CREST error

[tahamasoodi]

Hi,

Can anybody help me to sort out the following error in CREST structural variation suite;

sort: open failed: /home/taha/Softwares/CREST/tmp/FIP4ZomcPu.fa.cap.contigs.clip.fa.psl: No such file or directory
can't open /home/taha/Softwares/CREST/tmp/FIP4ZomcPu.fa.cap.contigs.clip.fa.psl.sorted:No such file or directory at CREST.pl line 608

[GenoMax]

Error message looks pretty clear. Does this file (/home/taha/Softwares/CREST/tmp/FIP4ZomcPu.fa.cap.contigs.clip.fa.psl) actually exist?

[tahamasoodi]

Thanks GenoMax,
No, this file is not present in this location. Actually, when the program runs, it generates many temporary files which get stored in /home/taha/Softwares/CREST/tmp/ folder. Although this folder contains the file called FIP4ZomcPu.fa.cap.contigs.clip.fa but there is no file with .psl

[GenoMax]

It looks like blat search (which should generate the PSL files) is not working? Do you have blat installed and working correctly?

Is this problem happening with just one set of data (are other sets working ok)?

[tahamasoodi]

Thanks, yes i think it seems problem with the Blat. Now I'm getting the following error, when I re installed everything. How can I check whether Blat is working or not?

Sorry, the BLAT/iPCR server seems to be down. Please try again later.
chr10 1225800 + 2
Couldn't find host sjblat. h_errno 2
Resource temporarily unavailable

[GenoMax]

Have you installed the gfServer (from CREST README)?

2. The pipeline uses gfServer to mimic a standard blat server, so you need
to setup your own gfServer. Details on setting up the server can be found in
the BLAT package.