# Hail unable to see sample vcf files
**URL:** https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174
**Category:** Help \[0.1\]
**Created:** [March 28, 2017, 6:55pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174 "2017-03-28T18:55:17Z")
**Posts on this page:** 14
**Page:** 1
### Author:  [@mweiner](https://discuss.hail.is/u/mweiner)
#### Post date: [March 28, 2017, 6:55pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/1 "2017-03-28T18:55:17Z")
In running through the ‘Getting Started’ i am trying to import the included sample.vcf into Hail’s .vds format, run: but when i run the command in the python interperter i get the error:
[cloudera@quickstart hail]$ python2.7
Python 2.7.13 (default, Mar 28 2017, 10:26:54)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type “help”, “copyright”, “credits” or “license” for more information.
> > > from hail import \*
> > > hc = HailContext()
> > > Setting default log level to “WARN”.
> > > To adjust logging level use sc.setLogLevel(newLevel).
> > > hc.import\_vcf(‘src/test/resources/sample.vcf’).write(‘sample.vds’)
> > > hail: info: SparkUI: [http://192.168.40.130:4040](http://192.168.40.130:4040)
> > > hail: warning: `src/test/resources/sample.vcf’ refers to no files
> > > Traceback (most recent call last):
> > > File “”, line 1, in
> > > File “”, line 2, in import\_vcf
> > > File “/home/cloudera/hail/python/hail/java.py”, line 110, in handle\_py4j
> > > raise FatalError(msg)
> > > hail.java.FatalError: arguments refer to no files
and i can not go beyond that without getting into more errors. Any thoughts ?
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### Author:  [@tpoterba](https://discuss.hail.is/u/tpoterba)
#### Post date: [March 28, 2017, 7:29pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/2 "2017-03-28T19:29:27Z")
Hi Michael,
I’ve seen this kind of error before when using a system with an HDFS file system installed – this is the default file system in Spark, so `src/test/resources/sample.vcf` will look in the hdfs home directory.
If this is the case, try importing this file by using `file://` followed by the fully clarified path to `sample.vcf`.
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### Author:  [@mweiner](https://discuss.hail.is/u/mweiner)
#### Post date: [March 28, 2017, 7:58pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/3 "2017-03-28T19:58:38Z")
Thank you, Tim, i will try that suggestion - i hadnt even considered that
Michael
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### Author:  [@mweiner](https://discuss.hail.is/u/mweiner)
#### Post date: [March 29, 2017, 11:04am UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/4 "2017-03-29T11:04:09Z")
Well that got me a little further:
> > > hc.import\_vcf(‘file:///home/cloudera/hail/src/test/resources/sample.vcf’).write(‘sample.vds’)
> > > Traceback (most recent call last):
> > > File “”, line 1, in
> > > File “”, line 2, in import\_vcf
> > > File “/home/cloudera/hail/python/hail/java.py”, line 110, in handle\_py4j
> > > raise FatalError(msg)
> > > hail.java.FatalError: UnsupportedClassVersionError: is/hail/io/compress/BGzipCodec : Unsupported major.minor version 52.0
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### Author:  [@tpoterba](https://discuss.hail.is/u/tpoterba)
#### Post date: [March 29, 2017, 2:34pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/5 "2017-03-29T14:34:28Z")
Looks like you don’t have Java 8, running `java -version` will tell you what you’ve got.
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### Author:  [@mweiner](https://discuss.hail.is/u/mweiner)
#### Post date: [March 29, 2017, 2:35pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/6 "2017-03-29T14:35:39Z")
Ack you are right, i thought i changed the JAVA\_HOME to point to 1.8.0 before starting this. Thank you for pointing that out.
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### Author:  [@klong](https://discuss.hail.is/u/klong)
#### Post date: [July 17, 2017, 6:55pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/7 "2017-07-17T18:55:40Z")
I have a similar issue but my java home is set. The error is a a little different:
“Hail version: 0.1-5661c35
Error summary: UnsupportedClassVersionError: is/hail/io/compress/BGzipCodec : Unsupported major.minor version 52.0”
“echo $JAVA\_HOME
/opt/jdk1.8.0\_131
echo $JRE\_HOME
/opt/jdk1.8.0\_131/jre”
Mentions this in the error “UnsupportedClassVersionError: is/hail/io/compress/BGzipCodec : Unsupported major.minor version 52.0”
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### Author:  [@tpoterba](https://discuss.hail.is/u/tpoterba)
#### Post date: [July 17, 2017, 7:14pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/8 "2017-07-17T19:14:45Z")
Is it possible that your jar wasn’t compiled with java 8?
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### Author:  [@klong](https://discuss.hail.is/u/klong)
#### Post date: [July 17, 2017, 7:24pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/9 "2017-07-17T19:24:46Z")
I can compile it again to test that theory.
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### Author:  [@klong](https://discuss.hail.is/u/klong)
#### Post date: [July 18, 2017, 1:28pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/10 "2017-07-18T13:28:28Z")
Compiled it again making sure Java was set to version 8. Still have the same issue.
Hail version: 0.1-5661c35
Error summary: UnsupportedClassVersionError: is/hail/io/compress/BGzipCodec : Unsupported major.minor version 52.0
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### Author:  [@danking](https://discuss.hail.is/u/danking)
#### Post date: [July 18, 2017, 3:51pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/11 "2017-07-18T15:51:16Z")
Hi @klong,
Please see this [Stack Overflow post](https://stackoverflow.com/a/42027100/6823256) about setting the JDK version for a Spark cluster. Setting `JAVA_HOME` only modifies the JDK on the driver node (the node on which you’ve set `JAVA_HOME`). You must also set the appropriate JDK for all of the worker nodes. This can be done with a `spark2-submit` `--conf` parameter:
```nohighlight
--conf spark.executorEnv.JAVA_HOME=/path/on/executor/to/jdk1.8
```
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### Author:  [@klong](https://discuss.hail.is/u/klong)
#### Post date: [July 18, 2017, 7:28pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/12 "2017-07-18T19:28:07Z")
Awesome. I am passed this hurdle now. If remove the $SPARK\_CLASSPATH from my env what do I set these equal?
–conf spark.executor.extraClassPath= /path/to/Spark???
–conf spark.driver.extraClassPath=???
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### Author:  [@tpoterba](https://discuss.hail.is/u/tpoterba)
#### Post date: [July 18, 2017, 7:37pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/13 "2017-07-18T19:37:39Z")
Both should have the path to the Hail jar, I think. That should have been the old value of $SPARK\_CLASSPATH
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### Author:  [@klong](https://discuss.hail.is/u/klong)
#### Post date: [July 18, 2017, 7:47pm UTC](https://discuss.hail.is/t/hail-unable-to-see-sample-vcf-files/174/14 "2017-07-18T19:47:08Z")
Thank you for the quick answer.