Comments (5)
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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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!
from mixcr.
Whats the difference between the commands you have tried? Can you please share what another error you got?
from mixcr.
Hi, were you able to resolve the issue?
from mixcr.
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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