Andrew Erzunov
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Activity overview
Latest activity by Andrew Erzunov-
Andrew Erzunov commented,
Hello Genevieve,After running BaseRecalibrator tool, I got the following result (BaseRecalibrator was able to recalibrate 0 reads):https://drive.google.com/file/d/1mVtbBjgUcA9WFNaI3bOZYiXc-yH-KqtK/...
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Andrew Erzunov commented,
Hi Genevieve,I tried to add PU field:And after running the following command:I got this error: Faithfully,Andrew
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Andrew Erzunov commented,
Hello, Genevieve.After applying the following command, i got the following output: Faithfully,Andrew
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Andrew Erzunov commented,
Hello, Genevieve.I am attaching the log file after running the following command: ./gatk-4.2.6.1/gatk ReadsPipelineSpark -I /media/gene/sdb/cromwell/gatk_wdl/genome/genome_align.bam -R /media/gene/...
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Andrew Erzunov commented,
Thank you very much for your response, Genevieve.Using the Java argument -Xmx really helped to solve "java.lang.OutOfMemoryError" problem. ReadsPipelineSpark successfully executed on exome data, bu...
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Andrew Erzunov commented,
Hi Genevieve, Thanks a lot for your response.I tried to run ReadsPipelineSpark within GATK locally. Here is a command i used: docker run -v /xchg/local/pipelines/references/cromwell/gatk_wdl/exome_...
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Andrew Erzunov created a post,
ReadsPipelineSparkMulticore.wdl, Unrecognized runtime attribute keys: discs, cpu
AnsweredHello, while running ReadsPipelineSparkMulticore.wdl (https://github.com/broadinstitute/gatk/tree/master/scripts/spark_wdl) encountered the following problem. I would like to know what could be the...