Question: Galaxy Tool Error Report From Johnwu@Ibms.Sinica.Edu.Tw
0
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 377 from history id 2
You should be able to view the history containing the related history
item
176: Cuffcompare on data 175: transcript accuracy
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:
While executing cuffcompare, I encountered this error message:
Error running cuffcompare. [Errno 2] No such file or directory:
'cc_output'
I was practicing RNA-seq analysis steps on newly installed galaxy to
test if i could easily analyze my data.
I could run cufflinks and cuffdiff through galaxy, but i'm unable to
run cuffcompare.
how should i solve this problem?
thanks a lot!
job id: 126
tool id: cuffcompare
job command line:
python
/home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py
-s --ref_file="None" --dbkey=hg19
--index_dir=/home/galaxy/software/galaxy_dist/tool-data
/home/galaxy/software/galaxy_dist/database/files/000/dataset_376.dat
job stderr:
Error running cuffcompare. [Errno 2] No such file or directory:
'cc_output'
job stdout:
cuffcompare v1.0.3 (2403)
cuffcompare -o cc_output -s
/home/galaxy/data/galaxy_data/sam_index/hg19.fa ./input1
job info:
None
job traceback:
None
(This is an automated message).
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modified 7.5 years ago
by
Nate Coraor ♦ 3.2k
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written
7.5 years ago by
galaxy-user@lists.bx.psu.edu • 10
