Hello Di Nguyen,
Without seeing your history, my initial guess is that the SAM output
from the mapping runs need to be sorted before running Cufflinks.
(Tophat, which is designed to map spliced RNA-seq data, sorts the SAM
output as part of the data processing, but BWA and Bowtie do not).
The workflow provided on this FAQ can be followed to sort SAM files for
Cufflinks:
https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2
If you continue to have problems, please submit a bug report (click on
"green bug" icon from the error Cufflinks dataset as run on the main
public Galaxy instance (http://usegalaxy.org), leave all inputs and the
error dataset undeleted, note this email address in the comments if it
differs from your Galaxy account email address (so that I can link the
two issues together), and we can provide more feedback.
http://wiki.g2.bx.psu.edu/Support#Error_from_tools
Hopefully this helps,
Jen
Galaxy team
On 6/20/12 1:28 PM, Di Nguyen wrote:
Hi Jen,
I mapped with BWA and Bowtie for my RNAseq but Cufflink DID not run.
This is the error message:
"An error occurred running this job: /cufflinks v1.3.0
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8
-b /galaxy/data/hg19/sam_index/hg19.fa
Error running cufflinks.
return code = 1
cufflinks: /lib64/libz.so.1: no version information available
(required by cufflinks)"
/What should I do?/
Di Nguyen
/
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
