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mizraelson avatar mizraelson commented on July 18, 2024

Hi, it looks like the issue is not with CPU or memory, but the storage. Can you try the following option:
--use-local-temp and let me know if it works.

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xmy1990 avatar xmy1990 commented on July 18, 2024

hi @mizraelson,
I added --use-local-temp, but another error was as follow:

Example: mixcr -Xmx40g analyze exome-seq --species hsa --threads 8 --use-local-temp test.bam out
This run used approximately 308m of memory

Then I tried

mixcr -Xmx40g analyze exome-seq --species hsa --threads 8 --use-local-temp test.bam out

The error befor happened again:

java.lang.IllegalStateException: Unexpected buffer behaviour. This might be a sign that you ran out of storage in the output or tmp folder.
        at com.milaboratory.o.zR.completed(SourceFile:1582)
        at com.milaboratory.o.Bk$a.completed(SourceFile:1163)
        at java.base/sun.nio.ch.Invoker.invokeUnchecked(Invoker.java:127)
        at java.base/sun.nio.ch.SimpleAsynchronousFileChannelImpl$3.run(SimpleAsynchronousFileChannelImpl.java:389)
        at java.base/java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1426)
        at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290)
        at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020)
        at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656)
        at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594)
        at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183)

Thanks!

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mizraelson avatar mizraelson commented on July 18, 2024

Whats the difference between the commands you have tried? Can you please share what another error you got?

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mizraelson avatar mizraelson commented on July 18, 2024

Hi, were you able to resolve the issue?

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xmy1990 avatar xmy1990 commented on July 18, 2024

Hi @mizraelson,

I have not resolved the storage issue which may be caused by our 50+ Gb WES data.
Even though some samples successfully got VDJ rearrangement results with MIXCR, the time is as long as 10+ hours which was unbearable.
I have just done an initial exploration for VDJ rearrangement and I may continue to solve this issue in the future.

Thank you for your kind help!

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