Hello Andreas,>Did you do some investigation what dependency providing liblapack.so and>libblas.so are needed (see my mail from yesterday)?Yes, I tried to run the test with different packages installed, and here are results:packages | result | user time------------------------------------------------------------ ---------------------- libatlas-base-dev | Successful run | 11m24.204slibopenblas-dev | Successful run | 10m31.860slibblas-dev+liblapack-dev | Successful run | 10m34.368sIt seems that libatlas-base-dev is less effective, but I'm not sure if we should exclude it from Depends, so I left if for nowOn Tue, Mar 28, 2017 at 11:29 PM, Andreas Tille <andreas@an3as.eu> wrote:[Changed subject to split up to topics in one thread]
Hi Nadiya,
On Tue, Mar 28, 2017 at 10:23:00PM -0700, Nadiya Sitdykova wrote:
> 1) I read the paper about mapdamage and figured out that with given pe.sam
> file the reference TGAAAACGA wouldn't make sense as the particular type of
> substitutions is specific for ancient DNA damages. So further for tests I
> used reference CGATACGA -- which contains all types of nucleotides and make
> sense regarding specifics of DNA damage.
>
> 2) But even after fixing (1) I still got an error (log attached). The
> problem is that on given dataset from pe_test mapdamage produces data with
> NaNs and then tries to compute quantiles on this data. I think that on real
> date NaNs also could be produced, so I treated this issue as a bug and made
> a patch which changes the way how quantiles are computed --- now it removes
> NaNs [1]
>
> 3) I wrote about all this to upstream as a comments to earlier created
> issue and asked if it's really was a bug in their opinion
>
> 4) FInally, move forward to fixing mapdamage test suite
Pretty good job. That's exactly the contribution I'm envisioning for the
Outreachy project. I've just added the URL of the upstream issue to the
patch.
> 11: stop("missing values and NaN's not allowed if 'na.rm' is FALSE")
> 10: quantile.default(newX[, i], ...)
> 9: FUN(newX[, i], ...)
> 8: apply(X, 1, quantile, c(0.025))
> 7: data.frame(x = 1:nrow(da), pos = da[, "Pos"], mea = apply(X,
> 1, mean), med = apply(X, 1, median), loCI = apply(X, 1, quantile,
> c(0.025)), hiCI = apply(X, 1, quantile, c(0.975)))
> 6: calcSampleStats(da, CTs)
> 5: postPredCheck(dat, mcmcOut)
> 4: eval(expr, envir, enclos)
> 3: eval(ei, envir)
> 2: withVisible(eval(ei, envir))
> 1: source(paste(path_to_mapDamage_stats, "main.R", sep = ""))
> The Bayesian statistics program failed to finish
> Traceback (most recent call last):
> File "/usr/local/bin/mapDamage", line 382, in <module>
> sys.exit(main())
> File "/usr/local/bin/mapDamage", line 365, in main
> mapdamage.rscript.run_stats(options)
> File "/usr/local/lib/python2.7/dist-packages/mapdamage/rscript. py", line 144, in run_stats
> raise e
> subprocess.CalledProcessError: Command '['Rscript', '/usr/local/lib/python2.7/dist-packages/mapdamage/Rscripts/ stats/runGeneral.R', '--args', '30', '10000', '10', '50000', '0', '0', '1', '1', '0', '0', '1', '12', 'results_pe/', '/usr/local/lib/python2.7/dist -packages/mapdamage/Rscripts/ stats/', 'results_pe/Stats_out', '0', '0', '0', 'results_pe/acgt_ratio.csv', '0', '0']' returned non-zero exit status 1
I'd recommend to manually run this script.
Did you do some investigation what dependency providing liblapack.so and
libblas.so are needed (see my mail from yesterday)?
Kind regards
Andreas.
--
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