I've downloaded the Suite of Velvet assembler tools at
and installed them as detailed in
I've then run velveth in Galaxy using two files - a file each of corresponding
left and right paired-end reads which gives me the following output:
0.000001] Reading FastQ file
[0.003878] 1538 reads found.
[0.003889] Reading FastQ file
[0.007500] 1538 reads found.
[0.007533] Reading read set file
[0.008571] 3076 sequences found
[0.018791] 3076 sequences in total.
[0.018825] Writing into roadmap file
[0.021716] Inputting sequences...
[0.021719] Inputting sequence 0 / 3076
[0.169007] Done inputting sequences
[0.169017] Destroying splay table
[0.177049] Splay table destroyed
I then go to the velvetg tool and select my velveth output file as the input to
velvetg, use 'auto' as the -ins_length and -ins_length_sd, and then leave the
remaining ins_length fields blank. I leave the final values (from -exp_cov to
Minimum Read-Pair Validation) as the default values.
When I execute the job it runs and finishes almost instantly and the only
output for 'velvetg on data X' is:
[0.000001] Unknown option: -ins_length3
The output files Contigs, Contig Stats and Unused Reads are all empty and the
LastGraph file has the error:
ERROR: /opt/galaxy_dist/database/files/002/dataset_2457_files/LastGraph not
The version of Velvet that I have installed and that is in the path is
I was wondering if anyone could give me some help here or has any suggestions.
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
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