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/
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