Thank you Peter. I changed the dataset and succeeded this time. Appreciated for you help.
Cheers, Tyler On Thu, Apr 19, 2012 at 12:40 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > On Thu, Apr 19, 2012 at 7:13 PM, JIE CHEN <jiechenable1...@gmail.com> > wrote: > > Hi Peter, > > > > Here is the full log: > > > > Excellent :) > > The good news is MIRA seems to be installed and running > fine - it just didn't like your test data, and I understand why: > > > ... > > > > Sanger will load 1 reads. > > Longest Sanger: 36 > > Longest 454: 0 > > Longest IonTor: 0 > > Longest PacBio: 0 > > Longest Solexa: 0 > > Longest Solid: 0 > > Longest overall: 36 > > Total reads to load: 1 > > ... > > Sanger total bases:36 used bases in used reads: 0 > > 454 total bases:0 used bases in used reads: 0 > > IonTor total bases:0 used bases in used reads: 0 > > PacBio total bases:0 used bases in used reads: 0 > > Solexa total bases:0 used bases in used reads: 0 > > Solid total bases:0 used bases in used reads: 0 > > > > .. > > > > Fatal error (may be due to problems of the input data or parameters): > > > > "No read can be used for assembly." > > > > ... > > Then finally some information my wrapper script adds: > > > MIRA took 0.00 minutes > > Return error code 1 from command: > > mira --job=denovo,genome,accurate SANGER_SETTINGS > -LR:lsd=1:mxti=0:ft=fastq > > -FN:fqi=/media/partition2_/galaxydb_data/000/dataset_290.dat > COMMON_SETTINGS > > -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 -OUT:rrot=1:rtd=1 > > It appears you are trying to run MIRA with a single 36bp read, > telling MIRA this is a Sanger read. That is very odd (not least > because a 36bp read sounds more likely to be an early > Solexa/Illumina read from the length). > > Has something gone wrong with loading the data into Galaxy? > Or did you just want to try a trivial test case? If so, it was too > simple and MIRA has stopped because it thinks it is bad input. > > The MIRA output log file (which is actually written to the stout > if you run MIRA yourself at the command line) is quite verbose, > but it is incredibly useful for diagnosing problems. That is why > I collect it as one of the output files in Galaxy. > > You should be able to try some larger realistic examples, e.g. > a virus or a bacterial genome depending on your server's > capabilities. And if they fail, have a look through the log file > for why MIRA said it failed. > > Also keep in mind that the Galaxy wrapper is deliberately a > simplified front end - MIRA has dozens of command line > options which are not available via my wrapper for simplicity. > > Regards, > > Peter >
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