Hello, I am running into an error when trying to write a larger-sized VEP annotated Hail Table. I know that there are some other topics that mention this, however the error message I’m receiving is different and I was hoping I could get some guidance.
Specs being used (on DNAnexus platform):
- 112 total # of cores
- 128 GB of memory
- 600 GB of storage
- Hail v 0.2.78
- VEP v 1.0.3
original MatrixTable specs (imported from pVCF):
- 469835 samples
- 2283839 variants
- 2506 partitions
Code:
from pyspark.sql import SparkSession
import hail as hl
builder = (
SparkSession
.builder
.enableHiveSupport()
)
spark = builder.getOrCreate()
hl.init(sc=spark.sparkContext)
mt = hl.read_matrix_table(mt_url)
ann_mt = hl.vep(mt, "path/to/config.json")
ann_tb = ann_mt.rows()
ann_tb.write(url)
I have been able to run the above code successfully for a smaller, truncated version of the same dataset (200000 samples + 100000 variants). However, when I try to run it with the data described in the “original MatrixTable specs” above, I get the following error message:
FatalError: HailException: VEP command 'docker run -i -v /cluster/vep:/root/.vep dnanexus/dxjupyterlab-vep ./vep --format vcf --json --everything --allele_number --no_stats --cache --offline --minimal --assembly GRCh38 -o STDOUT --check_existing --dir_cache /root/.vep/ --fasta /root/.vep/homo_sapiens/103_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --plugin LoF,loftee_path:/root/.vep/Plugins/loftee, human_ancestor_fa:/root/.vep/human_ancestor.fa,conservation_file:/root/.vep/loftee.sql, gerp_bigwig:/root/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw' failed with non-zero exit status 2
VEP Error output:
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 175.
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 214.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 191.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 194.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 238.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 241.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
Use of uninitialized value in uc at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 3801 in stage 1.0 failed 4 times, most recent failure: Lost task 3801.3 in stage 1.0 (TID 9137, ip-10-60-155-202.eu-west-2.compute.internal, executor 24): is.hail.utils.HailException: VEP command 'docker run -i -v /cluster/vep:/root/.vep dnanexus/dxjupyterlab-vep ./vep --format vcf --json --everything --allele_number --no_stats --cache --offline --minimal --assembly GRCh38 -o STDOUT --check_existing --dir_cache /root/.vep/ --fasta /root/.vep/homo_sapiens/103_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --plugin LoF,loftee_path:/root/.vep/Plugins/loftee, human_ancestor_fa:/root/.vep/human_ancestor.fa,conservation_file:/root/.vep/loftee.sql, gerp_bigwig:/root/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw' failed with non-zero exit status 2
VEP Error output:
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 175.
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 214.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 191.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 194.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 238.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 241.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
Use of uninitialized value in uc at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:11)
at is.hail.utils.package$.fatal(package.scala:78)
at is.hail.methods.VEP$.waitFor(VEP.scala:72)
at is.hail.methods.VEP$$anonfun$7$$anonfun$apply$4.apply(VEP.scala:226)
at is.hail.methods.VEP$$anonfun$7$$anonfun$apply$4.apply(VEP.scala:171)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:69)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:69)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:221)
at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at is.hail.sparkextras.ContextRDD.iterator(ContextRDD.scala:390)
at is.hail.rvd.BroadcastRVD.computePartition(RVD.scala:1558)
at __C684collect_distributed_array.apply_region13_43(Unknown Source)
at __C684collect_distributed_array.apply(Unknown Source)
at __C684collect_distributed_array.apply(Unknown Source)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1$$anonfun$apply$1.apply(BackendUtils.scala:31)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1$$anonfun$apply$1.apply(BackendUtils.scala:30)
at is.hail.utils.package$.using(package.scala:638)
at is.hail.annotations.RegionPool.scopedRegion(RegionPool.scala:144)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1.apply(BackendUtils.scala:30)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1.apply(BackendUtils.scala:28)
at is.hail.backend.spark.SparkBackendComputeRDD.compute(SparkBackend.scala:730)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:123)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:2001)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1984)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1983)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1983)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:1033)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:1033)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1033)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2223)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2172)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2161)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:823)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:945)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
at org.apache.spark.rdd.RDD.collect(RDD.scala:944)
at is.hail.backend.spark.SparkBackend.parallelizeAndComputeWithIndex(SparkBackend.scala:286)
at is.hail.backend.BackendUtils.collectDArray(BackendUtils.scala:28)
at __C608Compiled.__m610split_CollectDistributedArray_region1_29(Emit.scala)
at __C608Compiled.__m610split_CollectDistributedArray(Emit.scala)
at __C608Compiled.apply(Emit.scala)
at is.hail.expr.ir.CompileAndEvaluate$$anonfun$_apply$1.apply$mcV$sp(CompileAndEvaluate.scala:57)
at is.hail.expr.ir.CompileAndEvaluate$$anonfun$_apply$1.apply(CompileAndEvaluate.scala:57)
at is.hail.expr.ir.CompileAndEvaluate$$anonfun$_apply$1.apply(CompileAndEvaluate.scala:57)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:57)
at is.hail.expr.ir.CompileAndEvaluate$.evalToIR(CompileAndEvaluate.scala:30)
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.evaluate$1(LowerOrInterpretNonCompilable.scala:30)
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.is$hail$expr$ir$LowerOrInterpretNonCompilable$$rewrite$1(LowerOrInterpretNonCompilable.scala:67)
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.apply(LowerOrInterpretNonCompilable.scala:72)
at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.transform(LoweringPass.scala:69)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:16)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:16)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:16)
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:14)
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)
at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:14)
at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.apply(LoweringPass.scala:64)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:15)
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:13)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:13)
at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:47)
at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:381)
at is.hail.backend.spark.SparkBackend$$anonfun$8$$anonfun$apply$4.apply(SparkBackend.scala:417)
at is.hail.backend.spark.SparkBackend$$anonfun$8$$anonfun$apply$4.apply(SparkBackend.scala:414)
at is.hail.backend.ExecuteContext$$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$8.apply(SparkBackend.scala:414)
at is.hail.backend.spark.SparkBackend$$anonfun$8.apply(SparkBackend.scala:413)
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:750)
is.hail.utils.HailException: VEP command 'docker run -i -v /cluster/vep:/root/.vep dnanexus/dxjupyterlab-vep ./vep --format vcf --json --everything --allele_number --no_stats --cache --offline --minimal --assembly GRCh38 -o STDOUT --check_existing --dir_cache /root/.vep/ --fasta /root/.vep/homo_sapiens/103_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --plugin LoF,loftee_path:/root/.vep/Plugins/loftee, human_ancestor_fa:/root/.vep/human_ancestor.fa,conservation_file:/root/.vep/loftee.sql, gerp_bigwig:/root/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw' failed with non-zero exit status 2
VEP Error output:
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 175.
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 214.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 191.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 194.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 238.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 241.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
Use of uninitialized value in uc at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
at is.hail.utils.ErrorHandling$class.fatal(ErrorHandling.scala:11)
at is.hail.utils.package$.fatal(package.scala:78)
at is.hail.methods.VEP$.waitFor(VEP.scala:72)
at is.hail.methods.VEP$$anonfun$7$$anonfun$apply$4.apply(VEP.scala:226)
at is.hail.methods.VEP$$anonfun$7$$anonfun$apply$4.apply(VEP.scala:171)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:69)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:409)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:69)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:221)
at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1165)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:1091)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1156)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:882)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:335)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:286)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at is.hail.sparkextras.ContextRDD.iterator(ContextRDD.scala:390)
at is.hail.rvd.BroadcastRVD.computePartition(RVD.scala:1558)
at __C684collect_distributed_array.apply_region13_43(Unknown Source)
at __C684collect_distributed_array.apply(Unknown Source)
at __C684collect_distributed_array.apply(Unknown Source)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1$$anonfun$apply$1.apply(BackendUtils.scala:31)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1$$anonfun$apply$1.apply(BackendUtils.scala:30)
at is.hail.utils.package$.using(package.scala:638)
at is.hail.annotations.RegionPool.scopedRegion(RegionPool.scala:144)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1.apply(BackendUtils.scala:30)
at is.hail.backend.BackendUtils$$anonfun$collectDArray$1.apply(BackendUtils.scala:28)
at is.hail.backend.spark.SparkBackendComputeRDD.compute(SparkBackend.scala:730)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:123)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Hail version: 0.2.78-b17627756568
Error summary: HailException: VEP command 'docker run -i -v /cluster/vep:/root/.vep dnanexus/dxjupyterlab-vep ./vep --format vcf --json --everything --allele_number --no_stats --cache --offline --minimal --assembly GRCh38 -o STDOUT --check_existing --dir_cache /root/.vep/ --fasta /root/.vep/homo_sapiens/103_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --plugin LoF,loftee_path:/root/.vep/Plugins/loftee, human_ancestor_fa:/root/.vep/human_ancestor.fa,conservation_file:/root/.vep/loftee.sql, gerp_bigwig:/root/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw' failed with non-zero exit status 2
VEP Error output:
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 175.
Smartmatch is experimental at /root/.vep/Plugins/loftee/de_novo_donor.pl line 214.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 191.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 194.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 238.
Smartmatch is experimental at /root/.vep/Plugins/loftee/splice_site_scan.pl line 241.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
Use of uninitialized value in uc at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 906.
