No PDF output files

[Hongxi]

Hi,

I am new here, and I have some problems when I ran  SolexaQA++v3.1.7.1.

I used the example data (bad_MiSeq_dataset.fq.zip & good_MiSeq_dataset.fq.zip), but I couldn't get any pdf output files. Here is my command:

./SolexaQA++ analysis -h 20 --illumina -b /Users/penghongxi/Downloads/bad_MiSeq_dataset.fq 

Does anyone know why? Any suggestions will be thankful.

[Mauro Truglio]

Hi Hongxi,

Welcome. I just tried to reproduce your problem on a couple of PCs, but everything here is working fine, using the exact command line and input that you used. Four PDF files are produced, as expected.

Can you please specify which Operative System you are using, and if there is an error message during the execution?
Also, could you try that command on another machine?

Thanks

Mauro

[Hongxi]

Hi Mauro,

Thank you for your reply. I am using macOS Sierra 10.12.6, and there is an error message during the execution. The message is shown below.

wirelessprv-10-192-203-15:SolexaQA++ penghongxi$ ./SolexaQA++ analysis -h 20 --illumina -b /Users/penghongxi/Downloads/bad_MiSeq_dataset.fq 

SolexaQA++ v3.1.7.1

Released under GNU General Public License version 3

C++ version developed by Mauro Truglio (M.Tr...@massey.ac.nz)

Running with h=20

sh: Rscript: command not found

Subsidiary program R not found in your PATH. Line graphs, histogram and heatmap will not be produced.

Working on /Users/penghongxi/Downloads/bad_MiSeq_dataset.fq

User defined format: Illumina FASTQ format, Illumina pipeline 1.3+

Info: Phred value of 20.000000 converted to a probability value of 0.010000

BWA threshold 20

100% [==================================================]

Writing results....

Analysis complete

After analysis complete, I only get 3 output files with the suffix of *.matrix, *.quality, and *.segments.

I have R in my PC, do you know how I can fix it?

Thanks!

Hongxi

[Hongxi]

Hi Mauro,

I try again, and it works. Turns out that I accidentally delete R, after I reinstall R, I can get all the pdf files. Thank you again.

Best,

hongxi

On Friday, February 9, 2018 at 11:31:17 AM UTC-6, Mauro Truglio wrote: