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Unable to create .adam from .sam #1717

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Rokshan2016 opened this Issue Sep 12, 2017 · 8 comments

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@Rokshan2016

Rokshan2016 commented Sep 12, 2017

Can anyone help for this---

Exception in thread "main" java.io.FileNotFoundException: Couldn't find any files matching /home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-co/src/test/resources/small.sam. If you are trying to glob a directory of Parquet files, you need to glob inside the directory as well (e.g., "glob.me..adam/", instead of "glob.me.*.adam".

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heuermh Sep 12, 2017

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Sure, what is the call that causes this exception?

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heuermh commented Sep 12, 2017

Sure, what is the call that causes this exception?

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Rokshan2016 Sep 12, 2017

Thanks for quick reply
I am trying to convert .sam to .adam

./adam-submit transformAlignments /home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-co/src/test/resources/small.sam /home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-core/src/test/resources/small.adam

Rokshan2016 commented Sep 12, 2017

Thanks for quick reply
I am trying to convert .sam to .adam

./adam-submit transformAlignments /home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-co/src/test/resources/small.sam /home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-core/src/test/resources/small.adam

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You might have a typo:

/home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-co/src/test/resources/small.sam

to

/home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-core/src/test/resources/small.sam

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heuermh commented Sep 12, 2017

You might have a typo:

/home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-co/src/test/resources/small.sam

to

/home/rokshan.jahan/project/spark-genome-alignment-demo/build/adam/adam-core/src/test/resources/small.sam

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Rokshan2016 Sep 12, 2017

ok , let me check that, thanks

Rokshan2016 commented Sep 12, 2017

ok , let me check that, thanks

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Rokshan2016 Sep 12, 2017

error.txt

Please find the full stack trace
Thanks

Rokshan2016 commented Sep 12, 2017

error.txt

Please find the full stack trace
Thanks

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If you are using Spark on YARN over a cluster, then the paths need to be on shared storage, such as HDFS.

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heuermh commented Sep 12, 2017

If you are using Spark on YARN over a cluster, then the paths need to be on shared storage, such as HDFS.

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Rokshan2016 Sep 12, 2017

ok, let me try that

Thanks

Rokshan2016 commented Sep 12, 2017

ok, let me try that

Thanks

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Rokshan2016 Sep 12, 2017

It works .
Thanks:)

Rokshan2016 commented Sep 12, 2017

It works .
Thanks:)

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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