Bug Fixes
fq2bam, fq2bam_meth, deepvariant, deepsomatic, and pangenome_aware_deepvariant:
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In the
4.6.0-2release we have fixed a bug which caused the above tools to crash on DGX Spark unless performance parameters were manually set.
fq2bam and fq2bam_meth:
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In the
4.6.0-2release we have fixed a memory leak which occurred during CPU recovery. -
Resolved potential deadlock conditions that could occur when work queues become saturated.
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Fixed error which could trigger if
--bwa-cpu-thread-poolwas set to 1 thread. -
Fixed benign error which was reported when setting the environment variable CUDA_LOG_FILE=stderr.
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Fixed a memory leak when the
--align-onlyoption is on and outputs an unsorted bam file.
fq2bam, fq2bam_meth, giraffe, minimap2, rna_fq2bam:
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Fixed a missing comparison between the sum of base qualities and
INT8_MAX / 2in mark duplicates.
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Fixed a bug where batches could fail to enter CPU recovery mode when an error occurred during GPU extension.
Known Issues:
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fq2bam, fq2bam_meth, giraffe, minimap2, rna_fq2bam, bamsort, and associated pipelines: The parameter
--gpuwriteis not recommended for use on DGX Spark as it may fail.