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Hi everyone,
I'd like to use CREST for SV detection, but during the analysis, after half a minute, the program suddenly hangs at one position (for over 12 hours now). The last output is:
2 71865166 - 8
Output is in /tmp/n128E1meup/4apwtkgGLM.fa.cap.contigs.clip.fa.psl
Then it will not go on, although the process is still 100% active. The previous step extractSClip.pl worked well, BLAT server is running. All optional parameters have the default setting. No errors anywhere, and I can't see that this position is very complicated; alignment visualization shows me a simple inversion with 8 soft-clippped reads. Looks pretty much standard.
Does anyone here experience this as well? And are there any parameters in CREST, that influence this behaviour?
Would be great, if someone has an idea.
Thanks in advance!
Christoph
I'd like to use CREST for SV detection, but during the analysis, after half a minute, the program suddenly hangs at one position (for over 12 hours now). The last output is:
2 71865166 - 8
Output is in /tmp/n128E1meup/4apwtkgGLM.fa.cap.contigs.clip.fa.psl
Then it will not go on, although the process is still 100% active. The previous step extractSClip.pl worked well, BLAT server is running. All optional parameters have the default setting. No errors anywhere, and I can't see that this position is very complicated; alignment visualization shows me a simple inversion with 8 soft-clippped reads. Looks pretty much standard.
Does anyone here experience this as well? And are there any parameters in CREST, that influence this behaviour?
Would be great, if someone has an idea.
Thanks in advance!
Christoph