[galaxy-user] cuffcompare error in galaxy

[吳正華]

Dear galaxy team:

 

I was testing local galaxy of our lab by analyzing RNA-seq data in Jeremy’s
RNA-seq tutorial.

 

http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

 

I could run TopHat, cufflinks, and cuffdiff and got results correctly, 

but when I executed cuffcompare through galaxy, the following error
occurred:

 

Tool execution generated the following error message:

Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output'

The tool produced the following additional output:

cuffcompare v1.0.3 (2403)

cuffcompare -o cc_output  -s
/home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1

 

and error messages in log file (galaxy.log) are:

 

galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched

galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: 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_398.dat

 

galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished:
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_398.dat

 

galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move
/home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_outp
ut to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat
as directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move
/home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.
tmap to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat
as directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move
/home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.
refmap to
/home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat as
directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved
/home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_outp
ut.combined.gtf to
/home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat as
directed by from_work_dir

galaxy.jobs DEBUG 2011-06-10 14:02:28,174 

 

job 130 ended

 

 

I’ve tried to manually execute cuffcompare to analyze dataset_398.dat
(which is the output of tophat) and I could get correct cuffcompare output.

 

$ cuffcompare -o cc_output  -s /home/galaxy/data/galaxy_data/sam_index/hg19.
fasta dataset_398.dat

 

It seems that the coffcompare_wrapper might have something to do with this
error…

 

Thanks in advance for your help!

 

 

Best

John Wu

 

 

 

 

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