Re: Outreachy 2017 (Round 14)
Hello Nadiya,
On Sat, Mar 25, 2017 at 08:31:24PM -0700, Nadiya Sitdykova wrote:
> Thank you for instructions for using dch, I hope now I got it right.
I think so (except the blank line in the beginning which was probably
a typo).
> 1) I edited patch use_debian_packaged_seqtk.patch so I guess the problem
> with seqtk should be resolved now.
Yes, this works now for me.
> 2) I have this error on Ubuntu xenial, Debian jessie and after you
> mentioned that it's better to use unstable version, I tried Debian sid
> (amd64) and still got problems with RcppGSL.
> That stand-alone test returns exit code 1 with message "Missing the
> following R library RcppGSL".
This is very strange. I can confirm that there is really a problem
if I run
LANG=C . run-unit-test 2>&1 | tee > run-unit-test.out
I get the attached build log - but this does not contain the string
Rcpp. This needs to be investigated.
> And for commented tests in run-unit-test file
> the message is "Cannot use --stats-only with missing R libraries".
I think it would be the best to stick to the not commented tests
and make sure we get the same results. Could you please also
create the exact output if your test?
Kind regards
Andreas.
--
http://fam-tille.de
bash: cd: /tmp/mapdamage-test.lMvam8: No such file or directory
gzip: pulse-PKdhtXMmr18n: Permission denied
gzip: ssh-pgBy7Zg4S5zX/agent.3114: No such device or address
gzip: systemd-private-517cc73010a84c8dbec2b18fedc67d02-apache2.service-grolbu: Permission denied
gzip: systemd-private-517cc73010a84c8dbec2b18fedc67d02-colord.service-VKfwve: Permission denied
gzip: systemd-private-517cc73010a84c8dbec2b18fedc67d02-rtkit-daemon.service-uoqkYG: Permission denied
[fai_load] build FASTA index.
..
----------------------------------------------------------------------
Ran 2 tests in 0.058s
OK
Started with the command: /usr/bin/mapDamage -i rescale_test/pe_test/pe.sam -r rescale_test/pe_test/ref.fa
No length distributions are available, plotting length distribution only works for single-end reads
Performing Bayesian estimates
The ACGT frequencies must be in the range 0 to 1
Error in getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt) :
Calls: source -> withVisible -> eval -> eval -> getPmat
7: (function (e)
{
traceback(2)
quit(status = 1)
})()
6: stop()
5: getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt)
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
Reading from 'rescale_test/pe_test/pe.sam'
Writing results to 'results_pe/'
pdf results_pe/Fragmisincorporation_plot.pdf generated
Traceback (most recent call last):
File "/usr/bin/mapDamage", line 382, in <module>
sys.exit(main())
File "/usr/bin/mapDamage", line 365, in main
mapdamage.rscript.run_stats(options)
File "/usr/lib/python2.7/dist-packages/mapdamage/rscript.py", line 144, in run_stats
raise e
subprocess.CalledProcessError: Command '['Rscript', '/usr/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/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
pdf result exists
Started with the command: /usr/bin/mapDamage -d results_pe -y 0.1 --plot-only
No length distributions are available, plotting length distribution only works for single-end reads
pdf results_pe/Fragmisincorporation_plot.pdf generated
checking stdin redirect...
Started with the command: /usr/bin/mapDamage -i - -r rescale_test/pe_test/ref.fa
No length distributions are available, plotting length distribution only works for single-end reads
Performing Bayesian estimates
The ACGT frequencies must be in the range 0 to 1
Error in getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt) :
Calls: source -> withVisible -> eval -> eval -> getPmat
7: (function (e)
{
traceback(2)
quit(status = 1)
})()
6: stop()
5: getPmat(cu_pa$Theta, cu_pa$Rho, cu_pa$acgt)
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
Reading from '-'
Writing results to 'results_-/'
pdf results_-/Fragmisincorporation_plot.pdf generated
Traceback (most recent call last):
File "/usr/bin/mapDamage", line 382, in <module>
sys.exit(main())
File "/usr/bin/mapDamage", line 365, in main
mapdamage.rscript.run_stats(options)
File "/usr/lib/python2.7/dist-packages/mapdamage/rscript.py", line 144, in run_stats
raise e
subprocess.CalledProcessError: Command '['Rscript', '/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/runGeneral.R', '--args', '30', '10000', '10', '50000', '0', '0', '1', '1', '0', '0', '1', '12', 'results_-/', '/usr/lib/python2.7/dist-packages/mapdamage/Rscripts/stats/', 'results_-/Stats_out', '0', '0', '0', 'results_-/acgt_ratio.csv', '0', '0']' returned non-zero exit status 1
Reply to: