CREST outputs: what's wrong?

[lethalfang]

Spent many days to get all the CREST dependencies to run, and anyone knows what this means?

CREST.pl -f tumor.bam.cover.somatic.cover -d tumor.bam -g normal.bam --ref_genome human_g1k_v37_decoy.fasta -t human_g1k_v37_decoy.2bit --blatserver localhost --blatport 2014 -r 1

I got a bunch of stuff like:

SV filter starting....
low compexity filter
-seq value = query.fa
-repsiz range value = 2,8
-repsiz values = 2 to 8
-minrep value = 4
 INFO: Program read 167 bases 
 total bases read=167 
Sorting 2 repeat records
End 1st sort
Filtering repeats
nreps=2
AFTER FILTERS nreps=2
 End of Sequence file!
 total bases read=0 
 End of nucleotides. Exiting!
Type distance filter
1       223254531       +       hs37d5  33068960        -       14      hs37d5  33068960        +       1       223254531       -       19      CTX     0       0
Germline sclip filter
Loaded 201 letters in 1 sequences
Searched 1260 bases in 47 sequences
FAILED
SV filter starting....
low compexity filter
-seq value = query.fa
-repsiz range value = 2,8
-repsiz values = 2 to 8
-minrep value = 4
 INFO: Program read 106 bases 
 total bases read=106 
 End of Sequence file!
 total bases read=0 
 End of nucleotides. Exiting!
Type distance filter
Germline sclip filter
Loaded 201 letters in 1 sequences
Searched 398 bases in 17 sequences
FAILED

tumor.bam.predSV.txt file is empty.

What's wrong here? Any idea?

[gaoyf]

hello,I have met the same question. The .predSV.txt is empty. Do you have solved it? Can you help me?

[lethalfang]

hello,I have met the same question. The .predSV.txt is empty. Do you have solved it? Can you help me?

I forgot what my original problem was.
The .predSV.txt file is pretty small, sometimes only ~ 50 lines for the whole genome.
Have you tried the whole genome and saw an empty file?