hiddenMarkovPloidyShell.R error
Closed this issue · 7 comments
peterdfields commented
Hi,
I've been trying to run the hiddenMarkovPloidyShell.R script on a set of genomes. The species has a genome size that's relatively small, ~ 20Mbp. The data is around 20X coverage. When I run the script with pretty much default parameters I get the following error:
Error in seq.default(loci[1], loci[length(loci) - 1], minSize) :
'to' must be a finite number
Calls: windowsBuilder -> seq -> seq.default
Execution halted
I tried running the example generated through using the simulation script and the script finished successfully so I assume that I might be doing something incorrectly in either generating the mpileups or the way these pileups are being handled by the genotypelikelihood script? Anyway, please let me know if additional info would be useful in troubleshooting this error.
SamueleSoraggi commented
Hi, thanks for highlighting a problem :)
I am actually working on a final version to send it for publication, but
however the function that gives you problems is still the same, so let's
look at it.
I think you got the genotype likelihood function working alright, it looks
like the software has been reading its output files in, but just to be
sure, could you send me just some of the first lines of the output file
from the genotype likelihood function?
It is probable that you have a window of loci with no SNP. Try to change
the parameter 'wind' to a larger value than it is now, such as
'wind=100000' to specify the size of a window of loci. If the window is
larger, it is more likely to get SNPs into it.
Let me know what happens - in the meanwhile I will implement a check for
solving the problem of missing loci in windows for the new version.
Cheers,
Samuele
Den søn. 26. maj 2019 kl. 23.33 skrev peterdfields <notifications@github.com
…:
Hi,
I've been trying to run the hiddenMarkovPloidyShell.R script on a set of
genomes. The species has a genome size that's relatively small, ~ 20Mbp.
The data is around 20X coverage. When I run the script with pretty much
default parameters I get the following error:
Error in seq.default(loci[1], loci[length(loci) - 1], minSize) :
'to' must be a finite number
Calls: windowsBuilder -> seq -> seq.default
Execution halted
I tried running the example generated through using the simulation script
and the script finished successfully so I assume that I might be doing
something incorrectly in either generating the mpileups or the way these
pileups are being handled by the genotypelikelihood script? Anyway, please
let me know if additional info would be useful in troubleshooting this
error.
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peterdfields commented
Hi Samuele,
Thank you for getting back to me about this. First, a few lines from one of the genolikes files:
contig-0001 23 1 C 7 C G 4 3 -29.546180618212716 -38.47318403662433 -29.546180618212716 -4.852929694697231 -38.47318403662433 -29.546180618212716 -4.9185838524274095 -5.611531933164633 -38.47318403662433 -29.546180618212716 -5.310387976793086 -4.852929694697231
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contig-0001 29 1 A 9 A G 5 4 -37.322551304877244 -48.09262088789451 -37.322551304877244 -6.240238097597288 -48.09262088789451 -37.322551304877244 -6.423298994489124 -7.116746181486449 -48.09262088789451 -37.322551304877244 -6.984596963043472 -6.240238097597288
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contig-0001 31 1 A 10 A G 5 5 -47.63140083908785 -48.32257282443038 -47.63140083908785 -6.933112259052867 -48.32257282443038 -47.63140083908785 -7.521723263333335 -7.5219215117477365 -48.32257282443038 -47.63140083908785 -8.370799660803966 -6.933112259052867
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contig-0001 33 1 C 11 C T 6 5 -48.33815223623277 -53.565441823043464 -48.33815223623277 -7.63661735785008 -53.565441823043464 -48.33815223623277 -7.940351708691136 -8.625500433637177 -53.565441823043464 -48.33815223623277 -8.672669849735 -7.63661735785008 -9.757094021923859 -53.565441823043464 -48.33815223623277 -9.401287785987362 -7.660129815767198 -8.06114740121917 -10.767678320638774 -53.565441823043464 -48.338152236232766 -10.067904908549696 -7.940351708691136 -7.63661735785008 -8.625500433637175 -11.65192946185854 -53.56544182304346
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contig-0001 50 1 G 12 G A 6 6 -54.02587765896604 -59.11684608920717 -54.02587765896604 -8.335816190673084 -59.11684608920717 -54.02587765896604 -9.033929240292911 -9.046596358880086 -59.11684608920717 -54.02587765896604 -10.044703937345947 -8.335816190673084
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contig-0001 53 1 A 13 A T 7 6 -59.10423403376158 -64.56508882890974 -59.10423403376158 -9.020609583060734 -64.56508882890974 -59.10423403376158 -9.441585438763886 -10.128391402981455 -64.56508882890974 -59.10423403376158 -10.343639542034946 -9.020609583060734
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contig-0001 102 1 G 23 A G 14 9 -86.3360340808479 -136.03808097096726 -86.3360340808479 -15.945550652201419 -136.03808097096726 -86.3360340808479 -15.566954016959196 -19.03236574964768 -136.03808097096726 -86.3360340808479 -16.506596807572443 -15.945550652201419
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contig-0001 356 1 A 32 A C 16 16 -151.13099690274137 -155.5090349408413 -151.13099690274137 -22.187146148192063 -155.5090349408413 -151.13099690274137 -24.07008849386364 -24.071651983505177 -155.5090349408413 -151.13099690274137 -26.786525010268026 -22.187146148192063
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contig-0001 362 1 C 32 C T 18 14 -130.28378740078176 -172.46472406234133 -130.28378740078176 -22.202324345922378 -172.46472406234133 -130.28378740078176 -22.69182515676477 -25.476486359671547 -172.46472406234133 -130.28378740078176 -24.590148707124015 -22.202324345922378
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contig-0001 367 1 G 33 A G 17 16 -153.89945185499536 -156.60524982047804 -153.89945185499536 -22.882262903367923 -156.60524982047804 -153.89945185499536 -24.47921498421295 -25.17004973498719 -156.60524982047804 -153.89945185499536 -27.078964532716984 -22.882262903367923
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The snp density is relatively high in the sample. I tried increasing window size but the error remains the same. One thing I want to note in case it's the basis of the problem is I've generated a genolike file for each individual rather than a combine genolike file for all individuals. Could this be the cause of the problem?
Cheers
Peter
SamueleSoraggi commented
I think your genotype likelihoods file looks fine, and I can see indeed
that SNPs are there. Can I see the command you use to run the software?
Regarding the genolike file, if you generate it for only one individual,
then you will estimate population frequencies only using the information
from one individual, and not from all of them, but this should not be the
cause of any error.
Den man. 27. maj 2019 kl. 12.34 skrev peterdfields <notifications@github.com
…:
Hi Samuele,
Thank you for getting back to me about this. First, a few lines from one
of the genolikes files:
contig-0001 23 1 C 7 C G 4 3 -29.546180618212716 -38.47318403662433 -29.546180618212716 -4.852929694697231 -38.47318403662433 -29.546180618212716 -4.9185838524274095 -5.611531933164633 -38.47318403662433 -29.546180618212716 -5.310387976793086 -4.852929694697231
-6.408646329792864 -38.47318403662433 -29.546180618212716 -5.721530332894191 -4.7930919521503155 -5.198446446799095 -7.107327002251342 -38.47318403662433 -29.54618061821271 -6.105063111625855 -4.9185838524274095 -4.85292969469723 -5.611531933164631 -7.71386401875268 -38.473184036624325
contig-0001 29 1 A 9 A G 5 4 -37.322551304877244 -48.09262088789451 -37.322551304877244 -6.240238097597288 -48.09262088789451 -37.322551304877244 -6.423298994489124 -7.116746181486449 -48.09262088789451 -37.322551304877244 -6.984596963043472 -6.240238097597288
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contig-0001 31 1 A 10 A G 5 5 -47.63140083908785 -48.32257282443038 -47.63140083908785 -6.933112259052867 -48.32257282443038 -47.63140083908785 -7.521723263333335 -7.5219215117477365 -48.32257282443038 -47.63140083908785 -8.370799660803966 -6.933112259052867
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contig-0001 33 1 C 11 C T 6 5 -48.33815223623277 -53.565441823043464 -48.33815223623277 -7.63661735785008 -53.565441823043464 -48.33815223623277 -7.940351708691136 -8.625500433637177 -53.565441823043464 -48.33815223623277 -8.672669849735 -7.63661735785008 -9.757094021923859 -53.565441823043464 -48.33815223623277 -9.401287785987362 -7.660129815767198 -8.06114740121917 -10.767678320638774 -53.565441823043464 -48.338152236232766 -10.067904908549696 -7.940351708691136 -7.63661735785008 -8.625500433637175 -11.65192946185854 -53.56544182304346
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contig-0001 53 1 A 13 A T 7 6 -59.10423403376158 -64.56508882890974 -59.10423403376158 -9.020609583060734 -64.56508882890974 -59.10423403376158 -9.441585438763886 -10.128391402981455 -64.56508882890974 -59.10423403376158 -10.343639542034946 -9.020609583060734
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contig-0001 102 1 G 23 A G 14 9 -86.3360340808479 -136.03808097096726 -86.3360340808479 -15.945550652201419 -136.03808097096726 -86.3360340808479 -15.566954016959196 -19.03236574964768 -136.03808097096726 -86.3360340808479 -16.506596807572443 -15.945550652201419
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contig-0001 142 1 T 24 G C 14 10 -96.24913443302742 -124.75588369414069 -96.24913443302742 -16.681890270495344 -124.75588369414069 -96.24913443302742 -16.71946552262098 -19.459548338037965 -124.75588369414069 -96.24913443302742 -17.95026801261409 -16.681890270495344
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contig-0001 292 1 A 22 A T 13 9 -85.64462068195719 -128.03243076471173 -85.64462068195719 -15.252456350899335 -128.03243076471173 -85.64462068195719 -15.161196343692524 -17.934138579161925 -128.03243076471173 -85.64462068195719 -16.21834775310332 -15.252456350899335
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contig-0001 356 1 A 32 A C 16 16 -151.13099690274137 -155.5090349408413 -151.13099690274137 -22.187146148192063 -155.5090349408413 -151.13099690274137 -24.07008849386364 -24.071651983505177 -155.5090349408413 -151.13099690274137 -26.786525010268026 -22.187146148192063
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contig-0001 362 1 C 32 C T 18 14 -130.28378740078176 -172.46472406234133 -130.28378740078176 -22.202324345922378 -172.46472406234133 -130.28378740078176 -22.69182515676477 -25.476486359671547 -172.46472406234133 -130.28378740078176 -24.590148707124015 -22.202324345922378
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contig-0001 367 1 G 33 A G 17 16 -153.89945185499536 -156.60524982047804 -153.89945185499536 -22.882262903367923 -156.60524982047804 -153.89945185499536 -24.47921498421295 -25.17004973498719 -156.60524982047804 -153.89945185499536 -27.078964532716984 -22.882262903367923
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The snp density is relatively high in the sample. I tried increasing
window size but the error remains the same. One thing I want to note in
case it's the basis of the problem is I've generated a genolike file for
each individual rather than a combine genolike file for all individuals.
Could this be the cause of the problem?
Cheers
Peter
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peterdfields commented
The specific command is:
Rscript ~/popgen/HMMploidy/hiddenMarkovPloidyShell.R fileList=pop.filelist wind=100000
R version 3.4.4 and Rcpp_1.0.1 data.table_1.12.2 pracma_2.2.5
Would it be better to generate a pileup and genotype likelihood for all individuals that the test is to be run on?
SamueleSoraggi commented
A single pileup and then genolike file is better in term of analysis,
because you get better population frequency estimates. The method usually
works well only when there are more individuals at the same time.
The script as you run it is fine, as I imagined.
Do you think I could get to use your mpileup file to debug, so that I can
better point to the problem?
Den man. 27. maj 2019 kl. 14.52 skrev peterdfields <notifications@github.com
…:
The specific command is:
Rscript ~/popgen/HMMploidy/hiddenMarkovPloidyShell.R fileList=pop.filelist
wind=100000
R version 3.4.4 and Rcpp_1.0.1 data.table_1.12.2 pracma_2.2.5
Would it be better to generate a pileup and genotype likelihood for all
individuals that the test is to be run on?
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peterdfields commented
Sure. Do you have an email address I could send a link to you for a google drive folder?
SamueleSoraggi commented
The problem was due to the presence of multiple contigs in the same file. HMMploidy used to assume analysis on a single chromosome at a time, but now an automatic parser to work with multiple contigs in the same file has been implemented, so that
- windows of loci are not overlapping on two or more contigs,
- contigs with no SNPs are removed,
- contigs shorter than the window size are automatically considered as an entire window of reduced size.
The output plot in pdf format will show, on the x axis, positions for each contig in at least two points. This is done only with at most 50 labels for the x axis, that will otherwise have no text, since it would anyway be unreadable.
Feel free to open another issue if new problems pop up.
Cheers.