Create pdf screenshots GConf warning

[avilella]

Hi again @dariober ,

I have a bash loop that will create pdf screenshots of a list of regions for one bam file. This is the command-line I came up with:

cat $myregions | while read region; do echo $region; ASCIIGenome -fa $fa -ni -r $region -x "BSseq && save ${i}.$region.ascii.pdf" $i 1>/dev/null; done

When I run this on a CentOS machine that I ssh into, I get this warning:

GConf Error: Failed to contact configuration server; some possible causes are that you need to enable TCP/IP networking for ORBit, or you have stale NFS locks due to a system crash. See http://projects.gnome.org/gconf/ for information. (Details —  1: Failed to get connection to session: /bin/dbus-launch terminated abnormally with the following error: PuTTY X11 proxy: MIT-MAGIC-COOKIE-1 data did not matchAutolaunch error: X11 initialization failed.

Any ideas?

[dariober]

Hello- A couple of things... For looping over a number of regions consider using the -b/--batch option, see an example [here] (ttp://asciigenome.readthedocs.io/en/latest/examples.html#batch-and-non-interactive-mode). This is faster than re-starting ASCIIGenome from scratch for each region since you don't need to re-start the JVM, ASCIIGenome, loading files etc.

About the error you are getting, could you try to pin it down more? E.g. does this minimal run cause the issue:

ASCIIGenome -ni -x 'save tmp.pdf'

## Or
ASCIIGenome -ni -x 'save tmp.pdf' aln.bam