btmartin721 / clinehelpr Goto Github PK

crazy.a and crazy.b are the columns listing whether the loci were significant with both outlier tests. Should rename these to something more intuitive, like e.g., snps$both.a and snps$both.b

Hello.
Thanks for this great package to visualize and explore bgc output.
I'm having a visualization issue with the phi plot that I haven't been able to figure out.
The image seems to be missing the portions of the curves extending from hybrid index = 0.95.
Can you help?
Regards

Hi there! Hope you are doing well. I'm fairly new to this and attempting to use the ClineHelpR functions on my bgc outputs, but keep running into the same error when I get to the get_bgc_ouliers step(see output below).

It fails my run each time at this step and never creates the gene.outliers object. I did make sure to include "loci.file=NULL" in my code and I'm only really interested in outputting the Phi Plots. So I'm not quite sure how to fix this issue. Any guidance would be fantastic. Thank you!

Hi Bradley,

thank you for your fantastic tool.

I am getting errors when running run_bgc.sh, and I have no idea where to look for the problem:

After:
Initializing MCMC chain
gsl: ../gsl/gsl_vector_int.h:182: ERROR: index out of range

I attached my input files and I'd be most grateful for any pointers.

Kind regards

Ludo

bgc_p1in.txt
bgc_p0in.txt
bgc_loci.txt
bgc_admixedin.txt
bgc_settings.txt

Hello,

I'm trying to convert my vcf file (from ipyrad) to bcg using vcf2bgc.py file. For this, I'm using your example data files download from DRYAD but I get an error:

./vcf2bgc.py -v eatt.trans.finalfilt.recode.vcf -m eatt.bgc.popmap_final.txt --p1 PureEA --p2 PureTT --admixed EATT -o example_tutorial

P1 population has 8 individuals...

P2 population has 8 individuals...

Admixed populalation has 85 individuals...

Processing 233 records in VCF file...

Traceback (most recent call last):
File "./vcf2bgc.py", line 378, in
main()
File "./vcf2bgc.py", line 140, in main
normalize_linkagemap(pos_list, pos_min, pos_max, chrom_number, linkage_fh, locus_list)
File "./vcf2bgc.py", line 192, in normalize_linkagemap
mylist[i] = (val - nmin) / (nmax - nmin)
ZeroDivisionError: integer division or modulo by zero

Does anybody have an idea what is wrong? Any help would be appreciated.
The same error occurs with my own data.

The package is really helpful, congrats!
Thank you!

Not sure it is only me but I had to change jinja2 version in environment.yml to 2.11.3 else conda could not resolve the environment

Hi! I would like to know whether there is a way to provide the hybrid index (admixture coefficient), calculated in previous analysis, in ClineHelpR like in HIEST: https://cran.r-project.org/web/packages/HIest/HIest.pdf

The idea is to avoid classifying individuals in discrete populations, but rather use a continuous measure of admixture coefficient.

Thank you so much!

Hi!

I'm in the process of creating my bgc input files. The genind2bgc function is taking a long time to run in RStudio, so I thought I would run the R script on our remote servers to free up my laptop.

I'm running the Rscript through the ClineHelpR conda environment, and I'm getting an error that the "genind2bgc" command is not recognized: Error in genind2bgc(gen = hybrid_0.8gmiss_0.3imiss_minDP5_srich_sp_remove, : could not find function "genind2bgc"

It looks like the genind2bgc is not included in any of the dependencies that were required for the ClineHelpR conda environment. Is there an R package conda install of ClineHelpR that I can install within the ClineHelpR environment?

Thanks!

Dear Martin:
I used the docker to run the bgc:
./bgc -a ~/test_file/YJS_newhybrids_chr10_filter_p0in.txt -b ~/test_file/YJS_newhybrids_chr10_filter_p1in.txt -h ~/test_file/YJS_newhybrids_chr10_filter_admixedin.txt -M ~/test_file/YJS_newhybrids_chr10_filter_map.txt -O 0 -x 50000 -n 25000 -p 1 -q 1 -N 1 -m 1 -D 0.5 -t 5 -E 0.0001 -d 1 -s 1 -I 0 -u 0.04

but it have something wrong like:

Reading input files
Number of loci: 1090786
Number of admixed populations: 1
Number of individuals: 6
Using the linkage model for locus effects
Allowing for uncertainty in allele counts
Allocating memory
gsl: init_source.c:40: ERROR: failed to allocate space for block data
Default GSL error handler invoked.
Aborted (core dumped)

I don't know how to deal with it, any guidance would be fantastic. Thank you!

Hi! I am trying to run vcf2bgc and I found this error:
$ vcf2bgc.py -v chr22_ldna.recode.vcf -m population_map.txt --p1 P1 --p2 P2 --admixed ADMIXED --outprefix clines_chr22

P1 population has 6 individuals...

P2 population has 8 individuals...

Admixed populalation has 67 individuals...

Processing 1563 records in VCF file...

Traceback (most recent call last):
File "/home/user/app/src/scripts/vcf2bgc.py", line 240, in get_allele_depth
alleles = call.data[2].split(",")
AttributeError: 'int' object has no attribute 'split'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/user/app/src/scripts/vcf2bgc.py", line 422, in
main()
File "/home/user/app/src/scripts/vcf2bgc.py", line 172, in main
write_output(record, popsamples, ref, alt, locus, args.outprefix, admix, p1, p2)
File "/home/user/app/src/scripts/vcf2bgc.py", line 285, in write_output
admix_output = get_allele_depth(record, "Admixed", ref, alt, sampledict)
File "/home/user/app/src/scripts/vcf2bgc.py", line 254, in get_allele_depth
raise AttributeError("Error with parsing allele depths!")
AttributeError: Error with parsing allele depths!

My vcf was generated with GATK 4. Any idea on what is going on?
Thank you so much!
Best wishes

Users are having issues when using Docker with the vcf2bgc.py script because I updated it. Need to rebuild the Docker image.

This function assumes that the lnl output suffix includes "LnL" but using the docker image the output in the suffix has "lnl" (lowercase).
Workaround: rename the output files changing the lnl to LnL

example:
bgc produces: test_stat_lnl_1
change it to: test_stat_LnL_1

Hello,

This R package helps me a lot!
I am trying to plot an Ideogram with the output of bgc. The species I am working on has a draft genome and I aligned this to the chromosome level before running bgc. Is it possible to plot the output with our fasta data which we mapped the reads or something, instead of pafscaff output file? Alternatively. perhaps I can create a dummy file of .scaffold.tdt in pafscaff. Can you give me details of the contents of the .scaffold.tdt?

Thank your very much in advance!

Hello,

First of all, thank you for giving us the opportunity to run BGC so easily.

I am having some trouble understanding my results. I attached the log likelihood and hybrid index graphs that I obtained from two runs (100000 burn-in / 200000 MCMC iterations). I did it only as a test and want to add more runs and probably also more MCMC iterations.

Could you help me understand why my two runs give quite different log likelihood and hybrid index. It looks to me like the model found convergence inside each run but is not coherent between runs.

All the best,

Loïc
ABH_hi_convergence.pdf
ABH_LnL_convergence.pdf

Hi btmartin,
I have already run BGC and plot BGC results, see below. How can I get the outlier SNP position in each chromosome?

All the best,
Danqi Li

estpost names the LnL file as Ln1. Need to fix. Ln1 doesn't make any sense.

I got it running with genind2bcg, but once I try to run:

bcg.genes I got an error although I have the files in the indicated directory.

Any ideas on what is wrong?
Thank you very much!

Add your vcf2bgc script to scripts/