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