Did anyone run MetaSV with local assembly option on successfully especially for duplication variants?
Four types of variants are supported with local assembly: DEL, INS, INV, DUP. For my analysis, DEL, INS, INV could be finished within a few hours, but not DUP. Even 1 duplication variant could not finished over a day. The job is still running when I write this post.
The following are the details about parameters and output information.
My input parameters: --svs_to_assemble DUP --svs_to_softclip DUP
Where I am now from output information
INFO 2017-02-14 17:02:34,915 metasv.sv_interval Loading SV intervals from /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/MantaBreakdancer_metaSV/test_DUP.vcf
WARNING 2017-02-14 17:02:34,923 metasv.sv_interval Skipping Record(CHROM=1, POS=821604, REF=T, ALT=[DUP:TANDEM]) due to small size
WARNING 2017-02-14 17:02:34,923 metasv.sv_interval Skipping Record(CHROM=1, POS=2324462, REF=G, ALT=[DUP:TANDEM]) due to small size
WARNING 2017-02-14 17:02:34,924 metasv.sv_interval Skipping Record(CHROM=1, POS=3714245, REF=T, ALT=[DUP:TANDEM]) due to small size
WARNING 2017-02-14 17:02:34,924 metasv.sv_interval Skipping Record(CHROM=1, POS=4789624, REF=T, ALT=[DUP:TANDEM]) due to small size
INFO 2017-02-14 17:02:34,924 metasv.main SV types are set(['DUP'])
INFO 2017-02-14 17:02:34,924 metasv.main Output per-tool VCFs
INFO 2017-02-14 17:02:34,925 metasv.main Outputting single tool VCF for Manta
INFO 2017-02-14 17:02:34,976 metasv.main Indexing single tool VCF for Manta
INFO 2017-02-14 17:02:35,050 metasv.main Do merging
INFO 2017-02-14 17:02:35,050 metasv.main Processing SVs of type DUP
INFO 2017-02-14 17:02:35,050 metasv.main Intra-tool Merging SVs of type DUP
INFO 2017-02-14 17:02:35,050 metasv.main First level merging for DUP for tool Manta
INFO 2017-02-14 17:02:35,050 metasv.main Inter-tool Merging SVs of type DUP
INFO 2017-02-14 17:02:35,051 metasv.main Output merged VCF without assembly
INFO 2017-02-14 17:02:35,103 metasv.main ('DUP', 'LowQual', 'IMPRECISE', ('Manta',)):1
INFO 2017-02-14 17:02:35,103 metasv.main Running assembly
INFO 2017-02-14 17:02:35,103 metasv.main Creating directory /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/MantaBreakdancer_metaSV/metasv_work_test5DUP/spades
INFO 2017-02-14 17:02:35,111 metasv.main Creating directory /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/MantaBreakdancer_metaSV/metasv_work_test5DUP/age
INFO 2017-02-14 17:02:35,122 metasv.main Generating Soft-Clipping intervals.
INFO 2017-02-14 17:02:35,122 parallel_generate_sc_intervals-<_MainProcess(MainProcess, started)> SVs to soft-clip: set(['DUP', 'INV', 'DEL', 'INS'])
INFO 2017-02-14 17:02:35,315 get_bp_intervals-<_MainProcess(MainProcess, started)> 2 total candidate bp intervals in other methods
INFO 2017-02-14 17:02:35,325 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> Generating candidate intervals from /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/input/HCC4017_Clone4.DupsMarked_RG.bam for chromsome 1
INFO 2017-02-14 17:27:36,793 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 6949907 candidate reads
INFO 2017-02-14 17:28:07,973 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 574885 candidate NONE reads
INFO 2017-02-14 17:28:07,974 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> Gather intervals from breakpoints in other methods
INFO 2017-02-14 17:28:12,076 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 574885 bps in other methods
INFO 2017-02-14 17:44:31,879 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 127 unresolved intervals
INFO 2017-02-14 17:44:33,931 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 94 merged unresolved intervals
INFO 2017-02-14 17:44:34,789 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 94 filtered unresolved intervals
INFO 2017-02-14 17:44:34,935 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 79 coverage filtered unresolved intervals
INFO 2017-02-14 17:44:36,884 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 58 coverage filtered unresolved intervals
INFO 2017-02-14 17:57:45,636 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 179755 merged intervals with left bp support
Thanks,
Justin
Four types of variants are supported with local assembly: DEL, INS, INV, DUP. For my analysis, DEL, INS, INV could be finished within a few hours, but not DUP. Even 1 duplication variant could not finished over a day. The job is still running when I write this post.
The following are the details about parameters and output information.
My input parameters: --svs_to_assemble DUP --svs_to_softclip DUP
Where I am now from output information
INFO 2017-02-14 17:02:34,915 metasv.sv_interval Loading SV intervals from /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/MantaBreakdancer_metaSV/test_DUP.vcf
WARNING 2017-02-14 17:02:34,923 metasv.sv_interval Skipping Record(CHROM=1, POS=821604, REF=T, ALT=[DUP:TANDEM]) due to small size
WARNING 2017-02-14 17:02:34,923 metasv.sv_interval Skipping Record(CHROM=1, POS=2324462, REF=G, ALT=[DUP:TANDEM]) due to small size
WARNING 2017-02-14 17:02:34,924 metasv.sv_interval Skipping Record(CHROM=1, POS=3714245, REF=T, ALT=[DUP:TANDEM]) due to small size
WARNING 2017-02-14 17:02:34,924 metasv.sv_interval Skipping Record(CHROM=1, POS=4789624, REF=T, ALT=[DUP:TANDEM]) due to small size
INFO 2017-02-14 17:02:34,924 metasv.main SV types are set(['DUP'])
INFO 2017-02-14 17:02:34,924 metasv.main Output per-tool VCFs
INFO 2017-02-14 17:02:34,925 metasv.main Outputting single tool VCF for Manta
INFO 2017-02-14 17:02:34,976 metasv.main Indexing single tool VCF for Manta
INFO 2017-02-14 17:02:35,050 metasv.main Do merging
INFO 2017-02-14 17:02:35,050 metasv.main Processing SVs of type DUP
INFO 2017-02-14 17:02:35,050 metasv.main Intra-tool Merging SVs of type DUP
INFO 2017-02-14 17:02:35,050 metasv.main First level merging for DUP for tool Manta
INFO 2017-02-14 17:02:35,050 metasv.main Inter-tool Merging SVs of type DUP
INFO 2017-02-14 17:02:35,051 metasv.main Output merged VCF without assembly
INFO 2017-02-14 17:02:35,103 metasv.main ('DUP', 'LowQual', 'IMPRECISE', ('Manta',)):1
INFO 2017-02-14 17:02:35,103 metasv.main Running assembly
INFO 2017-02-14 17:02:35,103 metasv.main Creating directory /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/MantaBreakdancer_metaSV/metasv_work_test5DUP/spades
INFO 2017-02-14 17:02:35,111 metasv.main Creating directory /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/MantaBreakdancer_metaSV/metasv_work_test5DUP/age
INFO 2017-02-14 17:02:35,122 metasv.main Generating Soft-Clipping intervals.
INFO 2017-02-14 17:02:35,122 parallel_generate_sc_intervals-<_MainProcess(MainProcess, started)> SVs to soft-clip: set(['DUP', 'INV', 'DEL', 'INS'])
INFO 2017-02-14 17:02:35,315 get_bp_intervals-<_MainProcess(MainProcess, started)> 2 total candidate bp intervals in other methods
INFO 2017-02-14 17:02:35,325 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> Generating candidate intervals from /work/s167568/MGRAK_2016_10_17_WGS14_1507_0_MetaSV/input/HCC4017_Clone4.DupsMarked_RG.bam for chromsome 1
INFO 2017-02-14 17:27:36,793 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 6949907 candidate reads
INFO 2017-02-14 17:28:07,973 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 574885 candidate NONE reads
INFO 2017-02-14 17:28:07,974 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> Gather intervals from breakpoints in other methods
INFO 2017-02-14 17:28:12,076 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 574885 bps in other methods
INFO 2017-02-14 17:44:31,879 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 127 unresolved intervals
INFO 2017-02-14 17:44:33,931 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 94 merged unresolved intervals
INFO 2017-02-14 17:44:34,789 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 94 filtered unresolved intervals
INFO 2017-02-14 17:44:34,935 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 79 coverage filtered unresolved intervals
INFO 2017-02-14 17:44:36,884 resolve_none_svs-<Process(PoolWorker-1, started daemon)> 58 coverage filtered unresolved intervals
INFO 2017-02-14 17:57:45,636 generate_sc_intervals-<Process(PoolWorker-1, started daemon)> 179755 merged intervals with left bp support
Thanks,
Justin