I'm looking to automate some steps of my pipeline (including these) so any help would be greatly appreciated!

Best,
Shannon

[janawold1]

Massive upvote as I'm having the same issue, but don't have another machine to try it on. :(

@shannonekj were you able to resolve this issue?

[zactobias44]

I was experiencing this same issue, @janawold1! Did you find a solution? It also seems to be related to #385. I was able to resolve this using the singularity container provided by @James-S-Santangelo. If your HPC is set up for Singularity, I'd recommend running angsd and all related tools using James' singularity recipe. https://cloud.sylabs.io/library/james-s-santangelo

If you make the saf files from within the container and also use the realSFS print command from within the container, you can access the data.

[janawold1]

Hi @zactobias44 cheers for the singularity recipe. Sadly, I did not make any progress with this. I'll double check to see if our HPC is set up for Singularity, but I don't think it is. Either way, I'll just have to give it a go!

Thanks again!