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
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