8000 FusorSV stuck when starting posterior estimate on partition · Issue #32 · TheJacksonLaboratory/SVE · GitHub
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FusorSV stuck when starting posterior estimate on partition #32

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xmeng opened this issue Oct 7, 2019 · 0 comments
Open

FusorSV stuck when starting posterior estimate on partition #32

xmeng opened this issue Oct 7, 2019 · 0 comments

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@xmeng
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xmeng commented Oct 7, 2019

Hello,

Thanks for developing this tool. Does it work on bacteria genome? I tried several times and the program hang at line "starting posterior estimate on partition: t=7 b=8". It never produces any outputs.

I'd appreciate if you give any hints to debug.

Thanks.
xmeng

$python /tools/SVE/scripts/FusorSV/FusorSV.py -C -f /tools/SVE/scripts/FusorSV/data/models/default.pickle -r ../NCBI-GCA_000011065_1.fa -i out_sv/ -o /mnt/PRISM/out_vcf
no contig directory specified
using default stage id exclude list:[1, 36]
processing samples ['out_sv/BBNORM_TRIMMED_BT-tn2923-rep1_R_S18.vcf', 'out_sv/BBNORM_TRIMMED_BT-tn2923-rep1_R_S10.vcf', 'out_sv/BBNORM_TRIMMED_BT-tn2923-rep1_R_S11.vcf', 'out_sv/BBNORM_TRIMMED_BT-tn2923-rep1_R_S17.vcf']
for chroms ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y', 'MT']
merging the svmask regions
svmask regions merged in 0.0 sec
reading, parsing, partitioning and writing sample VCFs
reading sample sample1_S18.vcf
reading sample sample1_S10.vcf
reading sample sample1_S11.vcf
reading sample sample1_S17.vcf
finished reading 4 out of 4 samples generating 0 partitions in 1.06 sec
starting posterior estimate on partition: t=0 b=0
posterior estimate on partition: t=0 b=0 28.32 sec alpha=1.0
starting posterior estimate on partition: t=0 b=1
posterior estimate on partition: t=0 b=1 30.54 sec alpha=1.0
starting posterior estimate on partition: t=0 b=2
starting posterior estimate on partition: t=0 b=3
starting posterior estimate on partition: t=0 b=4
starting posterior estimate on partition: t=0 b=5
starting posterior estimate on partition: t=0 b=6
starting posterior estimate on partition: t=0 b=7
starting posterior estimate on partition: t=0 b=8
starting posterior estimate on partition: t=1 b=0
starting posterior estimate on partition: t=1 b=1
starting posterior estimate on partition: t=1 b=2
starting posterior estimate on partition: t=1 b=3
starting posterior estimate on partition: t=2 b=0
starting posterior estimate on partition: t=2 b=1
starting posterior estimate on partition: t=2 b=2
starting posterior estimate on partition: t=2 b=3
starting posterior estimate on partition: t=2 b=4
starting posterior estimate on partition: t=2 b=5
starting posterior estimate on partition: t=2 b=6
starting posterior estimate on partition: t=2 b=7
starting posterior estimate on partition: t=2 b=8
starting posterior estimate on partition: t=2 b=9
starting posterior estimate on partition: t=2 b=10
starting posterior estimate on partition: t=2 b=11
starting posterior estimate on partition: t=2 b=12
starting posterior estimate on partition: t=2 b=13
starting posterior estimate on partition: t=2 b=14
starting posterior estimate on partition: t=2 b=15
starting posterior estimate on partition: t=2 b=16
starting posterior estimate on partition: t=3 b=0
starting posterior estimate on partition: t=3 b=1
starting posterior estimate on partition: t=3 b=2
starting posterior estimate on partition: t=3 b=3
starting posterior estimate on partition: t=3 b=4
starting posterior estimate on partition: t=3 b=5
starting posterior estimate on partition: t=3 b=6
starting posterior estimate on partition: t=3 b=7
starting posterior estimate on partition: t=4 b=0
starting posterior estimate on partition: t=4 b=1
starting posterior estimate on partition: t=4 b=2
starting posterior estimate on partition: t=4 b=3
starting posterior estimate on partition: t=4 b=4
starting posterior estimate on partition: t=4 b=5
starting posterior estimate on partition: t=4 b=6
starting posterior estimate on partition: t=4 b=7
starting posterior estimate on partition: t=4 b=8
starting posterior estimate on partition: t=5 b=0
starting posterior estimate on partition: t=5 b=1
starting posterior estimate on partition: t=5 b=2
starting posterior estimate on partition: t=5 b=3
starting posterior estimate on partition: t=5 b=4
starting posterior estimate on partition: t=5 b=5
starting posterior estimate on partition: t=5 b=6
starting posterior estimate on partition: t=5 b=7
starting posterior estimate on partition: t=5 b=8
starting posterior estimate on partition: t=5 b=9
starting posterior estimate on partition: t=5 b=10
starting posterior estimate on partition: t=5 b=11
starting posterior estimate on partition: t=5 b=12
starting posterior estimate on partition: t=5 b=13
starting posterior estimate on partition: t=5 b=14
starting posterior estimate on partition: t=6 b=0
starting posterior estimate on partition: t=6 b=1
starting posterior estimate on partition: t=6 b=2
starting posterior estimate on partition: t=6 b=3
starting posterior estimate on partition: t=6 b=4
starting posterior estimate on partition: t=6 b=5
starting posterior estimate on partition: t=6 b=6
starting posterior estimate on partition: t=6 b=7
starting posterior estimate on partition: t=6 b=8
starting posterior estimate on partition: t=7 b=0
starting posterior estimate on partition: t=7 b=1
starting posterior estimate on partition: t=7 b=2
starting posterior estimate on partition: t=7 b=3
starting posterior estimate on partition: t=7 b=4
starting posterior estimate on partition: t=7 b=5
starting posterior estimate on partition: t=7 b=6
starting posterior estimate on partition: t=7 b=7
starting posterior estimate on partition: t=7 b=8
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