simonhmartin / dfs Goto Github PK

Hello-
I would like to ask for clarification as to how P1 and P2 are determined? I have been able to run DFS successfully for a few different populations within my dataset and was able to get DFS plots from R. However, I am not sure if P1 and P2 are determined by the order in which they are given in -FSpops flag in the sfs.py command line below? Or if somewhere in the various scripts there is someway the programs chose which population is P1 and P2, or somewhere else in another command line. In my case if the real phylogeny is (A,C)B,OutGroup, I listed the the populations in the --FSpops group as A C B to try to mimic the order of P1 P2 P3. Thank you for clarification.

python genomics_general-0.4/sfs.py -i mydata.basecounts.tsv.gz --inputType baseCounts \
--outgroup OG  --FSpops P1 P2 P3 --subsample 10 10 2 --pref mydata. --suff .subsample10.sfs

I have one plot where the red line that indicates the overall D value is not appearing. Haploid number is above 10 for P1 P2 and P3.
I can supply the input if needed for the R code. I was just wondering if this can happen for some datasets and why the line might not appear in the plot.

thank you.

Dear Simon,

I would like to explore DFS on the local shiny app but I seem to have issue with visualising the plot. Whenever I click the 'Run diffusion approximation and plot DFS', I get an error saying 'no lines available in input'. The corresponding R code given below:

"python3 sim_SFS_moments.py --Nsam 10 30 30 --twoPopPeriod T=0.1 N1=1 N2=1 m12=0 m21=0 --threePopPeriod T=0.1 N1=1 N2=1 N3=1 m12=0 m21=0 m23=0 m32=0 m13=0 m31=0 --threePopPeriod T=0.1 N1=1 N2=1 N3=1 m12=0.4 m21=0.4 m23=0 m32=0 m13=0 m31=0  2> /dev/null"
Warning in system(command, intern = TRUE, ignore.stderr = FALSE) :
  running command 'python3 sim_SFS_moments.py --Nsam 10 30 30 --twoPopPeriod T=0.1 N1=1 N2=1 m12=0 m21=0 --threePopPeriod T=0.1 N1=1 N2=1 N3=1 m12=0 m21=0 m23=0 m32=0 m13=0 m31=0 --threePopPeriod T=0.1 N1=1 N2=1 N3=1 m12=0.4 m21=0.4 m23=0 m32=0 m13=0 m31=0  2> /dev/null' had status 1
Warning: Error in read.table: no lines available in input

If I ignore the problems and click 'Save plots and data', I get an error going 'Warning: Error in segments: invalid fourth argument'

Any help would be greatly appreciated.

Dear Martin,

I have three species, for example, A, B, and C.
C could be the hybrid species between A and B.
I want to know the gene flow direction and introgression time in part of the hybrid genome of C (for example, the FST islands).
Is it ok to use Dfs? Is it robust to use Dfs in genomic windows?

Best regards,
Sandy

Hi, when I sun freq.py, there is an error：
Process Process-1:
Traceback (most recent call last):
File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib64/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/data/user003/soft/dfs/genomics_general-0.4/freq.py", line 55, in freqs_wrapper
baseFreqs = popAlns[pop].siteFreqs(asCounts=asCounts)
File "/data/user003/soft/dfs/genomics_general-0.4/genomics.py", line 1008, in siteFreqs
return np.array([binBaseFreqs(self.numArray[:,x][self.nanMask[:,x]], asCounts=asCounts) for x in sites])
File "/data/user003/soft/dfs/genomics_general-0.4/genomics.py", line 576, in binBaseFreqs
if asCounts: return np.bincount(numArr, minlength=4)
MemoryError
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written
37904 slices queued | 37903 slices analysed | 37903 slices written | 106800441 lines written

When I reduced threads to 1, the same error still appears. My genome is very large (10 Gb) and I don't know why this happen. Can you help me?