hgLoadMaf zoom in error

[Farre Belmonte, Marta]

Hi,

I’m trying to upload maf files to my mirror site. I’m doing this:

[mfbelmonte@login1(rvchpc1)]$ hgLoadMaf bosTau6 cetaRum_maf -loadFile=all_cetaRum.maf

Indexing and tabulating ./all_cetaRum.maf

Loading cetaRum_maf into database

Loaded 13038345 mafs in 1 files from

And then the summary, by doing this:

[mfbelmonte@login1(rvchpc1)]$ hgLoadMafSummary bosTau6 mafSummary all_cetaRum.maf

Indexing and tabulating all_cetaRum.maf

Created 3037065 summary blocks from 91521867 components and 13038345 mafs from all_cetaRum.maf

Loading into bosTau6 table mafSummary...

I updated the trackDb.ra by adding this track information, as following:

track cetaRum_maf

shortLabel MAF_cetaRum

longLabel Multiple alignments cetaRum 31st July 2014

group cne_repeats 

priority 99

visibility full 

color 160,160,160

altcolor 160,160,160

type wigMaf 0.0 1.0

speciesOrder species1 species2 species3

summary mafSummary

Everything looks fine when zoom out in dense and full mode, but when I try to zoom in I get this error in the browser:

• External file ./all_cetaRum.maf cannot be opened or has wrong size. Old size 31493581798, new size -1, error No such file or directory

Could you please assist?

Thanks,

Marta

                    

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[Hiram Clawson]

Good Morning Marta:

Your maf file needs to appear in /gbdb/bosTau6/...

For example, in the directory where you built the maf file, symlink it to
the table name directory: '/gbdb/bosTau6/cetaRum'

$ mkdir /gbdb/bosTau6/cetaRum
$ ln -s `pwd`/all_cetaRum.maf /gbdb/bosTau6/cetaRum/

Then, loading any maf files from that directory:

$ hgLoadMaf bosTau5 cetaRum

The name of your table is now 'cetaRum', use this name in your 'track'
line of the trackDb.ra file.

To see the file path loaded for this file:

$ hgsql -e 'select * from extFile;' bosTau6 | grep cetaRum

Note examples of loading maf files in our documents, for example:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/hg/makeDb/doc/hg38.txt

Look for the 'hgLoadMaf' commands.

--Hiram

> * External file ./all_cetaRum.maf cannot be opened or has wrong size. Old size 31493581798, new size -1, error No such file or directory