Hi Leon,

What is the output of "ls -lah /mnt/galaxyIndices/alignments/maf/"?

Also, you may what to use additional sub-directory structure for your file 
locations in case you want to add more alignments later, e.g., 
/mnt/galaxyIndices/hg19/maf/10_way_multiz/ or similiar

Also, note that although you are only indexing (for extraction) for the 
specified listed species, the alignments will contain all of the species 
present in the original file (you list 46way multiZ as the source).


Thanks for using Galaxy,

Dan


On Sep 10, 2013, at 6:44 PM, Leon Mei wrote:

> Dear colleagues,
> 
> I am having some trouble installing MAF datasets at our server. When I
> run "Extract MAF blocks given a set of genomic intervals", I got this
> error message:
> 
> "Fatal Error: The MAF source specified (10_WAY_MULTIZ_hg19) appears to
> be invalid."
> 
> Below is what I did by following the wiki page:
> http://wiki.galaxyproject.org/Admin/Datatypes/Add%20MAFs
> 
> 1, download all mafs for hg19 from
> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/maf/
> 
> 2, index them using "maf_build_index.py --species=hg19,panTro2,
> gorGor1,ponAbe2,papHam1,calJac1,tarSyr1,micMur1,otoGar1,rheMac2
> $file". Our user requested primates only.
> 
> 3, Here is my maf_index.loc file:
> ==
> 10-way multiZ (hg19)    10_WAY_MULTIZ_hg19
> hg19,panTro2,gorGor1,ponAbe2,papHam1,calJac1,tarSyr1,micMur1,otoGar1,rheMac2
>  hg19,panTro2,gorGor1,ponAbe2,papHam1,calJac1,tarSyr1,micMur1,otoGar1,rheMac2
>   /mnt/galaxyIndices/alignments/maf/chr1.maf,/mnt/galaxyIndices/alignments/m
>   
> af/chr10.maf,/mnt/galaxyIndices/alignments/maf/chr11.maf,/mnt/galaxyIndices/alignments/maf/chr11_gl000202_random.maf,/mnt/galaxyIndices/ali
>   
> gnments/maf/chr12.maf,/mnt/galaxyIndices/alignments/maf/chr13.maf,/mnt/galaxyIndices/alignments/maf/chr14.maf,/mnt/galaxyIndices/alignments
>   
> /maf/chr15.maf,/mnt/galaxyIndices/alignments/maf/chr16.maf,/mnt/galaxyIndices/alignments/maf/chr17.maf,/mnt/galaxyIndices/alignments/maf/ch
>   
> r17_ctg5_hap1.maf,/mnt/galaxyIndices/alignments/maf/chr17_gl000203_random.maf,/mnt/galaxyIndices/alignments/maf/chr17_gl000204_random.maf,/
>   
> mnt/galaxyIndices/alignments/maf/chr17_gl000205_random.maf,/mnt/galaxyIndices/alignments/maf/chr17_gl000206_random.maf,/mnt/galaxyIndices/a
>   
> lignments/maf/chr18.maf,/mnt/galaxyIndices/alignments/maf/chr18_gl000207_random.maf,/mnt/galaxyIndices/alignments/maf/chr19.maf,/mnt/galaxy
>   
> Indices/alignments/maf/chr19_gl000208_random.maf,/mnt/galaxyIndices/alignments/maf/chr19_gl000209_random.maf,/mnt/galaxyIndices/alignments/
>   
> maf/chr1_gl000191_random.maf,/mnt/galaxyIndices/alignments/maf/chr1_gl000192_random.maf,/mnt/galaxyIndices/alignments/maf/chr2.maf,/mnt/gal
>   
> axyIndices/alignments/maf/chr20.maf,/mnt/galaxyIndices/alignments/maf/chr21.maf,/mnt/galaxyIndices/alignments/maf/chr21_gl000210_random.maf
>   
> ,/mnt/galaxyIndices/alignments/maf/chr22.maf,/mnt/galaxyIndices/alignments/maf/chr3.maf,/mnt/galaxyIndices/alignments/maf/chr4.maf,/mnt/gal
>   
> axyIndices/alignments/maf/chr4_ctg9_hap1.maf,/mnt/galaxyIndices/alignments/maf/chr4_gl000193_random.maf,/mnt/galaxyIndices/alignments/maf/c
>   
> hr4_gl000194_random.maf,/mnt/galaxyIndices/alignments/maf/chr5.maf,/mnt/galaxyIndices/alignments/maf/chr6.maf,/mnt/galaxyIndices/alignments
>   
> /maf/chr6_apd_hap1.maf,/mnt/galaxyIndices/alignments/maf/chr6_cox_hap2.maf,/mnt/galaxyIndices/alignments/maf/chr6_dbb_hap3.maf,/mnt/galaxyI
>   
> ndices/alignments/maf/chr6_mann_hap4.maf,/mnt/galaxyIndices/alignments/maf/chr6_mcf_hap5.maf,/mnt/galaxyIndices/alignments/maf/chr6_qbl_hap
>   
> 6.maf,/mnt/galaxyIndices/alignments/maf/chr6_ssto_hap7.maf,/mnt/galaxyIndices/alignments/maf/chr7.maf,/mnt/galaxyIndices/alignments/maf/chr
>   
> 7_gl000195_random.maf,/mnt/galaxyIndices/alignments/maf/chr8.maf,/mnt/galaxyIndices/alignments/maf/chr8_gl000196_random.maf,/mnt/galaxyIndi
>   ces/alignments/maf/chr8_gl000197_random.maf
> ==
> 
> Any hint on which step is wrong or missing is highly appreciate!
> 
> Thanks,
> Leon
> 
> 
> 
> 
> 
> -- 
> Hailiang (Leon) Mei
> Netherlands Bioinformatics Center
> BioAssist NGS Taskforce
> - http://ngs.nbic.nl
> Skype: leon_mei    Mobile: +31 6 41709231
> ___________________________________________________________
> 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/
> 
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to