Hi Dan,

Here are the output:
==
hmei@ubuntu:~$ ls -lah /mnt/galaxyIndices/alignments/maf/
total 236G
drwxrwsr-x 2 postgres postgres 4.0K Sep 10 00:08 .
drwxrwsr-x 4 postgres postgres 4.0K Sep  9 16:27 ..
-rw-rw-r-- 1 postgres postgres  13G Oct 31  2009 chr10.maf
-rw-rw-r-- 1 postgres postgres 189M Sep  9 17:29 chr10.maf.index
-rw-rw-r-- 1 postgres postgres 189M Sep  8 21:35 chr11_gl000202_random.maf
-rw-rw-r-- 1 postgres postgres  12G Oct 31  2009 chr11.maf
-rw-rw-r-- 1 postgres postgres 184M Sep  9 18:07 chr11.maf.index
-rw-rw-r-- 1 postgres postgres  12G Oct 31  2009 chr12.maf
-rw-rw-r-- 1 postgres postgres 186M Sep  9 18:31 chr12.maf.index
-rw-rw-r-- 1 postgres postgres 8.7G Oct 31  2009 chr13.maf
-rw-rw-r-- 1 postgres postgres 135M Sep  9 18:49 chr13.maf.index
-rw-rw-r-- 1 postgres postgres 8.3G Oct 31  2009 chr14.maf
-rw-rw-r-- 1 postgres postgres 125M Sep  9 19:05 chr14.maf.index
-rw-rw-r-- 1 postgres postgres 7.3G Oct 31  2009 chr15.maf
-rw-rw-r-- 1 postgres postgres 112M Sep  9 19:19 chr15.maf.index
-rw-rw-r-- 1 postgres postgres 7.1G Oct 31  2009 chr16.maf
-rw-rw-r-- 1 postgres postgres 108M Sep  9 19:32 chr16.maf.index
-rw-rw-r-- 1 postgres postgres  39M Oct 31  2009 chr17_ctg5_hap1.maf
-rw-rw-r-- 1 postgres postgres 456K Sep  9 19:45 chr17_ctg5_hap1.maf.index
-rw-rw-r-- 1 postgres postgres 753K Oct 31  2009 chr17_gl000203_random.maf
-rw-rw-r-- 1 postgres postgres  45K Sep  9 19:45 chr17_gl000203_random.maf.index
-rw-rw-r-- 1 postgres postgres 5.1M Oct 31  2009 chr17_gl000204_random.maf
-rw-rw-r-- 1 postgres postgres 101K Sep  9 19:45 chr17_gl000204_random.maf.index
-rw-rw-r-- 1 postgres postgres 1.6M Oct 31  2009 chr17_gl000205_random.maf
-rw-rw-r-- 1 postgres postgres  33K Sep  9 19:45 chr17_gl000205_random.maf.index
-rw-rw-r-- 1 postgres postgres 968K Oct 31  2009 chr17_gl000206_random.maf
-rw-rw-r-- 1 postgres postgres  24K Sep  9 19:45 chr17_gl000206_random.maf.index
-rw-rw-r-- 1 postgres postgres 7.3G Oct 31  2009 chr17.maf
-rw-rw-r-- 1 postgres postgres 112M Sep  9 19:45 chr17.maf.index
-rw-rw-r-- 1 postgres postgres 265K Oct 31  2009 chr18_gl000207_random.maf
-rw-rw-r-- 1 postgres postgres 3.5K Sep  9 19:59 chr18_gl000207_random.maf.index
-rw-rw-r-- 1 postgres postgres 7.0G Oct 31  2009 chr18.maf
-rw-rw-r-- 1 postgres postgres 106M Sep  9 19:59 chr18.maf.index
-rw-rw-r-- 1 postgres postgres 4.2K Oct 31  2009 chr19_gl000208_random.maf
-rw-rw-r-- 1 postgres postgres  193 Sep  9 20:05 chr19_gl000208_random.maf.index
-rw-rw-r-- 1 postgres postgres 2.6M Oct 31  2009 chr19_gl000209_random.maf
-rw-rw-r-- 1 postgres postgres  54K Sep  9 20:05 chr19_gl000209_random.maf.index
-rw-rw-r-- 1 postgres postgres 3.5G Oct 31  2009 chr19.maf
-rw-rw-r-- 1 postgres postgres  48M Sep  9 20:05 chr19.maf.index
-rw-rw-r-- 1 postgres postgres 4.1M Oct 31  2009 chr1_gl000191_random.maf
-rw-rw-r-- 1 postgres postgres 108K Sep  9 20:05 chr1_gl000191_random.maf.index
-rw-rw-r-- 1 postgres postgres  22M Oct 31  2009 chr1_gl000192_random.maf
-rw-rw-r-- 1 postgres postgres 376K Sep  9 20:06 chr1_gl000192_random.maf.index
-rw-rw-r-- 1 postgres postgres  21G Oct 31  2009 chr1.maf
-rw-rw-r-- 1 postgres postgres 330M Sep  9 17:13 chr1.maf.index
-rw-rw-r-- 1 postgres postgres 5.6G Oct 31  2009 chr20.maf
-rw-rw-r-- 1 postgres postgres  83M Sep  9 20:59 chr20.maf.index
-rw-rw-r-- 1 postgres postgres 342K Oct 31  2009 chr21_gl000210_random.maf
-rw-rw-r-- 1 postgres postgres  31K Sep  9 21:05 chr21_gl000210_random.maf.index
-rw-rw-r-- 1 postgres postgres 2.9G Oct 31  2009 chr21.maf
-rw-rw-r-- 1 postgres postgres  38M Sep  9 21:05 chr21.maf.index
-rw-rw-r-- 1 postgres postgres 2.8G Oct 31  2009 chr22.maf
-rw-rw-r-- 1 postgres postgres  37M Sep  9 21:10 chr22.maf.index
-rw-rw-r-- 1 postgres postgres  23G Oct 31  2009 chr2.maf
-rw-rw-r-- 1 postgres postgres 355M Sep  9 20:49 chr2.maf.index
-rw-rw-r-- 1 postgres postgres  19G Oct 31  2009 chr3.maf
-rw-rw-r-- 1 postgres postgres 291M Sep  9 21:45 chr3.maf.index
-rw-rw-r-- 1 postgres postgres 9.1M Oct 31  2009 chr4_ctg9_hap1.maf
-rw-rw-r-- 1 postgres postgres 150K Sep  9 22:16 chr4_ctg9_hap1.maf.index
-rw-rw-r-- 1 postgres postgres 4.8M Oct 31  2009 chr4_gl000193_random.maf
-rw-rw-r-- 1 postgres postgres 101K Sep  9 22:16 chr4_gl000193_random.maf.index
-rw-rw-r-- 1 postgres postgres 2.2M Oct 31  2009 chr4_gl000194_random.maf
-rw-rw-r-- 1 postgres postgres 112K Sep  9 22:16 chr4_gl000194_random.maf.index
-rw-rw-r-- 1 postgres postgres  17G Oct 31  2009 chr4.maf
-rw-rw-r-- 1 postgres postgres 257M Sep  9 22:16 chr4.maf.index
-rw-rw-r-- 1 postgres postgres  17G Oct 31  2009 chr5.maf
-rw-rw-r-- 1 postgres postgres 255M Sep  9 22:47 chr5.maf.index
-rw-rw-r-- 1 postgres postgres  44M Oct 31  2009 chr6_apd_hap1.maf
-rw-rw-r-- 1 postgres postgres 496K Sep  9 23:18 chr6_apd_hap1.maf.index
-rw-rw-r-- 1 postgres postgres  96M Oct 31  2009 chr6_cox_hap2.maf
-rw-rw-r-- 1 postgres postgres 1.1M Sep  9 23:18 chr6_cox_hap2.maf.index
-rw-rw-r-- 1 postgres postgres  86M Oct 31  2009 chr6_dbb_hap3.maf
-rw-rw-r-- 1 postgres postgres 926K Sep  9 23:18 chr6_dbb_hap3.maf.index
-rw-rw-r-- 1 postgres postgres  16G Oct 31  2009 chr6.maf
-rw-rw-r-- 1 postgres postgres 249M Sep  9 23:17 chr6.maf.index
-rw-rw-r-- 1 postgres postgres  78M Oct 31  2009 chr6_mann_hap4.maf
-rw-rw-r-- 1 postgres postgres 848K Sep  9 23:18 chr6_mann_hap4.maf.index
-rw-rw-r-- 1 postgres postgres  80M Oct 31  2009 chr6_mcf_hap5.maf
-rw-rw-r-- 1 postgres postgres 854K Sep  9 23:18 chr6_mcf_hap5.maf.index
-rw-rw-r-- 1 postgres postgres  87M Oct 31  2009 chr6_qbl_hap6.maf
-rw-rw-r-- 1 postgres postgres 949K Sep  9 23:18 chr6_qbl_hap6.maf.index
-rw-rw-r-- 1 postgres postgres  80M Oct 31  2009 chr6_ssto_hap7.maf
-rw-rw-r-- 1 postgres postgres 871K Sep  9 23:19 chr6_ssto_hap7.maf.index
-rw-rw-r-- 1 postgres postgres 2.4M Oct 31  2009 chr7_gl000195_random.maf
-rw-rw-r-- 1 postgres postgres  56K Sep  9 23:44 chr7_gl000195_random.maf.index
-rw-rw-r-- 1 postgres postgres  14G Oct 31  2009 chr7.maf
-rw-rw-r-- 1 postgres postgres 214M Sep  9 23:44 chr7.maf.index
-rw-rw-r-- 1 postgres postgres 551K Oct 31  2009 chr8_gl000196_random.maf
-rw-rw-r-- 1 postgres postgres  50K Sep 10 00:08 chr8_gl000196_random.maf.index
-rw-rw-r-- 1 postgres postgres 1.4M Oct 31  2009 chr8_gl000197_random.maf
-rw-rw-r-- 1 postgres postgres  56K Sep 10 00:08 chr8_gl000197_random.maf.index
-rw-rw-r-- 1 postgres postgres  13G Oct 31  2009 chr8.maf
-rw-rw-r-- 1 postgres postgres 201M Sep 10 00:08 chr8.maf.index
==

And thanks for the suggestion of adding an extra dir level, I will do that.

At the moment, I only need primates, but I couldn't find a way to get
subset of mafs (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/), so I
downloaded the 46 way files and index primates first. If you knows a
trick to get a selected subset, I would love to hear it.

Thanks!

Leon


On Wed, Sep 11, 2013 at 6:38 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> 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/
>



-- 
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/

Reply via email to