deseq_hts problems

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

deseq_hts problems

bravobih
Hi !
I'm trying to execute Galaxy DESeq2 on datasets created in other steps.
The script executed is deseq2-hts.sh (placed at shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/cec4b4fb30be/deseq_hts/deseq-hts_2.0/src). The first two steps - "Data preparation" and  "Read counting" are executed without problems, but the 3-rd step - "Differential testing"
reports an error
"Error in file(file, "rt") : cannot open the     connection
Calls: read.delim -> read.table -> file"

The error comes from script difftest_deseq2.R - it is getting three command arguments (and they are right) and attempts to read files INFILE_COUNTS.tab and INFILE_CONDITIONS.tab
(where INFILE - the second argument.)
But the problem that these two files are never created in the database/files/NNN !

Where can be the root of the problem?

It is a local installation of Galaxy
OS - CentOS 6.5 with all updates.




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/