...extracting tumor discordant reads
...extracting normal discordant reads
...extracting tumor split reads
...extracting normal split reads
RUNNING: /xchip/gistic/Jeremiah/GIT/speedseq/bin/speedseq sv -B /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam,/xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam -R /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta -t 2 -x /xchip/gistic/Jeremiah/GIT/lumpy-sv/exclude.bed -o lumpy_somatic
Sourcing executables from /xchip/gistic/Jeremiah/GIT/speedseq/bin/speedseq.config ...

        create temporary directory

Running LUMPY express
OUTPUT: lumpy_somatic.YHC9EE9l8IY5/lumpy_somatic.sv.vcf
Sourcing executables from /xchip/gistic/Jeremiah/GIT/speedseq/bin/speedseq.config ...

    create temporary directory
Calculating insert distributions... 
Library read groups: tumor-
Library read length: 101
done
1
Calculating insert distributions... 
Library read groups: id
Library read length: 101
done
1
Running LUMPY... 

/xchip/gistic/Jeremiah/GIT/speedseq//bin/lumpy  \
    -t lumpy_somatic.YHC9EE9l8IY5/temp_lumpyexpress/lumpy_somatic.sv.vcf \
    -msw 4 \
    -tt 0 \
    -x /xchip/gistic/Jeremiah/GIT/lumpy-sv/exclude.bed \
     -pe bam_file:tum.discordants.bam,histo_file:lumpy_somatic.YHC9EE9l8IY5/temp_lumpyexpress/lumpy_somatic.sv.vcf.sample1.lib1.x4.histo,mean:322.898687983,stdev:81.6018767025,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,id:tumor_sim,min_mapping_threshold:20,read_group:tumor- -pe bam_file:norm.discordants.bam,histo_file:lumpy_somatic.YHC9EE9l8IY5/temp_lumpyexpress/lumpy_somatic.sv.vcf.sample2.lib1.x4.histo,mean:314.997116293,stdev:72.077827909,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,id:HCC1143_BL,min_mapping_threshold:20,read_group:id \
     -sr bam_file:tum.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:tumor_sim,min_clip:20 -sr bam_file:norm.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:HCC1143_BL,min_clip:20 \
    > lumpy_somatic.YHC9EE9l8IY5/lumpy_somatic.sv.vcf
/xchip/gistic/Jeremiah/GIT/speedseq//bin/lumpy  -t lumpy_somatic.YHC9EE9l8IY5/temp_lumpyexpress/lumpy_somatic.sv.vcf -msw 4 -tt 0 -x /xchip/gistic/Jeremiah/GIT/lumpy-sv/exclude.bed  -pe bam_file:tum.discordants.bam,histo_file:lumpy_somatic.YHC9EE9l8IY5/temp_lumpyexpress/lumpy_somatic.sv.vcf.sample1.lib1.x4.histo,mean:322.898687983,stdev:81.6018767025,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,id:tumor_sim,min_mapping_threshold:20,read_group:tumor- -pe bam_file:norm.discordants.bam,histo_file:lumpy_somatic.YHC9EE9l8IY5/temp_lumpyexpress/lumpy_somatic.sv.vcf.sample2.lib1.x4.histo,mean:314.997116293,stdev:72.077827909,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,id:HCC1143_BL,min_mapping_threshold:20,read_group:id  -sr bam_file:tum.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:tumor_sim,min_clip:20 -sr bam_file:norm.splitters.bam,back_distance:10,min_mapping_threshold:20,weight:1,id:HCC1143_BL,min_clip:20 > lumpy_somatic.YHC9EE9l8IY5/lumpy_somatic.sv.vcf
LUMPY Express done
SV calling done.
...deleting norm.discordants and norm.splitters.bam
...deleting tum.discordants and tum.splitters.bam