LJA
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AntonBankevich
Assertion `in_edges==out_edges' failed. Child process crashed
07:07:30 167Mb INFO: Finished loading graph 07:07:31 500Mb INFO: Looking for unique edges 07:07:31 500Mb INFO: Marked 342 long edges as unique 07:07:31 500Mb INFO: Marking extra edges as unique based on read paths 07:12:57 0.5Gb INFO: Marked 342 edges as unique 07:12:57 0.5Gb INFO: Splitting graph with unique edges 07:12:57 0.5Gb INFO: Processing 2452 components 07:12:57 0.5Gb INFO: Finished unique edges search. Found 4444 unique edges 07:12:57 0.5Gb INFO: Analysing repeats of multiplicity 2 and looking for additional unique edges 07:12:57 0.5Gb INFO: Finished processing of repeats of multiplicity 2. Found 0 erroneous edges. 07:12:57 0.5Gb INFO: Resolving repeats 07:12:57 0.5Gb INFO: Constructing paths 07:13:01 0.6Gb INFO: Building graph === Stack Trace === /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(_Z16print_stacktracev+0x40) [0x45d7d0] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(_ZN17repeat_resolution12MultiplexDBG22FreezeUnpairedVerticesEv+0x117) [0x585147] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(_ZN17repeat_resolution12MultiplexDBGC2ERKSt6vectorINS_16SuccinctEdgeInfoESaIS2_EEmPNS_7RRPathsEb+0x9a8) [0x589a48] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(_ZN17repeat_resolution12MultiplexDBGC2ERN3dbg9SparseDBGEPNS_7RRPathsEmR19UniqueClassificator+0x33) [0x589b23] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(_ZN17repeat_resolution14RepeatResolver14ResolveRepeatsERN7logging6LoggerEm+0x1ad) [0x4760cd] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja() [0x45b67e] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(_Z9runInForkRKSt8functionIFvvEE+0x20) [0x45dea0] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(_Z9MDBGPhaseRN7logging6LoggerEmmmmmbRKNSt12experimental10filesystem2v14pathES7_S7_bb+0xf7) [0x4552f7] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja(main+0x13e2) [0x452562] /usr/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f0198864555] /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja() [0x454245] lja: /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/src/projects/repeat_resolution/mdbg.cpp:171: void repeat_resolution::MultiplexDBG::FreezeUnpairedVertices(): Assertion `in_edges==out_edges' failed. Child process crashed
Hi, thank you for this report. Can you please try the solution in https://github.com/AntonBankevich/LJA/issues/21#issuecomment-1074238528 ?
LJA reported the above problem when I input the entire data (size = 14GB). However, when I reduced the data size to 761M, LJA was fine.
The command line is as follows: /date/home/yang/Software/LJA/LJA-untagged-c539e6b1159980742576/bin/lja -o OutputDir --reads ./m64081_220225_235158.fasta -t 30
Hi, thank you for this report. Can you please try the solution in #21 (comment) ?
Thanks for your reply, I am running the program again according to your suggestion!
Hi, thank you for this report. Can you please try the solution in #21 (comment) ?
I have tried commenting out or deleting the line 171, but still report the same problem.
Hmm, sorry for that! :( Have you recompiled the project after commenting out the line?
I suggest trying the fix that @AntonBankevich has suggested in this comment https://github.com/AntonBankevich/LJA/issues/21#issuecomment-1074238528. Specifically to try version of LJA in branch bug_fix.