I am facing simialr issue with sff_extract. I downloaded SSAHA2 ver 2.5.3 , but It has no installation instructions, only programs ssaha2 ssaha2Build and ssahaSNP. Please explain, how did it work out for you? Regards, Ganga Jeena On Tue, Dec 14, 2010 at 1:31 AM, Artemus Harper <subanark@xxxxxxxxx> wrote: > Apparently I didn't have ssaha2 installed. It works now that it is > installed. > > > On Mon, Dec 13, 2010 at 7:07 AM, Cleo Ho <cleoho175@xxxxxxxxx> wrote: > >> I had the same problem before, and it turned out I didn't put ssaha2 in >> the correct directory. ssaha2 should be put in place where mira can call it >> directly by the its command line from any directory. Such directory may be >> usr/local/bin, for example, in a Linux system. Hope this helps. >> >> Cleo >> >> On 2010-12-13, at 1:31 AM, Artemus Harper <subanark@xxxxxxxxx> wrote: >> >> The error message is exactly as I've posted. Thats all the info it gives. >> It occurs after several seconds after starting. >> On Dec 12, 2010, at 5:29 PM, Sven Klages wrote: >> >> When does the error occur, immediately? What does the error say? >> >> 2010/12/10 Artemus Harper < <subanark@xxxxxxxxx>subanark@xxxxxxxxx> >> >>> I'm trying to use sff_extract, but I ran into an error: >>> $ sff_extract_0_2_8 -o cherry_454 -l linker.fasta -i >>> "insert_size:8000,insert_stdev:750" 454_paired_end_8kb_reads/GQKO24N02.sff >>> Working on '454_paired_end_8kb_reads/GQKO24N02.sff': >>> Creating temporary sequences from reads in >>> '454_paired_end_8kb_reads/GQKO24N02.sff' ... done. >>> Searching linker sequences with SSAHA2 (this may take a while) ... >>> >>> An error occured during the SSAHA2 execution, aborting. >>> >>> My linker file is: >>> >cherry_linker_1 >>> TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG >>> >cherry_linker_2 >>> AGCATATTGAAGCATATTACATACGATATGCTTCAATAATGC >>> >>> -- >>> Artemus Harper >>> >> >> >> > > > -- > Artemus Harper >