Run could not finish for DUP variant with option "--svs_to_assemble --svs_to_softclip" on

[justin-mbca]

I am running Metasv with local assembly for duplication variants. My input is only 5 duplication variants and 4 of them were skipped due to small size, so there is only 1 duplication will be processed for local assembly. I am wondering how much time this process will take. My job has been running over a day with 2 threads and 12G memory for each thread. Are there anyway to speed up this process? For other types of variant DEL,Inseration,Duplication, the same setting could be finished in a few hours with all variants from one chromosome. Thanks, Justin

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