Manta currently handles paired-end (FR) reads only.
Opened this issue · 2 comments
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
Hi，I have the same problem as you, did you solve it？
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