Hi, I've downloaded the Suite of Velvet assembler tools at http://community.g2.bx.psu.edu/ and installed them as detailed in http://gmod.827538.n3.nabble.com/attachment/868065/0/README?by-user=t 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 /opt/galaxy_dist/database/files/002/dataset_2411.dat [0.003878] 1538 reads found. [0.003881] Done [0.003889] Reading FastQ file /opt/galaxy_dist/database/files/002/dataset_2412.dat [0.007500] 1538 reads found. [0.007502] Done [0.007533] Reading read set file /opt/galaxy_dist/database/files/002/dataset_2456_files/Sequences; [0.008571] 3076 sequences found [0.018786] Done [0.018791] 3076 sequences in total. [0.018825] Writing into roadmap file /opt/galaxy_dist/database/files/002/dataset_2456_files/Roadmaps... [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 found! The version of Velvet that I have installed and that is in the path is velvet_1.0.18. I was wondering if anyone could give me some help here or has any suggestions. Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
