atomicbitvector assertion error in untangle

[esrice]

When running this command:

odgi untangle -i k_locus.og -r 'bGalGal1b#0#chrZ:11159192-11400491' -m 256 -P > test.bed

I receive the following error:

[odgi::untangle] warning: no step index specified. Building one with a sample rate of 8. This may take additional time. A step index can be provided via -a, --step-index. A step index can be built using odgi st
epindex.
[odgi::algorithms::stepindex] Collecting Steps Progress: 18.37% @ 1.84e+03/s elapsed: 00:00:00:00 remain: 00:[odgi::algorithms::stepindex] Collecting Steps Progress: 100.00% @ 1.06e+03/s elapsed: 00:00:00:00 re
main: 00:00:00:00
[odgi::algorithms::stepindex] Building Progress: 100.00% @ 1.05e+03/s elapsed: 00:00:00:00 remain: 00:00:00:00
[odgi::algorithms::untangle] untangling 294 queries with 1 targets
[odgi::algorithms::untangle] establishing initial cuts for 294 paths
odgi: /opt/conda/conda-bld/odgi_1671316371355/work/deps/atomicbitvector/include/atomic_bitvector.hpp:159: bool atomicbitvector::atomic_bv_t::set(size_t, std::memory_order): Assertion `idx < _size' failed.
Aborted

Running v0.8.2-0-g8715c55. Let me know if there's any other information that would be helpful. Thanks!

[ekg]

I would guess that there is a mismatch between yout BED file and the graph paths. Have you confirmed they match? You may need to apply odgi procbed if the graph is a subset of a larger one but the BED is not. Just a thought.

To be sure we can understand the best thing is to share the test case. Is this possible?

On Wed, Mar 29, 2023, 23:03 Edward S. Rice @.***> wrote:

When running this command:

odgi untangle -i k_locus.og -r 'bGalGal1b#0#chrZ:11159192-11400491' -m 256 -P > test.bed

I receive the following error:

[odgi::untangle] warning: no step index specified. Building one with a sample rate of 8. This may take additional time. A step index can be provided via -a, --step-index. A step index can be built using odgi st epindex. [odgi::algorithms::stepindex] Collecting Steps Progress: 18.37% @ 1.84e+03/s elapsed: 00:00:00:00 remain: 00:[odgi::algorithms::stepindex] Collecting Steps Progress: 100.00% @ 1.06e+03/s elapsed: 00:00:00:00 re main: 00:00:00:00 [odgi::algorithms::stepindex] Building Progress: 100.00% @ 1.05e+03/s elapsed: 00:00:00:00 remain: 00:00:00:00 [odgi::algorithms::untangle] untangling 294 queries with 1 targets [odgi::algorithms::untangle] establishing initial cuts for 294 paths odgi: /opt/conda/conda-bld/odgi_1671316371355/work/deps/atomicbitvector/include/atomic_bitvector.hpp:159: bool atomicbitvector::atomic_bv_t::set(size_t, std::memory_order): Assertion `idx < _size' failed. Aborted

Running v0.8.2-0-g8715c55. Let me know if there's any other information that would be helpful. Thanks!

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[esrice]

Thanks for the fast reply. I wasn't using a range from a bed file, but rather the argument to -r is the name of the path from "odgi paths" as recommended by the tutorial "Untangling the pangenome" under the "Linearize the C4 region" heading. The og is indeed a subgraph of a larger graph, but I'm trying to untangle using the whole path of bGalGal1b through the subgraph, as the tutorial does for the hg38 path. How might I go about doing this? Thanks!

On Thu, Mar 30, 2023, 7:36 AM Erik Garrison @.***> wrote:

I would guess that there is a mismatch between yout BED file and the graph paths. Have you confirmed they match? You may need to apply odgi procbed if the graph is a subset of a larger one but the BED is not. Just a thought.

To be sure we can understand the best thing is to share the test case. Is this possible?

On Wed, Mar 29, 2023, 23:03 Edward S. Rice @.***> wrote:

When running this command:

odgi untangle -i k_locus.og -r 'bGalGal1b#0#chrZ:11159192-11400491' -m 256 -P > test.bed

I receive the following error:

[odgi::untangle] warning: no step index specified. Building one with a sample rate of 8. This may take additional time. A step index can be provided via -a, --step-index. A step index can be built using odgi st epindex. [odgi::algorithms::stepindex] Collecting Steps Progress: 18.37% @ 1.84e+03/s elapsed: 00:00:00:00 remain: 00:[odgi::algorithms::stepindex] Collecting Steps Progress: 100.00% @ 1.06e+03/s elapsed: 00:00:00:00 re main: 00:00:00:00 [odgi::algorithms::stepindex] Building Progress: 100.00% @ 1.05e+03/s elapsed: 00:00:00:00 remain: 00:00:00:00 [odgi::algorithms::untangle] untangling 294 queries with 1 targets [odgi::algorithms::untangle] establishing initial cuts for 294 paths odgi: /opt/conda/conda-bld/odgi_1671316371355/work/deps/atomicbitvector/include/atomic_bitvector.hpp:159: bool atomicbitvector::atomic_bv_t::set(size_t, std::memory_order): Assertion `idx < _size' failed. Aborted

Running v0.8.2-0-g8715c55. Let me know if there's any other information that would be helpful. Thanks!

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