# Unable to utilize my vcf file **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [December 16, 2021, 8:25am UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409 "2021-12-16T08:25:36Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![jeji29](https://avatars.discourse-cdn.com/v4/letter/j/b5ac83/32.png) [@jeji29](https://discuss.hail.is/u/jeji29)\ **Post date:** [December 16, 2021, 8:25am UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/1 "2021-12-16T08:25:36Z")
Hello, I am trying to import by vcf file, but I am getting an error whenever I am trying to apply any function to my file. ```auto i_dir = '/Users/jeji/ASD_pQTL' vcf_path = '/'.join([i_dir, "SNUBH_ASD_210210.vcf.gz"]) mt = hl.import_vcf(vcf_path, reference_genome = 'GRCh38', force_bgz = True, min_partitions = n_cores*4) ``` This is how I imported my file. This is the error I get. For example, when I try: ```auto mt.show() ``` This is the error code I get: ```auto --------------------------------------------------------------------------- FatalError Traceback (most recent call last) /var/folders/6t/k806qy3120z5c974tdcphgrm0000gn/T/ipykernel_36666/2845130735.py in ----> 1 mt.show() in show(self, n_rows, n_cols, include_row_fields, width, truncate, types, handler) /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/matrixtable.py in show(self, n_rows, n_cols, include_row_fields, width, truncate, types, handler) 2631 col_key_type = self.col_key.dtype 2632 if len(col_key_type) == 1 and col_key_type[0] in (hl.tstr, hl.tint32, hl.tint64): -> 2633 cols = self.col_key[0].take(displayed_n_cols) 2634 entries = {repr(cols[i]): t.entries[i] 2635 for i in range(0, displayed_n_cols)} in take(self, n, _localize) /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/expr/expressions/base_expression.py in take(self, n, _localize) 1003 e = t.take(n, _localize=False).map(lambda r: r[name]) 1004 if _localize: -> 1005 return hl.eval(e) 1006 return e 1007 in eval(expression) /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/expr/expressions/expression_utils.py in eval(expression) 192 Any 193 """ --> 194 return eval_timed(expression)[0] 195 196 in eval_timed(expression) /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/expr/expressions/expression_utils.py in eval_timed(expression) 156 if ir_type != expression.dtype: 157 raise ExpressionException(f'Expression type and IR type differed: \n{ir_type}\n vs \n{expression_type}') --> 158 (tupled_ans, timing) = Env.backend().execute(tupled_expression._ir, True) 159 else: 160 uid = Env.get_uid() /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed) 108 raise HailUserError(message_and_trace) from None 109 --> 110 raise e /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed) 84 # print(self._hail_package.expr.ir.Pretty.apply(jir, True, -1)) 85 try: ---> 86 result_tuple = self._jhc.backend().executeEncode(jir, stream_codec) 87 (result, timings) = (result_tuple._1(), result_tuple._2()) 88 value = ir.typ._from_encoding(result) /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/py4j/java_gateway.py in __call__ (self, *args) 1302 1303 answer = self.gateway_client.send_command(command) -> 1304 return_value = get_return_value( 1305 answer, self.gateway_client, self.target_id, self.name) 1306 /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/hail/backend/py4j_backend.py in deco(*args, **kwargs) 27 raise FatalError('Error summary: %s' % (deepest,), error_id) from None 28 else: ---> 29 raise FatalError('%s\n\nJava stack trace:\n%s\n' 30 'Hail version: %s\n' 31 'Error summary: %s' % (deepest, full, hail. __version__ , deepest), error_id) from None FatalError: IllegalArgumentException: requirement failed Java stack trace: java.lang.IllegalArgumentException: requirement failed at scala.Predef$.require(Predef.scala:268) at is.hail.rvd.RVDPartitioner.(RVDPartitioner.scala:52) at is.hail.rvd.RVDPartitioner.extendKeySamePartitions(RVDPartitioner.scala:141) at is.hail.expr.ir.LoweredTableReader$$anon$2.coerce(TableIR.scala:383) at is.hail.expr.ir.GenericTableValue.toTableStage(GenericTableValue.scala:162) at is.hail.io.vcf.MatrixVCFReader.lower(LoadVCF.scala:1790) at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:407) at is.hail.expr.ir.lowering.LowerTableIR$.apply(LowerTableIR.scala:1199) at is.hail.expr.ir.lowering.LowerToCDA$.lower(LowerToCDA.scala:69) at is.hail.expr.ir.lowering.LowerToCDA$.apply(LowerToCDA.scala:18) at is.hail.expr.ir.lowering.LowerToDistributedArrayPass.transform(LoweringPass.scala:77) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.evaluate$1(LowerOrInterpretNonCompilable.scala:27) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:67) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:53) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.apply(LowerOrInterpretNonCompilable.scala:72) at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.transform(LoweringPass.scala:69) at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$3(LoweringPass.scala:16) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$1(LoweringPass.scala:16) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass.apply(LoweringPass.scala:14) at is.hail.expr.ir.lowering.LoweringPass.apply$(LoweringPass.scala:13) at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.apply(LoweringPass.scala:64) at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1(LoweringPipeline.scala:15) at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1$adapted(LoweringPipeline.scala:13) at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36) at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:38) at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:13) at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:47) at is.hail.backend.spark.SparkBackend._execute(SparkBackend.scala:381) at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$2(SparkBackend.scala:417) at is.hail.backend.ExecuteContext$.$anonfun$scoped$3(ExecuteContext.scala:47) at is.hail.utils.package$.using(package.scala:638) at is.hail.backend.ExecuteContext$.$anonfun$scoped$2(ExecuteContext.scala:47) at is.hail.utils.package$.using(package.scala:638) at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:17) at is.hail.backend.ExecuteContext$.scoped(ExecuteContext.scala:46) at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:275) at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$1(SparkBackend.scala:414) at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52) at is.hail.backend.spark.SparkBackend.executeEncode(SparkBackend.scala:413) 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:282) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:238) at java.lang.Thread.run(Thread.java:748) Hail version: 0.2.79-f141af259254 Error summary: IllegalArgumentException: requirement failed ``` I am not sure where I should approach the problem from. Any solutions? Thanks in advance πŸ™‚ ---
**Author:** ![johnc1231](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/johnc1231/32/286_2.png) [@johnc1231](https://discuss.hail.is/u/johnc1231)\ **Post date:** [December 16, 2021, 5:25pm UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/2 "2021-12-16T17:25:23Z")
This seems like probably a hail bug. Two things: 1. Is this VCF private? Or is it public data? 2. Can you try making the first line of your hail script: ```auto hl._set_flags(no_whole_stage_codegen='1') ``` and see if that works? ---
**Author:** ![johnc1231](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/johnc1231/32/286_2.png) [@johnc1231](https://discuss.hail.is/u/johnc1231)\ **Post date:** [December 16, 2021, 5:30pm UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/3 "2021-12-16T17:30:56Z")
Can you also share the hail log file with us? ---
**Author:** ![jeji29](https://avatars.discourse-cdn.com/v4/letter/j/b5ac83/32.png) [@jeji29](https://discuss.hail.is/u/jeji29)\ **Post date:** [December 16, 2021, 11:52pm UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/4 "2021-12-16T23:52:39Z")
1. It is a private VCF data! 2. Yes, it works when I initialize hail by that code! and I have attached my log file. Thanks πŸ˜ƒ [hail20211217.log](https://discuss.hail.is/uploads/short-url/j37spEZV6vFXj9mh5ag9pd9kuds.log) (312.6 KB) ---
**Author:** ![skose](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/skose/32/518_2.png) [@skose](https://discuss.hail.is/u/skose)\ **Post date:** [January 10, 2022, 6:26pm UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/5 "2022-01-10T18:26:59Z")
Hi all, [25d](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/3) I am running into a similar issue. If I use hl.\_set\_flags(no\_whole\_stage\_codegen=β€˜1’) however and initialise that way, I am then unable to intialise hail with build β€˜GRCh38’. Is there a way around this? Thanks ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [January 10, 2022, 6:28pm UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/6 "2022-01-10T18:28:59Z")
Hey @skose! I’m sorry to hear Hail is giving you a hard time. Can you share the full error message you get when you start hail with GRCh38 as the default genome reference? ---
**Author:** ![skose](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/skose/32/518_2.png) [@skose](https://discuss.hail.is/u/skose)\ **Post date:** [January 10, 2022, 6:55pm UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/7 "2022-01-10T18:55:46Z")
Hi @danking Thanks for the reply. I initialise hail as per usual but then get a java error. The file is bgzipped and tabixed. When I try mt.show() it gets an error. I can do analysis on the file suck as kinship etc, but when I try to show anything it does that. The initial thread says to initialise with hl.\_set\_flags(no\_whole\_stage\_codegen=β€˜1’), but then I cannot do the init with the reference build I wish to use (β€˜GRCh38’). ```auto $ ipython Python 3.6.13 | packaged by conda-forge | (default, Sep 23 2021, 07:55:15) Type 'copyright', 'credits' or 'license' for more information IPython 7.16.2 -- An enhanced Interactive Python. Type '?' for help. In [1]: import hail as hl In [2]: build='GRCh38' In [3]: hl.init(default_reference=build) WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.apache.spark.unsafe.Platform (file:/Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/pyspark/jars/spark-unsafe_2.12-3.1.2.jar) to constructor java.nio.DirectByteBuffer(long,int) WARNING: Please consider reporting this to the maintainers of org.apache.spark.unsafe.Platform WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 2022-01-10 06:01:49 WARN NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable Setting default log level to "WARN". To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel). 2022-01-10 06:01:50 WARN Hail:43 - This Hail JAR was compiled for Spark 3.1.1, running with Spark 3.1.2. Compatibility is not guaranteed. Running on Apache Spark version 3.1.2 SparkUI available at http://25229cgnlt:4040 Welcome to ____ <>__ / /_/ / ____ / / / __ / _ `/ / / /_/ /_/\_,_/_/_/ version 0.2.78-b17627756568 LOGGING: writing to /Users/adminskose/Desktop/hail-20220110-0601-0.2.78-b17627756568.log In [4]: mt = hl.import_vcf('final.vcf.gz',force_bgz=True) In [5]: mt.show() 2022-01-10 06:03:41 Hail: INFO: Coerced prefix-sorted dataset (10 + 5) / 15] --------------------------------------------------------------------------- FatalError Traceback (most recent call last) in ----> 1 mt.show() in show(self, n_rows, n_cols, include_row_fields, width, truncate, types, handler) /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/matrixtable.py in show(self, n_rows, n_cols, include_row_fields, width, truncate, types, handler) 2631 col_key_type = self.col_key.dtype 2632 if len(col_key_type) == 1 and col_key_type[0] in (hl.tstr, hl.tint32, hl.tint64): -> 2633 cols = self.col_key[0].take(displayed_n_cols) 2634 entries = {repr(cols[i]): t.entries[i] 2635 for i in range(0, displayed_n_cols)} in take(self, n, _localize) /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/expr/expressions/base_expression.py in take(self, n, _localize) 1003 e = t.take(n, _localize=False).map(lambda r: r[name]) 1004 if _localize: -> 1005 return hl.eval(e) 1006 return e 1007 in eval(expression) /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/expr/expressions/expression_utils.py in eval(expression) 192 Any 193 """ --> 194 return eval_timed(expression)[0] 195 196 in eval_timed(expression) /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 575 def wrapper(__original_func, *args, **kwargs): 576 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 577 return __original_func(*args_, **kwargs_) 578 579 return wrapper /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/expr/expressions/expression_utils.py in eval_timed(expression) 156 if ir_type != expression.dtype: 157 raise ExpressionException(f'Expression type and IR type differed: \n{ir_type}\n vs \n{expression_type}') --> 158 (tupled_ans, timing) = Env.backend().execute(tupled_expression._ir, True) 159 else: 160 uid = Env.get_uid() /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed) 108 raise HailUserError(message_and_trace) from None 109 --> 110 raise e /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/backend/py4j_backend.py in execute(self, ir, timed) 84 # print(self._hail_package.expr.ir.Pretty.apply(jir, True, -1)) 85 try: ---> 86 result_tuple = self._jhc.backend().executeEncode(jir, stream_codec) 87 (result, timings) = (result_tuple._1(), result_tuple._2()) 88 value = ir.typ._from_encoding(result) /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/py4j/java_gateway.py in __call__ (self, *args) 1303 answer = self.gateway_client.send_command(command) 1304 return_value = get_return_value( -> 1305 answer, self.gateway_client, self.target_id, self.name) 1306 1307 for temp_arg in temp_args: /Applications/anaconda3/envs/bioinfo/lib/python3.6/site-packages/hail/backend/py4j_backend.py in deco(*args, **kwargs) 29 raise FatalError('%s\n\nJava stack trace:\n%s\n' 30 'Hail version: %s\n' ---> 31 'Error summary: %s' % (deepest, full, hail. __version__ , deepest), error_id) from None 32 except pyspark.sql.utils.CapturedException as e: 33 raise FatalError('%s\n\nJava stack trace:\n%s\n' FatalError: IllegalArgumentException: requirement failed Java stack trace: java.lang.IllegalArgumentException: requirement failed at scala.Predef$.require(Predef.scala:268) at is.hail.rvd.RVDPartitioner.(RVDPartitioner.scala:52) at is.hail.rvd.RVDPartitioner.extendKeySamePartitions(RVDPartitioner.scala:141) at is.hail.expr.ir.LoweredTableReader$$anon$2.coerce(TableIR.scala:387) at is.hail.expr.ir.GenericTableValue.toTableStage(GenericTableValue.scala:162) at is.hail.io.vcf.MatrixVCFReader.lower(LoadVCF.scala:1790) at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:403) at is.hail.expr.ir.lowering.LowerTableIR$.apply(LowerTableIR.scala:1195) at is.hail.expr.ir.lowering.LowerToCDA$.lower(LowerToCDA.scala:69) at is.hail.expr.ir.lowering.LowerToCDA$.apply(LowerToCDA.scala:18) at is.hail.expr.ir.lowering.LowerToDistributedArrayPass.transform(LoweringPass.scala:77) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.evaluate$1(LowerOrInterpretNonCompilable.scala:27) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:67) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:53) at is.hail.expr.ir.LowerOrInterpretNonCompilable$.apply(LowerOrInterpretNonCompilable.scala:72) at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.transform(LoweringPass.scala:69) at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$3(LoweringPass.scala:16) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$1(LoweringPass.scala:16) at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81) at is.hail.expr.ir.lowering.LoweringPass.apply(LoweringPass.scala:14) at is.hail.expr.ir.lowering.LoweringPass.apply$(LoweringPass.scala:13) at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.apply(LoweringPass.scala:64) at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1(LoweringPipeline.scala:15) at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1$adapted(LoweringPipeline.scala:13) at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36) at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33) at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:38) at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:13) at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:47) at is.hail.backend.spark.SparkBackend._execute(SparkBackend.scala:381) at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$2(SparkBackend.scala:417) at is.hail.backend.ExecuteContext$.$anonfun$scoped$3(ExecuteContext.scala:47) at is.hail.utils.package$.using(package.scala:638) at is.hail.backend.ExecuteContext$.$anonfun$scoped$2(ExecuteContext.scala:47) at is.hail.utils.package$.using(package.scala:638) at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:17) at is.hail.backend.ExecuteContext$.scoped(ExecuteContext.scala:46) at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:275) at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$1(SparkBackend.scala:414) at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52) at is.hail.backend.spark.SparkBackend.executeEncode(SparkBackend.scala:413) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:282) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:238) at java.base/java.lang.Thread.run(Thread.java:834) Hail version: 0.2.78-b17627756568 Error summary: IllegalArgumentException: requirement failed ``` ---
**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:** [January 10, 2022, 7:04pm UTC](https://discuss.hail.is/t/unable-to-utilize-my-vcf-file/2409/8 "2022-01-10T19:04:58Z")
You can set flags after initializing. If you set flags before initializing, that will initialize automatically (and prevent you from re-initializing with different parameters). The solution here is to move the `_set_flags` line after the `hl.init` line, I think.