regarding MAKER

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

regarding MAKER

Nandita Pasari

Sir,

I am trying to run maker from bin.
I was successful in running the example data but as I proceeded to a second run from the bin folder I am getting an error as follows:


STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
mv: target `435.maker.output/mpi_blastdb/te_proteins%2Efasta.mpi.10.0/' is not a directory
mv: target `435.maker.output/mpi_blastdb/te_proteins%2Efasta.mpi.10/' is not a directory
ERROR: SplitDB not created correctly

 at /home/shams/Downloads/maker/bin/../lib/GI.pm line 1116.
        GI::split_db("/home/shams/Downloads/maker/data/te_proteins.fasta", "protein", 10, "/home/shams/Downloads/maker/bin/contig 435.maker.output/mpi_b"..., "C") called at maker line 518
--> rank=NA, hostname=shams-ThinkCentre-M90p

How can this be rectified?

Nandita Pasari
Pre Doctoral Fellow
Synthetic Biology and Biofuels Group
ICGEB
New Delhi

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: regarding MAKER

Carson Hinton Holt
Hi Nadita,

You appear to be using input files with spaces in their names.  It’s best
to avoid whitespace in file names for linux based programs, as they will
not always be interpreted correctly.

Thanks,
Carson


On 1/23/14, 3:23 AM, "Nandita Pasari" <[hidden email]> wrote:

>
>Sir,
>
>I am trying to run maker from bin.
>I was successful in running the example data but as I proceeded to a
>second run from the bin folder I am getting an error as follows:
>
>
>STATUS: Parsing control files...
>STATUS: Processing and indexing input FASTA files...
>mv: target `435.maker.output/mpi_blastdb/te_proteins%2Efasta.mpi.10.0/'
>is not a directory
>mv: target `435.maker.output/mpi_blastdb/te_proteins%2Efasta.mpi.10/' is
>not a directory
>ERROR: SplitDB not created correctly
>
> at /home/shams/Downloads/maker/bin/../lib/GI.pm line 1116.
> GI::split_db("/home/shams/Downloads/maker/data/te_proteins.fasta",
>"protein", 10, "/home/shams/Downloads/maker/bin/contig
>435.maker.output/mpi_b"..., "C") called at maker line 518
>--> rank=NA, hostname=shams-ThinkCentre-M90p
>
>How can this be rectified?
>
>Nandita Pasari
>Pre Doctoral Fellow
>Synthetic Biology and Biofuels Group
>ICGEB
>New Delhi
>

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org