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Manta currently handles paired-end (FR) reads only. #309

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hanqin580230 opened this issue Apr 13, 2023 · 2 comments
Open

Manta currently handles paired-end (FR) reads only. #309

hanqin580230 opened this issue Apr 13, 2023 · 2 comments

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@hanqin580230
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Hi.
I am running manta 1.6.0 and he manta options for the configManta.py I used was:
python2 configManta.py
--bam ERR5671305.srt.rmdup.real.bam
--referenceFasta mPpa.hic.fasta
--runDir Af45
My error is shown below:
[2023-04-13T06:05:13.557416Z] [cu16] [166827_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/home/yul20t1/.conda/envs/manta3/new/libexec/GetAlignmentStats --ref /home/yul20t1/ZhouJT.Dir/ReferenceGenome/black_leopard/mPpa.hic.fasta --output-file /home/yul20t1/ZhouJT.Dir/leopard_SV_VCF/manta/black_mapping/africa/Af45/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/yul20t1/ZhouJT.Dir/leopard_bams/black_mapping/africa/Af45/ERR5671305.srt.rmdup.real.bam'
[2023-04-13T06:05:13.564653Z] [cu16] [166827_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 10 stderr lines from task (of 10 total lines):
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.513808Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2023-Apr-13 14:05:13 /home/yul20t1/.conda/envs/manta3/manta-1.6.0.release_src/src/c++/lib/manta/ReadGroupStatsUtil.cpp(461): Throw in function void ReadGroupTracker::finalize()
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.515521Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::wrapexceptillumina::common::GeneralException
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.516487Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] std::exception::what: Unexpected consensus read orientation (Rm) for read group '' in bam file '/home/yul20t1/ZhouJT.Dir/leopard_bams/black_mapping/africa/Af45/ERR5671305.srt.rmdup.real.bam
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.517363Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] Manta currently handles paired-end (FR) reads only.
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.518116Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000]
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.518880Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000]
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.519724Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] cmdline: /home/yul20t1/.conda/envs/manta3/new/libexec/GetAlignmentStats --ref /home/yul20t1/ZhouJT.Dir/ReferenceGenome/black_leopard/mPpa.hic.fasta --output-file /home/yul20t1/ZhouJT.Dir/leopard_SV_VCF/manta/black_mapping/africa/Af45/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/yul20t1/ZhouJT.Dir/leopard_bams/black_mapping/africa/Af45/ERR5671305.srt.rmdup.real.bam
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.520455Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] version: 1.6.0
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.521143Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] buildTime: 2023-04-13T03:31:35.013871Z
[2023-04-13T06:05:13.566534Z] [cu16] [166827_1] [TaskManager] [ERROR] [2023-04-13T06:05:13.521809Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] compiler: g++-7.2.0
[2023-04-13T06:05:13.568620Z] [cu16] [166827_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2023-04-13T06:05:33.062584Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] Workflow terminated due to the following task errors:
[2023-04-13T06:05:33.065546Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/home/yul20t1/.conda/envs/manta3/new/libexec/GetAlignmentStats --ref /home/yul20t1/ZhouJT.Dir/ReferenceGenome/black_leopard/mPpa.hic.fasta --output-file /home/yul20t1/ZhouJT.Dir/leopard_SV_VCF/manta/black_mapping/africa/Af45/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/yul20t1/ZhouJT.Dir/leopard_bams/black_mapping/africa/Af45/ERR5671305.srt.rmdup.real.bam'
[2023-04-13T06:05:33.124008Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 10 stderr lines from task (of 10 total lines):
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.513808Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: 2023-Apr-13 14:05:13 /home/yul20t1/.conda/envs/manta3/manta-1.6.0.release_src/src/c++/lib/manta/ReadGroupStatsUtil.cpp(461): Throw in function void ReadGroupTracker::finalize()
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.515521Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] Dynamic exception type: boost::wrapexceptillumina::common::GeneralException
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.516487Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] std::exception::what: Unexpected consensus read orientation (Rm) for read group '' in bam file '/home/yul20t1/ZhouJT.Dir/leopard_bams/black_mapping/africa/Af45/ERR5671305.srt.rmdup.real.bam
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.517363Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] Manta currently handles paired-end (FR) reads only.
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.518116Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000]
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.518880Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000]
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.519724Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] cmdline: /home/yul20t1/.conda/envs/manta3/new/libexec/GetAlignmentStats --ref /home/yul20t1/ZhouJT.Dir/ReferenceGenome/black_leopard/mPpa.hic.fasta --output-file /home/yul20t1/ZhouJT.Dir/leopard_SV_VCF/manta/black_mapping/africa/Af45/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /home/yul20t1/ZhouJT.Dir/leopard_bams/black_mapping/africa/Af45/ERR5671305.srt.rmdup.real.bam
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.520455Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] version: 1.6.0
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.521143Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] buildTime: 2023-04-13T03:31:35.013871Z
[2023-04-13T06:05:33.126511Z] [cu16] [166827_1] [WorkflowRunner] [ERROR] [2023-04-13T06:05:13.521809Z] [cu16] [166827_1] [getAlignmentStats_generateStats_000] compiler: g++-7.2.0

Could you please provide some explanation what the problem is? Is there a way to call SVs anyways on this bam file?
Thank you for your support and best regards, Qin
@ssss123456789
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Hi，I have the same problem as you, did you solve it？

@hanqin580230
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Hi，I have the same problem as you, did you solve it？

I have tried all similar solutions to other problems, but still haven't solved it

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@ssss123456789 @hanqin580230