debreak does not output desirable results

[Huanle]

Hi @Maggi-Chen ,

I gave debreak (DeBreak_v1.0.2) a try, using the test dataset and I ran into the following error message (see below).

Seems to me 'test_out/tra-merged-*' and test_out/debreak_poa_workspace/ were not generated. I commented out line 227 of debreak, but the errors remain. Can you help me figure out what is going wrong?

Thanks a lot.

$ debreak --bam DeBreak/testdata/test_read.bam -o test_out/ --poa --rescue_large_ins --rescue_dup --ref 
DeBreak/testdata/test_ref.fa

Start to detect SV from DeBreak/testdata/test_read.bam chr1 is done with maplength: 22577500 chr1 - inv finished, time cost: 0.041229963302612305 chr1 -ins finished, time cost: 0.07404088973999023 chr1 - del finished, time cost: 0.07749056816101074 chr1 - dup finished, time cost: 0.07759332656860352 cat: 'test_out/tra-merged-*': No such file or directory [M::mm_idx_gen::0.0021.78] collected minimizers [M::mm_idx_gen::0.0032.23] sorted minimizers [M::main::0.0032.22] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.0032.15] mid_occ = 11 [M::mm_idx_stat] kmer size: 9; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.0032.13] distinct minimizers: 784 (97.58% are singletons); average occurrences: 1.034; average spacing: 5.319 [M::worker_pipeline::0.0042.07] mapped 45 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -k 9 -N 100 test_out/debreak_resdup_refseq/chr1__199998__157__45.fa test_out/debreak_resdup_insertseq/chr1__199998__157__45.fa [M::main] Real time: 0.005 sec; CPU: 0.009 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.0021.68] collected minimizers [M::mm_idx_gen::0.0032.25] sorted minimizers [M::main::0.0032.25] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.0042.19] mid_occ = 5 [M::mm_idx_stat] kmer size: 9; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.0042.15] distinct minimizers: 1123 (94.39% are singletons); average occurrences: 1.059; average spacing: 5.479 [M::worker_pipeline::0.0052.17] mapped 40 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -k 9 -N 100 test_out/debreak_resdup_refseq/chr1__249999__1257__45.fa test_out/debreak_resdup_insertseq/chr1__249999__1257__45.fa [M::main] Real time: 0.005 sec; CPU: 0.011 sec; Peak RSS: 0.004 GB ls: cannot access 'test_out/debreak_poa_workspace/*keepfile.ctg.fa': No such file or directory [M::mm_idx_gen::0.0201.05] collected minimizers [M::mm_idx_gen::0.0363.36] sorted minimizers [M::main::0.0363.35] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.0403.14] mid_occ = 63 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.0423.02] distinct minimizers: 75447 (96.98% are singletons); average occurrences: 1.124; average spacing: 5.306 [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -a -t 8 DeBreak/testdata/test_ref.fa test_out/debreak_poa_workspace/allfasta [M::main] Real time: 0.048 sec; CPU: 0.133 sec; Peak RSS: 0.010 GB Start to detect SVs from debreak_poa_workspace/allsvpoa.sam 8 finish chr1 [M::mm_idx_gen::0.0191.07] collected minimizers [M::mm_idx_gen::0.0353.56] sorted minimizers [M::main::0.0353.56] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.0373.38] mid_occ = 63 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.0393.29] distinct minimizers: 75447 (96.98% are singletons); average occurrences: 1.124; average spacing: 5.306 [M::worker_pipeline::0.046*2.93] mapped 1 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -a -t 8 --secondary=no DeBreak/testdata/test_ref.fa test_out/debreak_ins_workspace/debreak_rescuelargeins_merged.fa [M::main] Real time: 0.051 sec; CPU: 0.140 sec; Peak RSS: 0.010 GB Start to detect SVs from debreak_rescuelargeins_merged.sam