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Input Stream Error during mergeLocusGraph #99
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Thanks for the report, we reproduce the issue here. We'll send an update when this is sorted. |
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Note if you'd like a temporary workaround you can disable |
ctsa
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Aug 29, 2017
A bug was preventing the binary graph file from being written out by EstimateSVLoci when multi-region is used and no candidate SV content is found in the targeted regions. Fixed in this patch. Closes #99.
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We've finished the fix. This will be available in the next release. For now I've backported the patch onto the v1.1.1 release code here: https://github.com/Illumina/manta/tree/MANTA-1211-backport-for-v1.1.1 |
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@ctsa Thanks for the fix. |
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Hi,
During a recent somatic run, input stream error was encountered while executing megerLocusGraph. One empty bin file under "svLocusGraph.bin.tmpdir" could be causing the problem as excluding the file from the list resolves the issue. Please check what caused the file to be empty, or if there is some other cause.
Files can be download here.
Error code listed below.
[2017-08-24T02:02:51.978624] [gb203] [15523_1] [TaskManager] [ERROR] Failed to complete command task: 'mergeLocusGraph' lauched from master workflow, error code: 1, command: '/home/Share/softwares/manta_1.1.1/libexec/MergeSVLoci --output-file /home/liyuan/analysis_temp/CtDNA_SJY23_male/manta/workspace/svLocusGraph.bin --graph-file-list /home/liyuan/analysis_temp/CtDNA_SJY23_male/manta/workspace/svLocusGraph.bin.tmpdir/list.svLocusGraph.txt'[2017-08-24T02:02:51.980594] [gb203] [15523_1] [TaskManager] [ERROR] [mergeLocusGraph] Error Message:[2017-08-24T02:02:51.982736] [gb203] [15523_1] [TaskManager] [ERROR] [mergeLocusGraph] Last 6 stderr lines from task (of 6 total lines):[2017-08-24T02:02:51.982736] [gb203] [15523_1] [TaskManager] [ERROR] [2017-08-24T02:02:51.940472] [gb203] [15523_1] [mergeLocusGraph] FATAL_ERROR: EXCEPTION: input stream error[2017-08-24T02:02:51.982736] [gb203] [15523_1] [TaskManager] [ERROR] [2017-08-24T02:02:51.941467] [gb203] [15523_1] [mergeLocusGraph] ...caught in program.run()[2017-08-24T02:02:51.982736] [gb203] [15523_1] [TaskManager] [ERROR] [2017-08-24T02:02:51.942354] [gb203] [15523_1] [mergeLocusGraph] cmdline: /home/Share/softwares/manta_1.1.1/libexec/MergeSVLoci --output-file /home/liyuan/analysis_temp/CtDNA_SJY23_male/manta/workspace/svLocusGraph.bin --graph-file-list /home/liyuan/analysis_temp/CtDNA_SJY23_male/manta/workspace/svL ocusGraph.bin.tmpdir/list.svLocusGraph.txt[2017-08-24T02:02:51.982736] [gb203] [15523_1] [TaskManager] [ERROR] [2017-08-24T02:02:51.943041] [gb203] [15523_1] [mergeLocusGraph] version: 1.1.1[2017-08-24T02:02:51.982736] [gb203] [15523_1] [TaskManager] [ERROR] [2017-08-24T02:02:51.943712] [gb203] [15523_1] [mergeLocusGraph] buildTime: 2017-05-27T03:23:56.028559Z[2017-08-24T02:02:51.982736] [gb203] [15523_1] [TaskManager] [ERROR] [2017-08-24T02:02:51.944368] [gb203] [15523_1] [mergeLocusGraph] compiler: g++-4.8.5[2017-08-24T02:02:51.984443] [gb203] [15523_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.The text was updated successfully, but these errors were encountered: