ozborn commented 12 years ago

How fast does this program run?

I ran it on a ~150 GB BAM file and it finished in about 30 seconds or so which I think is far too quick and did not provide any entries in bp.fa. The mapped.sam and the all.bed just contain header information, despite reporting success. Any idea what is going on?

Lowering the min BP cluster size didn't add any more results, still nothing.

-John

INPUT INFORMATION

SAM FILE : X306_Merged_Lanes_realigned.bam

FASTA FILE : ./hg19.fa

JSON FILE : null

OUTPUT DIR : X306

BP FILTER PROCESSES : 2

MAX BREAKPOINT DIFF : 2

MIN BP CLUSTER SIZE : 5

MIN MEAN BASE QUAL : 5

MIN SEQ LENGTH : 10

BASES AROUND BREAK : 1000

MAX SV DIFF : 10

MIN SV CLUSTER SIZE : 10

MAPPER : bwa

MAPPER THREADS : 2

node /lustre/scratch/ozborn/schroeder/ngs/clipcrop/shinout-clipcrop-421d175/subs/rawbreaks.js X306_Merged_Lanes_realigned.bam --parallel 2 node /lustre/scratch/ozborn/schroeder/ngs/clipcrop/shinout-clipcrop-421d175/subs/bpfastagen.js X306/bp.bed ./hg19.fa -l 1000 -j bwa index X306/bp.fa bwa aln -t 2 X306/bp.fa X306/bp.fastq >X306/mapped.sai bwa samse -f X306/mapped.sam X306/bp.fa X306/mapped.sai X306/bp.fastq node /lustre/scratch/ozborn/schroeder/ngs/clipcrop/shinout-clipcrop-421d175/subs/cluster_svinfo.js ./hg19.fa X306 10 10 SUCCEEDED

ghost commented 12 years ago

Got similar issues, runs quite fast but all output is empty except for headers.

ratman commented 12 years ago

We have the same!