# java.lang.UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()

**URL:** <https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569>\
**Category:** Help \[0.1\]\
**Created:** [July 16, 2018, 5:29am UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569 "2018-07-16T05:29:48Z")\
**Posts on this page:** 16\
**Page:** 1

<div class="post-metadata">

**Author:** ![roise3000](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/roise3000/32/170_2.png) [@roise3000](https://discuss.hail.is/u/roise3000)\
**Post date:** [July 16, 2018, 5:29am UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/1 "2018-07-16T05:29:48Z")

</div>

Hi! I’m brand new to hail. I’m trhying to get the tutorial working “01-genome-wide-association-study”, but I’m stuck on this line in the notebook: “hl.utils.get\_1kg(‘data/’)”, with the follwoing error:

```
2018-07-15 22:23:13 Hail: INFO: downloading 1KG VCF ...
  Source: https://storage.googleapis.com/hail-tutorial/1kg.vcf.bgz
2018-07-15 22:23:14 Hail: INFO: importing VCF and writing to matrix table...
---------------------------------------------------------------------------
FatalError Traceback (most recent call last)
<ipython-input-3-414286e92795> in <module>()
----> 1 hl.utils.get_1kg('data/')

~/hail/python/hail/utils/tutorial.py in get_1kg(output_dir, overwrite)
     66 cluster_readable_vcf = Env.jutils().copyToTmp(jhc, local_path_uri(tmp_vcf), 'vcf')
     67 info('importing VCF and writing to matrix table...')
---> 68 hl.import_vcf(cluster_readable_vcf, min_partitions=16).write(matrix_table_path, overwrite=True)
     69 
     70 tmp_annot = os.path.join(tmp_dir, '1kg_annotations.txt')

~/hail/python/hail/typecheck/check.py in wrapper(*args, **kwargs)
    545 def wrapper(*args, **kwargs):
    546 args_, kwargs_ = check_all(f, args, kwargs, checkers, is_method=is_method)
--> 547 return f(*args_, **kwargs_)
    548 
    549 update_wrapper(wrapper, f)

~/hail/python/hail/methods/impex.py in import_vcf(path, force, force_bgz, header_file, min_partitions, drop_samples, call_fields, reference_genome, contig_recoding, array_elements_required, skip_invalid_loci)
   1799 joption(min_partitions), drop_samples, jset_args(call_fields),
   1800 joption(rg), joption(contig_recoding), array_elements_required,
-> 1801 skip_invalid_loci)
   1802 
   1803 return MatrixTable(jmt)

/usr/local/spark-2.2.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py in __call__ (self, *args)
   1131 answer = self.gateway_client.send_command(command)
   1132 return_value = get_return_value(
-> 1133 answer, self.gateway_client, self.target_id, self.name)
   1134 
   1135 for temp_arg in temp_args:

~/hail/python/hail/utils/java.py in deco(*args, **kwargs)
    194 raise FatalError('%s\n\nJava stack trace:\n%s\n'
    195 'Hail version: %s\n'
--> 196 'Error summary: %s' % (deepest, full, hail. __version__ , deepest)) from None
    197 except pyspark.sql.utils.CapturedException as e:
    198 raise FatalError('%s\n\nJava stack trace:\n%s\n'

FatalError: UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V

Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 2 in stage 1.0 failed 1 times, most recent failure: Lost task 2.0 in stage 1.0 (TID 3, localhost, executor driver): java.lang.UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V
	at is.hail.annotations.Region.nativeCtor(Native Method)
	at is.hail.annotations.Region.<init>(Region.scala:35)
	at is.hail.annotations.Region$.apply(Region.scala:15)
	at is.hail.rvd.RVDContext$.default(RVDContext.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:6)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD.is$hail$sparkextras$ContextRDD$$sparkManagedContext(ContextRDD.scala:129)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:138)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:137)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2062)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2087)
	at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
	at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
	at is.hail.sparkextras.ContextRDD.collect(ContextRDD.scala:143)
	at is.hail.rvd.OrderedRVD$.getPartitionKeyInfo(OrderedRVD.scala:563)
	at is.hail.rvd.OrderedRVD$.coerce(OrderedRVD.scala:656)
	at is.hail.rvd.OrderedRVD$.coerce(OrderedRVD.scala:640)
	at is.hail.io.vcf.LoadVCF$.apply(LoadVCF.scala:911)
	at is.hail.HailContext$$anonfun$importVCFs$2.apply(HailContext.scala:641)
	at is.hail.HailContext$$anonfun$importVCFs$2.apply(HailContext.scala:639)
	at is.hail.HailContext.forceBGZip(HailContext.scala:604)
	at is.hail.HailContext.importVCFs(HailContext.scala:639)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:280)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:214)
	at java.lang.Thread.run(Thread.java:745)java.lang.UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V
	at is.hail.annotations.Region.nativeCtor(Native Method)
	at is.hail.annotations.Region.<init>(Region.scala:35)
	at is.hail.annotations.Region$.apply(Region.scala:15)
	at is.hail.rvd.RVDContext$.default(RVDContext.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:6)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD.is$hail$sparkextras$ContextRDD$$sparkManagedContext(ContextRDD.scala:129)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:138)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:137)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Hail version: devel-2d767347e1ea
Error summary: UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V
```

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 16, 2018, 7:16pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/2 "2018-07-16T19:16:05Z")

</div>

we must have broken our deployment for MacOS. I’ll have a fix asap.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 16, 2018, 7:30pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/3 "2018-07-16T19:30:44Z")

</div>

[https://github.com/hail-is/hail/issues/3934](https://github.com/hail-is/hail/issues/3934)  
should fix

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 16, 2018, 7:31pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/4 "2018-07-16T19:31:14Z")

</div>

(there will probably be a fixed distribution available for download in a few hours)

---

<div class="post-metadata">

**Author:** ![roise3000](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/roise3000/32/170_2.png) [@roise3000](https://discuss.hail.is/u/roise3000)\
**Post date:** [July 17, 2018, 6:52am UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/5 "2018-07-17T06:52:36Z")

</div>

Thanks Tim!  
Where do I download the new dist from?  
The version in [https://storage.googleapis.com/hail-common/distributions/devel/Hail-devel-f7631a0c96cd-Spark-2.2.0.zip](https://storage.googleapis.com/hail-common/distributions/devel/Hail-devel-f7631a0c96cd-Spark-2.2.0.zip) still gives me the same error.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 17, 2018, 8:46am UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/6 "2018-07-17T08:46:51Z")

</div>

ok, that’s the version that should have fixed it. Hmm.

What operating system are you using?

---

<div class="post-metadata">

**Author:** ![roise3000](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/roise3000/32/170_2.png) [@roise3000](https://discuss.hail.is/u/roise3000)\
**Post date:** [July 17, 2018, 6:00pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/7 "2018-07-17T18:00:04Z")

</div>

macOS Sierra  
10.12.6 (16G1510)  
MacBook Pro (Retina, 15-inch, Mid 2015)  
Processor: 2.5 GHz Intel Core i7

Hail version: devel-f7631a0c96cd

```
(hail) mn-mklosi:hail mklosi$ python --version
Python 3.6.6 :: Anaconda, Inc.

(hail) mn-mklosi:hail mklosi$ conda list
# packages in environment at /Users/mklosi/miniconda/envs/hail:
#
# Name Version Build Channel
appnope 0.1.0 py36hf537a9a_0  
backcall 0.1.0 py36_0  
blas 1.0 mkl  
bleach 2.1.3 py36_0  
bokeh 0.13.0 py36_0  
ca-certificates 2018.03.07 0  
certifi 2018.4.16 py36_0  
cycler 0.10.0 py36hfc81398_0  
dbus 1.13.2 h760590f_1  
decorator 4.3.0 py36_0  
entrypoints 0.2.3 py36_2  
expat 2.2.5 hb8e80ba_0  
freetype 2.9.1 hb4e5f40_0  
gettext 0.19.8.1 h15daf44_3  
glib 2.56.1 h35bc53a_0  
html5lib 1.0.1 py36_0  
icu 58.2 h4b95b61_1  
intel-openmp 2018.0.3 0  
ipykernel 4.8.2 py36_0  
ipython 6.4.0 py36_1  
ipython_genutils 0.2.0 py36h241746c_0  
ipywidgets 7.2.1 py36_0  
jedi 0.12.0 py36_1  
jinja2 2.10 py36_0  
jpeg 9b he5867d9_2  
jsonschema 2.6.0 py36hb385e00_0  
jupyter 1.0.0 py36_4  
jupyter_client 5.2.3 py36_0  
jupyter_console 5.2.0 py36_1  
jupyter_core 4.4.0 py36_0  
kiwisolver 1.0.1 py36h0a44026_0  
libcxx 4.0.1 h579ed51_0  
libcxxabi 4.0.1 hebd6815_0  
libedit 3.1.20170329 hb402a30_2  
libffi 3.2.1 h475c297_4  
libgfortran 3.0.1 h93005f0_2  
libiconv 1.15 hdd342a3_7  
libpng 1.6.34 he12f830_0  
libsodium 1.0.16 h3efe00b_0  
markupsafe 1.0 py36h1de35cc_1  
matplotlib 2.2.2 py36hbf02d85_2  
mistune 0.8.3 py36h1de35cc_1  
mkl 2018.0.3 1  
mkl_fft 1.0.2 py36h6b9c3cc_0  
mkl_random 1.0.1 py36h5d10147_1  
nbconvert 5.3.1 py36_0  
nbformat 4.4.0 py36h827af21_0  
ncurses 6.1 h0a44026_0  
notebook 5.5.0 py36_0  
numpy 1.14.5 py36h648b28d_4  
numpy-base 1.14.5 py36ha9ae307_4  
openssl 1.0.2o h26aff7b_0  
packaging 17.1 py36_0  
pandas 0.23.2 py36h6440ff4_0  
pandoc 2.2.1 h1a437c5_0  
pandocfilters 1.4.2 py36_1  
parsimonious 0.8.1 <pip>
parso 0.2.1 py36_0  
patsy 0.5.0 py36_0  
pcre 8.42 h378b8a2_0  
pexpect 4.6.0 py36_0  
pickleshare 0.7.4 py36hf512f8e_0  
pip 10.0.1 py36_0  
prompt_toolkit 1.0.15 py36haeda067_0  
ptyprocess 0.6.0 py36_0  
py4j 0.10.6 py36hde0549a_1  
pygments 2.2.0 py36h240cd3f_0  
pyparsing 2.2.0 py36_1  
pyqt 5.9.2 py36h655552a_0  
pyspark 2.2.0 py36_0  
python 3.6.6 hc167b69_0  
python-dateutil 2.7.3 py36_0  
pytz 2018.5 py36_0  
pyyaml 3.12 py36h1de35cc_1  
pyzmq 17.0.0 py36h1de35cc_3  
qt 5.9.6 h74ce4d9_0  
qtconsole 4.3.1 py36hd96c0ff_0  
readline 7.0 hc1231fa_4  
scipy 1.1.0 py36hf1f7d93_0  
seaborn 0.8.1 py36_0  
send2trash 1.5.0 py36_0  
setuptools 39.2.0 py36_0  
simplegeneric 0.8.1 py36_2  
sip 4.19.8 py36h0a44026_0  
six 1.11.0 py36_1  
sqlite 3.24.0 ha441bb4_0  
statsmodels 0.9.0 py36h1d22016_0  
terminado 0.8.1 py36_1  
testpath 0.3.1 py36h625a49b_0  
tk 8.6.7 h35a86e2_3  
tornado 5.0.2 py36h1de35cc_0  
traitlets 4.3.2 py36h65bd3ce_0  
wcwidth 0.1.7 py36h8c6ec74_0  
webencodings 0.5.1 py36_1  
wheel 0.31.1 py36_0  
widgetsnbextension 3.2.1 py36_0  
xz 5.2.4 h1de35cc_4  
yaml 0.1.7 hc338f04_2  
zeromq 4.2.5 h0a44026_0  
zlib 1.2.11 hf3cbc9b_2
```

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 17, 2018, 6:20pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/8 "2018-07-17T18:20:34Z")

</div>

we’re a bit stumped here. What version of java are you running?

---

<div class="post-metadata">

**Author:** ![roise3000](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/roise3000/32/170_2.png) [@roise3000](https://discuss.hail.is/u/roise3000)\
**Post date:** [July 17, 2018, 10:08pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/9 "2018-07-17T22:08:14Z")

</div>

```
JAVA_VERSION="1.8.0_121"
OS_NAME="Darwin"
OS_VERSION="11.2"
OS_ARCH="x86_64"
SOURCE=" .:f2b5b6ab1f55 corba:386e9b79fcf5 deploy:7130ca3292fd hotspot:90f94521c351 hotspot/make/closed:bb6215e98e28 hotspot/src/closed:5c67a72be91c hotspot/test/closed:262c6cd71fd1 install:709a5016570e jaxp:b8d4e4724071 jaxws:5b8834cc3bb9 jdk:2974746e5619 jdk/make/closed:14736f778a50 jdk/src/closed:784a1cdcf90e jdk/test/closed:75844215d99a langtools:f634736433d9 nashorn:fd548ea7e156 pubs:6c3449393359 sponsors:d32775ed283a"
BUILD_TYPE="commercial"

```

I’ll try to setup everything from scratch

---

<div class="post-metadata">

**Author:** ![roise3000](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/roise3000/32/170_2.png) [@roise3000](https://discuss.hail.is/u/roise3000)\
**Post date:** [July 18, 2018, 2:27am UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/10 "2018-07-18T02:27:43Z")

</div>

@tpoterba I downloaded the newest Hail version: devel-56ea3941ae61, and recreated my environment from scratch. still the same error ☹ I’m reattaching output, just in case smth has changed.

```
2018-07-17 19:24:51 Hail: INFO: downloading 1KG VCF ...
  Source: https://storage.googleapis.com/hail-tutorial/1kg.vcf.bgz
2018-07-17 19:24:52 Hail: INFO: importing VCF and writing to matrix table...
---------------------------------------------------------------------------
FatalError Traceback (most recent call last)
<ipython-input-3-414286e92795> in <module>()
----> 1 hl.utils.get_1kg('data/')

~/hail/python/hail/utils/tutorial.py in get_1kg(output_dir, overwrite)
     66 cluster_readable_vcf = Env.jutils().copyToTmp(jhc, local_path_uri(tmp_vcf), 'vcf')
     67 info('importing VCF and writing to matrix table...')
---> 68 hl.import_vcf(cluster_readable_vcf, min_partitions=16).write(matrix_table_path, overwrite=True)
     69 
     70 tmp_annot = os.path.join(tmp_dir, '1kg_annotations.txt')

~/hail/python/hail/typecheck/check.py in wrapper(*args, **kwargs)
    545 def wrapper(*args, **kwargs):
    546 args_, kwargs_ = check_all(f, args, kwargs, checkers, is_method=is_method)
--> 547 return f(*args_, **kwargs_)
    548 
    549 update_wrapper(wrapper, f)

~/hail/python/hail/matrixtable.py in write(self, output, overwrite, stage_locally, _codec_spec)
   2116 """
   2117 
-> 2118 self._jvds.write(output, overwrite, stage_locally, _codec_spec)
   2119 
   2120 def globals_table(self) -> Table:

/usr/local/spark-2.2.0-bin-hadoop2.7/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py in __call__ (self, *args)
   1131 answer = self.gateway_client.send_command(command)
   1132 return_value = get_return_value(
-> 1133 answer, self.gateway_client, self.target_id, self.name)
   1134 
   1135 for temp_arg in temp_args:

~/hail/python/hail/utils/java.py in deco(*args, **kwargs)
    198 raise FatalError('%s\n\nJava stack trace:\n%s\n'
    199 'Hail version: %s\n'
--> 200 'Error summary: %s' % (deepest, full, hail. __version__ , deepest)) from None
    201 except pyspark.sql.utils.CapturedException as e:
    202 raise FatalError('%s\n\nJava stack trace:\n%s\n'

FatalError: UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V

Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 4 in stage 1.0 failed 1 times, most recent failure: Lost task 4.0 in stage 1.0 (TID 5, localhost, executor driver): java.lang.UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V
	at is.hail.annotations.Region.nativeCtor(Native Method)
	at is.hail.annotations.Region.<init>(Region.scala:35)
	at is.hail.annotations.Region$.apply(Region.scala:15)
	at is.hail.rvd.RVDContext$.default(RVDContext.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:6)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD.is$hail$sparkextras$ContextRDD$$sparkManagedContext(ContextRDD.scala:129)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:138)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:137)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2062)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2087)
	at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
	at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
	at is.hail.sparkextras.ContextRDD.collect(ContextRDD.scala:143)
	at is.hail.rvd.OrderedRVD$.getPartitionKeyInfo(OrderedRVD.scala:574)
	at is.hail.rvd.OrderedRVD$.makeCoercer(OrderedRVD.scala:669)
	at is.hail.io.vcf.MatrixVCFReader.coercer$lzycompute(LoadVCF.scala:972)
	at is.hail.io.vcf.MatrixVCFReader.coercer(LoadVCF.scala:972)
	at is.hail.io.vcf.MatrixVCFReader.apply(LoadVCF.scala:1004)
	at is.hail.expr.ir.MatrixRead.execute(MatrixIR.scala:413)
	at is.hail.expr.ir.Interpret$.apply(Interpret.scala:573)
	at is.hail.expr.ir.Interpret$.apply(Interpret.scala:39)
	at is.hail.expr.ir.Interpret$.apply(Interpret.scala:15)
	at is.hail.variant.MatrixTable.write(MatrixTable.scala:1717)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
	at py4j.Gateway.invoke(Gateway.java:280)
	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
	at py4j.commands.CallCommand.execute(CallCommand.java:79)
	at py4j.GatewayConnection.run(GatewayConnection.java:214)
	at java.lang.Thread.run(Thread.java:745)java.lang.UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V
	at is.hail.annotations.Region.nativeCtor(Native Method)
	at is.hail.annotations.Region.<init>(Region.scala:35)
	at is.hail.annotations.Region$.apply(Region.scala:15)
	at is.hail.rvd.RVDContext$.default(RVDContext.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:8)
	at is.hail.rvd.package$RVDContextIsPointed$.point(package.scala:6)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD$Weaken$$anonfun$apply$4.apply(ContextRDD.scala:64)
	at is.hail.sparkextras.ContextRDD.is$hail$sparkextras$ContextRDD$$sparkManagedContext(ContextRDD.scala:129)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:138)
	at is.hail.sparkextras.ContextRDD$$anonfun$run$1.apply(ContextRDD.scala:137)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$23.apply(RDD.scala:797)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Hail version: devel-56ea3941ae61
Error summary: UnsatisfiedLinkError: is.hail.annotations.Region.nativeCtor()V
```

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 18, 2018, 2:45am UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/11 "2018-07-18T02:45:21Z")

</div>

Ack, thanks for helping us figure this out! We discussed a bit today with no solution. I’ll try again to clone your problem locally tomorrow.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 18, 2018, 2:44pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/12 "2018-07-18T14:44:35Z")

</div>

We have someone else reporting this issue with our deployment on Google Cloud. Something nefarious is going on.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 18, 2018, 8:00pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/13 "2018-07-18T20:00:04Z")

</div>

We’ve isolated the problem, fix soon!

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 18, 2018, 9:28pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/14 "2018-07-18T21:28:35Z")

</div>

fix is in and building, should be live tonight.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 18, 2018, 9:28pm UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/15 "2018-07-18T21:28:52Z")

</div>

sorry about that!

---

<div class="post-metadata">

**Author:** ![roise3000](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/roise3000/32/170_2.png) [@roise3000](https://discuss.hail.is/u/roise3000)\
**Post date:** [July 19, 2018, 5:55am UTC](https://discuss.hail.is/t/java-lang-unsatisfiedlinkerror-is-hail-annotations-region-nativector/569/16 "2018-07-19T05:55:07Z")

</div>

no problem. thanks for fixing so attentively.

```
2018-07-18 22:52:55 Hail: INFO: downloading 1KG VCF ...
  Source: https://storage.googleapis.com/hail-tutorial/1kg.vcf.bgz
2018-07-18 22:52:57 Hail: INFO: importing VCF and writing to matrix table...
2018-07-18 22:52:59 Hail: INFO: Coerced sorted dataset
2018-07-18 22:53:02 Hail: INFO: wrote 10961 items in 16 partitions to data/1kg.mt
2018-07-18 22:53:02 Hail: INFO: downloading 1KG annotations ...
  Source: https://storage.googleapis.com/hail-tutorial/1kg_annotations.txt
2018-07-18 22:53:03 Hail: INFO: Done!

```

yey!