Hello Andreas, 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 Regards, Nadiya On Tue, Mar 28, 2017 at 4:55 PM, Nadiya Sitdykova <rovensk...@gmail.com> wrote: > Hello Andreas, > > 1) Actually I was wrong, after changing reference to TGAAAACGA the new > type of error arises, so I'm working on it for now > 2) I created an issue here https://github.com/ginolhac/mapDamage/issues/18 > > Regards, Nadiya > > On Tue, Mar 28, 2017 at 2:58 PM, Büşra Selin Pekişçi < > busra.peki...@gmail.com> wrote: > >> Hello Andreas, >> >> Sorry for wrong mail from Canberk's mail account.I was using his computer >> and missend mail from his account. >> >> 2017-03-29 0:56 GMT+03:00 Canberk Koç <canberk...@gmail.com>: >> >>> Hello Andreas, >>> >>> I was working on filo and find out something. Filo binaries goes to >>> /usr/lib/filo section and i think it is wrong . They make these changes >>> because binary names are too generic should i make link them to bin >>> directory with filo-* like name ? >>> >>> Best Regards >>> >>> >>> >>> Canberk Koç >>> [image: https://]about.me/canberkkoc >>> >>> <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links> >>> >>> >>> 2017-03-28 22:58 GMT+03:00 Andreas Tille <andr...@an3as.eu>: >>> >>>> Hi Büşra, >>>> >>>> On Tue, Mar 28, 2017 at 10:49:30PM +0300, Büşra Selin Pekişçi wrote: >>>> > I check Prank git and find out something i don't know if it is >>>> important. >>>> > At run-unit-test script you make a trap and give there $ADTTMP >>>> variable can >>>> > we use it instead of $AUTOPKGTEST_TMP variable. >>>> >>>> No. :-) >>>> >>>> > I was curious about it. >>>> >>>> Thanks for spotting this cut-n-pasto of mine. ADTTMP was the old name >>>> and I was just copying from other tests. However, if you add further >>>> tests please also make sure the temporary dir will be removed. >>>> >>>> > And >>>> > i start to work on filo package for your information . Thanks for >>>> help. >>>> >>>> Fine. >>>> >>>> Kind regards >>>> >>>> Andreas. >>>> >>>> -- >>>> http://fam-tille.de >>>> >>>> >>> >> >
Started with the command: /usr/local/bin/mapDamage -i pe.sam -r ref_T.fa [fai_load] build FASTA index. Reading from 'pe.sam' Writing results to 'results_pe/' pdf results_pe/Fragmisincorporation_plot.pdf generated No length distributions are available, plotting length distribution only works for single-end reads Performing Bayesian estimates Warning, To few substitutions to assess the nick frequency, using constant nick frequency instead Starting grid search, starting from random values Adjusting the proposal variance iteration 1 Adjusting the proposal variance iteration 2 Adjusting the proposal variance iteration 3 Adjusting the proposal variance iteration 4 Adjusting the proposal variance iteration 5 Adjusting the proposal variance iteration 6 Adjusting the proposal variance iteration 7 Adjusting the proposal variance iteration 8 Adjusting the proposal variance iteration 9 Adjusting the proposal variance iteration 10 Done burning, starting the iterations Done with the iterations, finishing up Writing and plotting to files Error in quantile.default(newX[, i], ...) : missing values and NaN's not allowed if 'na.rm' is FALSE Calls: source ... calcSampleStats -> data.frame -> apply -> FUN -> quantile.default 12: (function (e) { traceback(2) quit(status = 1) })() 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