# I cannot import the UKB 200K WGS VCFs in Hail due to an empty line in the VCF after the header lines **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [July 1, 2022, 1:35am UTC](https://discuss.hail.is/t/i-cannot-import-the-ukb-200k-wgs-vcfs-in-hail-due-to-an-empty-line-in-the-vcf-after-the-header-lines/2738 "2022-07-01T01:35:28Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![hnjr](https://avatars.discourse-cdn.com/v4/letter/h/76d3ee/32.png) [@hnjr](https://discuss.hail.is/u/hnjr)\ **Post date:** [July 1, 2022, 1:35am UTC](https://discuss.hail.is/t/i-cannot-import-the-ukb-200k-wgs-vcfs-in-hail-due-to-an-empty-line-in-the-vcf-after-the-header-lines/2738/1 "2022-07-01T01:35:28Z")
Hi all, I would like to process UK-Biobank 200K WGS data with hail. Unfortunately, I could not import vcf with the attached error. How can we import those vcf files? I appreciate any information about this Thank you so much. * * * ```python vcf = 'file:///mnt/project/Bulk/Whole genome sequences/Population level WGS variants, pVCF format - interim 200k release/ukb24304_c2_b1_v1.vcf.gz' mt = hl.import_vcf(vcf, force_bgz = True, reference_genome = 'GRCh38', find_replace = ('nul', '.'), array_elements_required = False) ``` * * * ```python FatalError Traceback (most recent call last) in 6 find_replace = ('nul', '.'), ----> 7 array_elements_required = False 8 ) 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, entry_float_type, filter, find_replace, n_partitions, block_size, _partitions) /opt/conda/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 /opt/conda/lib/python3.6/site-packages/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, entry_float_type, filter, find_replace, n_partitions, block_size, _partitions) 2370 skip_invalid_loci, force_bgz, force, filter, find_replace, 2371 _partitions) -> 2372 return MatrixTable(ir.MatrixRead(reader, drop_cols=drop_samples)) 2373 2374 /opt/conda/lib/python3.6/site-packages/hail/matrixtable.py in __init__ (self, mir) 556 self._entry_indices = Indices(self, {self._row_axis, self._col_axis}) 557 --> 558 self._type = self._mir.typ 559 560 self._global_type = self._type.global_type /opt/conda/lib/python3.6/site-packages/hail/ir/base_ir.py in typ(self) 359 def typ(self): 360 if self._type is None: --> 361 self._compute_type() 362 assert self._type is not None, self 363 return self._type /opt/conda/lib/python3.6/site-packages/hail/ir/matrix_ir.py in _compute_type(self) 59 60 def _compute_type(self): ---> 61 self._type = Env.backend().matrix_type(self) 62 63 /opt/conda/lib/python3.6/site-packages/hail/backend/spark_backend.py in matrix_type(self, mir) 284 285 def matrix_type(self, mir): --> 286 jir = self._to_java_matrix_ir(mir) 287 return tmatrix._from_java(jir.typ()) 288 /opt/conda/lib/python3.6/site-packages/hail/backend/spark_backend.py in _to_java_matrix_ir(self, ir) 270 271 def _to_java_matrix_ir(self, ir): --> 272 return self._to_java_ir(ir, self._parse_matrix_ir) 273 274 def _to_java_blockmatrix_ir(self, ir): /opt/conda/lib/python3.6/site-packages/hail/backend/spark_backend.py in _to_java_ir(self, ir, parse) 260 r = CSERenderer(stop_at_jir=True) 261 # FIXME parse should be static --> 262 ir._jir = parse(r(ir), ir_map=r.jirs) 263 return ir._jir 264 /opt/conda/lib/python3.6/site-packages/hail/backend/spark_backend.py in _parse_matrix_ir(self, code, ref_map, ir_map) 238 239 def _parse_matrix_ir(self, code, ref_map={}, ir_map={}): --> 240 return self._jbackend.parse_matrix_ir(code, ref_map, ir_map) 241 242 def _parse_blockmatrix_ir(self, code, ref_map={}, ir_map={}): /cluster/spark/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py in __call__ (self, *args) 1255 answer = self.gateway_client.send_command(command) 1256 return_value = get_return_value( -> 1257 answer, self.gateway_client, self.target_id, self.name) 1258 1259 for temp_arg in temp_args: /opt/conda/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: StringIndexOutOfBoundsException: String index out of range: 0 Java stack trace: java.lang.StringIndexOutOfBoundsException: String index out of range: 0 at java.lang.String.charAt(String.java:658) at scala.collection.immutable.StringOps$.apply$extension(StringOps.scala:37) at is.hail.io.vcf.LoadVCF$$anonfun$getHeaderLines$1$$anonfun$apply$5.apply(LoadVCF.scala:1293) at is.hail.io.vcf.LoadVCF$$anonfun$getHeaderLines$1$$anonfun$apply$5.apply(LoadVCF.scala:1293) at scala.collection.Iterator$$anon$16.hasNext(Iterator.scala:600) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409) at scala.collection.Iterator$class.foreach(Iterator.scala:891) at scala.collection.AbstractIterator.foreach(Iterator.scala:1334) at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104) at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48) at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310) at scala.collection.AbstractIterator.to(Iterator.scala:1334) at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302) at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334) at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289) at scala.collection.AbstractIterator.toArray(Iterator.scala:1334) at is.hail.io.vcf.LoadVCF$$anonfun$getHeaderLines$1.apply(LoadVCF.scala:1295) at is.hail.io.vcf.LoadVCF$$anonfun$getHeaderLines$1.apply(LoadVCF.scala:1291) at is.hail.io.fs.FS$$anonfun$readLines$1.apply(FS.scala:221) at is.hail.io.fs.FS$$anonfun$readLines$1.apply(FS.scala:212) at is.hail.utils.package$.using(package.scala:638) at is.hail.io.fs.FS$class.readLines(FS.scala:211) at is.hail.io.fs.HadoopFS.readLines(HadoopFS.scala:70) at is.hail.io.vcf.LoadVCF$.getHeaderLines(LoadVCF.scala:1291) at is.hail.io.vcf.MatrixVCFReader$.apply(LoadVCF.scala:1573) at is.hail.io.vcf.MatrixVCFReader$.fromJValue(LoadVCF.scala:1665) at is.hail.expr.ir.MatrixReader$.fromJson(MatrixIR.scala:90) at is.hail.expr.ir.IRParser$.matrix_ir_1(Parser.scala:1720) at is.hail.expr.ir.IRParser$$anonfun$matrix_ir$1.apply(Parser.scala:1646) at is.hail.expr.ir.IRParser$$anonfun$matrix_ir$1.apply(Parser.scala:1646) at is.hail.utils.StackSafe$More.advance(StackSafe.scala:64) at is.hail.utils.StackSafe$.run(StackSafe.scala:16) at is.hail.utils.StackSafe$StackFrame.run(StackSafe.scala:32) at is.hail.expr.ir.IRParser$$anonfun$parse_matrix_ir$1.apply(Parser.scala:1986) at is.hail.expr.ir.IRParser$$anonfun$parse_matrix_ir$1.apply(Parser.scala:1986) at is.hail.expr.ir.IRParser$.parse(Parser.scala:1973) at is.hail.expr.ir.IRParser$.parse_matrix_ir(Parser.scala:1986) at is.hail.backend.spark.SparkBackend$$anonfun$parse_matrix_ir$1$$anonfun$apply$22.apply(SparkBackend.scala:660) at is.hail.backend.spark.SparkBackend$$anonfun$parse_matrix_ir$1$$anonfun$apply$22.apply(SparkBackend.scala:659) at is.hail.backend.ExecuteContext$$anonfun$scoped$1$$anonfun$apply$1.apply(ExecuteContext.scala:47) at is.hail.backend.ExecuteContext$$anonfun$scoped$1$$anonfun$apply$1.apply(ExecuteContext.scala:47) at is.hail.utils.package$.using(package.scala:638) at is.hail.backend.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:47) at is.hail.backend.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:46) at is.hail.utils.package$.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$$anonfun$parse_matrix_ir$1.apply(SparkBackend.scala:659) at is.hail.backend.spark.SparkBackend$$anonfun$parse_matrix_ir$1.apply(SparkBackend.scala:658) at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52) at is.hail.utils.ExecutionTimer$.logTime(ExecutionTimer.scala:59) at is.hail.backend.spark.SparkBackend.parse_matrix_ir(SparkBackend.scala:658) 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: 0.2.78-b17627756568 Error summary: StringIndexOutOfBoundsException: String index out of range: 0 ``` ---
**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:** [July 6, 2022, 2:53pm UTC](https://discuss.hail.is/t/i-cannot-import-the-ukb-200k-wgs-vcfs-in-hail-due-to-an-empty-line-in-the-vcf-after-the-header-lines/2738/2 "2022-07-06T14:53:09Z")
Does that VCF have empty lines? I’m pretty sure that’s a violation of the VCF spec. ---
**Author:** ![hnjr](https://avatars.discourse-cdn.com/v4/letter/h/76d3ee/32.png) [@hnjr](https://discuss.hail.is/u/hnjr)\ **Post date:** [July 7, 2022, 5:13pm UTC](https://discuss.hail.is/t/i-cannot-import-the-ukb-200k-wgs-vcfs-in-hail-due-to-an-empty-line-in-the-vcf-after-the-header-lines/2738/3 "2022-07-07T17:13:57Z")
Thanks! I found some [discssion](https://community.dnanexus.com/s/question/0D5t000003vBuLhCAK/have-questions-about-the-200k-wgs-joint-variant-call-data-release-ask-them-here) about this. It looks the issues of vcf file. Thank you for suggestion!