Question: Unable to get kmergenie to work, but make check seems fine
0
gravatar for jeremycfd
2.4 years ago by
jeremycfd0
United States
jeremycfd0 wrote:

Hello all,

After a fresh install of kmergenie, I've attempted to run the program on a couple of different files of different sizes, all to no success. Essentially it asks me to run make check, but as far as I can tell make check returns no errors. Any insights on how to get this working?

./kmergenie ELJC31_pc001_1_final.fastq --diploid
running histogram estimation
Linear estimation: ~96 M distinct 71-mers are in the reads
K-mer sampling: 1/18
| processing                                                                                         |
[going to estimate histograms for values of k: 121 111 101 91 81 71 61 51 41 31 21
------------------------------------------------------------------------------------------------------------------------Total time Wallclock  1144.9343 s
fitting model to histograms to estimate best k
could not fit histograms-k101.histo
could not fit histograms-k31.histo
could not fit histograms-k121.histo
could not fit histograms-k41.histo
could not fit histograms-k111.histo
could not fit histograms-k21.histo
could not fit histograms-k51.histo
could not fit histograms-k81.histo
could not fit histograms-k71.histo
could not fit histograms-k61.histo
could not fit histograms-k91.histo
could not predict a best k value
Execution of decide failed (return code 0). If this is a fresh Kmergenie install, try running 'make check'.

 

make check
scripts/test_install
Testing presence of specialk....
OK
Testing presence of Rscript....
R scripting front-end version 3.0.2 (2013-09-25)
OK
Testing basic Rscript functionality....
Rscript --no-init-file -e 'rnorm(1)'
[1] "rnorm(1)"
OK
Testing a simple KmerGenie example....

OK
Test successful. KmerGenie is ready, type `./kmergenie`.

kmergenie • 893 views
ADD COMMENTlink modified 2.4 years ago by rchikhi0 • written 2.4 years ago by jeremycfd0
0
gravatar for rchikhi
2.4 years ago by
rchikhi0
United States
rchikhi0 wrote:

Hello, given the output, it seems that your install is fine. It displayed that "try running make check" message by mistake, This will be fixed in the next version. However, it appears that kmergenie could not estimate a best k on your dataset.

- Please try without the --diploid option

- If it still fails, could you please post or email me (kmergenie@cse.psu.edu) the HTML report generated by Kmergenie?

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by rchikhi0
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