Question: Galaxy Tool Error Report From Johnwu@Ibms.Sinica.Edu.Tw
0
"mailto:galaxy-user"@lists.bx.psu.edu • 10 wrote:
GALAXY TOOL ERROR REPORT
This error report was sent from the Galaxy instance hosted on the
server
"192.168.0.36:8080"
This is in reference to dataset id 316 from history id 2
You should be able to view the history containing the related history
item
121: Cufflinks on data 92: gene expression
by logging in as a Galaxy admin user to the Galaxy instance referenced
above
and pointing your browser to the following link.
192.168.0.36:8080/history/view?id=f597429621d6eb2b
The user 'johnwu@ibms.sinica.edu.tw' provided the following
information:
Hi galaxy dev team:
I just installed galaxy on my ubuntu box and tried to do RNA-seq
analysis according to Jeremy's excellent tutorial
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
however, I encountered following error messages when I was trying to
execute Cufflinks in galaxy..
job id: 106
tool id: cufflinks
job command line:
python
/home/galaxy/software/galaxy_dist/tools/ngs_rna/cufflinks_wrapper.py
--input=/home/galaxy/software/galaxy_dist/database/files/000/dataset_2
87.dat --assembled-isoforms-output=/home/galaxy/software/g
alaxy_dist/database/files/000/dataset_318.dat --num-
threads="4" -I 300000 -F 0.05 -j
0.05 -b
--ref_file="None" --dbkey=hg19
--index_dir=/home/galaxy/software/galaxy_dist/tool-data
job stderr:
Error running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf'
job stdout:
cufflinks v1.0.3
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 4
-b
job info:
None
job traceback:
None
(This is an automated message).