SOLiD alignment browser

[alig]

Just wondering if anyone has tried to run any of the ABI SOLiD open source software as I cannot even get started. I get a long list of errors starting with the output below

Alison/ABISOLiD/solidbrowser/bin/get-real-path: not found
Reading config file conf/apollo.cfg
Can't find tiers file fly.tiers--looking in jar
Creating Alison/ABISOLiD/solidbrowser/conf/fly.tiers from /fly.tiers
Couldn't get fly.tiers from jar
Error on line 54 of conf/fly.style:
Types file fly.tiers not found!
Can't find tiers file fly.tiers--looking in jar

thanks alig

[westerman]

Which software is giving you problems? We run the corona_lite and browser packages successfully.

[alig]

SOLiD alignment browser

I'm trying to run Applied Biosystems SOLiD System Alignment Browser (SAB) downloaded from Applied Biosystems website

alig

[westerman]

Solid Alignment Browser work on Linux & Solaris, at least.

I can't help troubleshoot your problem but can say that we run SAB on both Linux and Solaris. The initial message says:

This is Applied Biosystems SOLiD Alignment Browser v2.0.0, last updated Sep 26 2008. Based on Apollo Genome Annotation and Curation Tool, version 1.6.4.

If you do not even get that far then you may need to re-download and re-install the software. Or something. But the program does work and so the problems must be on your end instead of being global.

[lellabioinfo]

Hi, I get a long list of errors after the installation of SOLID ALIGNMENT BROWSER. Did anyone find the same problem?

APOLLO_ROOT: /appliedbiosystems/solidbrowser
OS name: Linux
OS arch: amd64
Java version: 1.6.0_0
Cannot run program "/appliedbiosystems/solidbrowser/bin/get-real-path": java.io.IOException: error=2, No such file or directory
Reading config file conf/apollo.cfg
Can't find tiers file fly.tiers--looking in jar
Creating /appliedbiosystems/solidbrowser/conf/fly.tiers from /fly.tiers
Couldn't get fly.tiers from jar
Error on line 54 of conf/fly.style:
Types file fly.tiers not found!
Can't find tiers file fly.tiers--looking in jar
Creating /appliedbiosystems/solidbrowser/conf/fly.tiers from /fly.tiers
Couldn't get fly.tiers from jar
Error on line 56 of conf/chado.style:
Types file fly.tiers not found!
Can't find tiers file rice.tiers--looking in jar
Creating /appliedbiosystems/solidbrowser/conf/rice.tiers from /rice.tiers
Couldn't get rice.tiers from jar
Error on line 54 of conf/rice.style:
Types file rice.tiers not found!
warning - unable to find chado jdbc adapter config file chado-adapter.xml
Can't find tiers file ensj.tiers--looking in jar
Creating /appliedbiosystems/solidbrowser/conf/ensj.tiers from /ensj.tiers
Couldn't get ensj.tiers from jar
Error on line 2 of conf/gff.style:
Types file ensj.tiers not found!
....

Thanks a lot!

[westerman]

...
Cannot run program "/appliedbiosystems/solidbrowser/bin/get-real-path": java.io.IOException: error=2, No such file or directory
...

As usual when the first error you encounter is 'no such file' then I suggest checking your PATH to make sure that it points to the corona_lite/bin directory. One way to do this is via the corona shell script. I run tcsh and have in my .cshrc

setenv CORONAROOT /phillip/corona_lite
source $CORONAROOT/etc/profile.d/corona.csh

Similar commands are available to bash, etc.

If you want for us to do more troubleshooting of your problem then please do an:

echo $PATH
echo $CORONAROOT

And paste in the results into your message.

[jsun529]

SOLiD

When run corona_lite matching and SNP pipeline, there are several known snp indels have not been picked up , what are the parameters to fiddle ? Thanks

[westerman]

In regards to missing SNPs, I know of no parameters to fiddle with. Oh, there is the mysterious '-pt' parameters but as far as I can tell it does not make much of a difference.

Do check the snp_prob.dat file to see if your SNP was even potentially discovered.

There is the diBayes program which is available from the Solid software web site. I haven't had much luck with the program but perhaps I need to try an different approach.