rpetrovski
commented
8 years ago There is an issue with vigorous gap realignment which I am debugging at the moment. This feature makes sense for RNA. If you are running DNA, you should get reasonable gaps without turning it on.
Roman.
On 12 Sep 2016 17:12, "shamsudheen kv" notifications@github.com wrote:
I was doing an aligning an exome data with the following command.
$ /_home/shamsion/softwarelibrary/isaac2-master/build/bin/isaac-align -r /home/shamsion/softwarelibrary/FormatVersion6_iSAAC-02_15_07_25690771/sorted-reference.xml -b ../Rao_P2RX7_Family/ --base-calls-format fastq-gz --base-quality-cutoff 20 -m 120 -j 32 -o H10alighned --realign-vigorously yes
The command exit with an error 2016-09-12 21:26:48 [7fc0444bb700] ERROR: ***\ Internal Program Error - assertion (undoneAlignmentPos <= long(undoPivotGap.getEndPos(false).getPosition())) failed in isaac::build::GapRealigner::GapChoice isaac::build::GapRealigner::findBetterGapsChoice(const isaac::build::gapRealigner::GapsRange&, const isaac::reference::ReferencePosition&, const isaac::reference::ReferencePosition&, const std::vectorisaac::reference::Contig&, const isaac::io::FragmentAccessor&, const isaac::build::PackedFragmentBuffer::Index&, unsigned int&):/home/shamsion/softwarelibrary/isaac2-master/src/c++/lib/build/GapRealigner.cpp(1089): undoPivotPos pos ReferencePosition(0:3212350:0f) overlapped by an existing deletion PackedFragmentBuffer::Index(ReferencePosition(0:3212350:0f),64583823do 64583562mdo, 48M2510D52M) Segmentation fault (core dumped)
Where as when i run with only by using --realign-gaps yes instead of --realign-vigorously yes, it is working fine. Why this core dump error is coming? If I want to use both the option what is the preferable commandline/input
Thanks Shams
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I was doing an aligning an exome data with the following command.
$ /_home/shamsion/softwarelibrary/isaac2-master/build/bin/isaac-align -r /home/shamsion/softwarelibrary/FormatVersion6_iSAAC-02_15_07_25690771/sorted-reference.xml -b ../Rao_P2RX7_Family/ --base-calls-format fastq-gz --base-quality-cutoff 20 -m 120 -j 32 -o H10alighned --realign-vigorously yes
The command exit with an error 2016-09-12 21:26:48 [7fc0444bb700] ERROR: ***\ Internal Program Error - assertion (undoneAlignmentPos <= long(undoPivotGap.getEndPos(false).getPosition())) failed in isaac::build::GapRealigner::GapChoice isaac::build::GapRealigner::findBetterGapsChoice(const isaac::build::gapRealigner::GapsRange&, const isaac::reference::ReferencePosition&, const isaac::reference::ReferencePosition&, const std::vectorisaac::reference::Contig&, const isaac::io::FragmentAccessor&, const isaac::build::PackedFragmentBuffer::Index&, unsigned int&):/home/shamsion/softwarelibrary/isaac2-master/src/c++/lib/build/GapRealigner.cpp(1089): undoPivotPos pos ReferencePosition(0:3212350:0f) overlapped by an existing deletion PackedFragmentBuffer::Index(ReferencePosition(0:3212350:0f),64583823do 64583562mdo, 48M2510D52M) Segmentation fault (core dumped)
Where as when i run with only by using --realign-gaps yes instead of --realign-vigorously yes, it is working fine. Why this core dump error is coming? If I want to use both the option what is the preferable commandline/input
Thanks Shams