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assertion fail with TwoBit reference (query past end of contig) #1214

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akiezun opened this issue Dec 2, 2015 · 0 comments
Closed

assertion fail with TwoBit reference (query past end of contig) #1214

akiezun opened this issue Dec 2, 2015 · 0 comments
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@droazen
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bug
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alpha

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@akiezun
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akiezun commented Dec 2, 2015

command

spark-submit \
  --master $SPARK_MASTER \
  --driver-memory 8G \
  --num-executors ${1} \
  --executor-cores 4 \
  --executor-memory 20G \
  --conf spark.driver.maxResultSize=0 \
  --conf spark.driver.userClassPathFirst=true \
  --conf spark.executor.userClassPathFirst=true \
  --conf spark.io.compression.codec=lzf \
  --conf spark.yarn.executor.memoryOverhead=600 \
      $JAR BaseRecalibratorSpark \
        --input hdfs:///user/akiezun/CEUTrio.HiSeq.WEx.b37.NA12892.bam \
        --output bqsr_out_${1}.bam \
        -R hdfs:///user/droazen/bqsr/human_g1k_v37.2bit \
        --knownSites hdfs:////user/akiezun/dbsnp_138.b37.excluding_sites_after_129.vcf \
        --joinStrategy BROADCAST \
        --apiKey $API_KEY \
        --sparkMaster $SPARK_MASTER

fails with

java.lang.AssertionError: assertion failed
    at scala.Predef$.assert(Predef.scala:165)
    at org.bdgenomics.adam.util.TwoBitFile.extract(TwoBitFile.scala:112)
    at org.bdgenomics.adam.util.TwoBitFile.extract(TwoBitFile.scala:170)
    at org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSource.getReferenceBases(ReferenceTwoBitSource.java:48)
    at org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource.getReferenceBases(ReferenceMultiSource.java:99)
    at org.broadinstitute.hellbender.engine.spark.BroadcastJoinReadsWithRefBases.lambda$addBases$c54addeb$1(BroadcastJoinReadsWithRefBases.java:53)
...
@akiezun akiezun added the bug label Dec 2, 2015
@akiezun akiezun added this to the alpha milestone Dec 2, 2015
droazen added a commit that referenced this issue Dec 2, 2015
@droazen
Truncate queries in ReferenceTwoBitSource at contig ends when necessary
de53bfa 
The TwoBit API can't handle queries beyond the ends of contigs (we get
an assertion failure). This changes ReferenceTwoBitSource to truncate query
intervals at contig ends as necessary.

Resolves #1214
@droazen droazen mentioned this issue Dec 2, 2015
Merged
droazen added a commit that referenced this issue Dec 2, 2015
@droazen
Truncate queries in ReferenceTwoBitSource at contig ends when necessary
e25ca19 
The TwoBit API can't handle queries beyond the ends of contigs (we get
an assertion failure). This changes ReferenceTwoBitSource to truncate query
intervals at contig ends as necessary.

Resolves #1214
droazen added a commit that referenced this issue Dec 3, 2015
@droazen
Truncate queries in ReferenceTwoBitSource at contig ends when necessary
d4ceabd 
The TwoBit API can't handle queries beyond the ends of contigs (we get
an assertion failure). This changes ReferenceTwoBitSource to truncate query
intervals at contig ends as necessary.

Resolves #1214
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