Spent many days to get all the CREST dependencies to run, and anyone knows what this means?
I got a bunch of stuff like:
tumor.bam.predSV.txt file is empty.
What's wrong here? Any idea?
Code:
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
Code:
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
What's wrong here? Any idea?
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