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java.io.FileNotFoundException when file exists #1385

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akmorrow13 opened this Issue Feb 8, 2017 · 5 comments

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akmorrow13 commented Feb 8, 2017

I have been having issues reading hdfs files via sc.loadFeatures() and sc.loadAlignments() in ADAMContext. However, I am able to load in the same file location using sc.textFile().

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Hi @akmorrow13! Could you post a stack trace?

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fnothaft commented Feb 8, 2017

Hi @akmorrow13! Could you post a stack trace?

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scala> import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.ADAMContext._

scala> val f = sc.loadFeatures("hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam")
java.io.FileNotFoundException: Couldn't find any files matching hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam
        at org.bdgenomics.adam.rdd.ADAMContext.getFsAndFilesWithFilter(ADAMContext.scala:477)
        at org.bdgenomics.adam.rdd.ADAMContext.loadAvroSequences(ADAMContext.scala:290)
        at org.bdgenomics.adam.rdd.ADAMContext.loadParquetFeatures(ADAMContext.scala:1223)
        at org.bdgenomics.adam.rdd.ADAMContext.loadFeatures(ADAMContext.scala:1372)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:30)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:35)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:37)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:39)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:41)
        at $iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:43)
        at $iwC$$iwC$$iwC$$iwC.<init>(<console>:45)
        at $iwC$$iwC$$iwC.<init>(<console>:47)
        at $iwC$$iwC.<init>(<console>:49)
        at $iwC.<init>(<console>:51)
        at <init>(<console>:53)
        at .<init>(<console>:57)
        at .<clinit>(<console>)
        at .<init>(<console>:7)
        at .<clinit>(<console>)
        at $print(<console>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.spark.repl.SparkIMain$ReadEvalPrint.call(SparkIMain.scala:1045)
        at org.apache.spark.repl.SparkIMain$Request.loadAndRun(SparkIMain.scala:1326)
        at org.apache.spark.repl.SparkIMain.loadAndRunReq$1(SparkIMain.scala:821)
        at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:852)
        at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:800)
        at org.apache.spark.repl.SparkILoop.reallyInterpret$1(SparkILoop.scala:857)
        at org.apache.spark.repl.SparkILoop.interpretStartingWith(SparkILoop.scala:902)
        at org.apache.spark.repl.SparkILoop.command(SparkILoop.scala:814)
        at org.apache.spark.repl.SparkILoop.processLine$1(SparkILoop.scala:657)
        at org.apache.spark.repl.SparkILoop.innerLoop$1(SparkILoop.scala:665)
        at org.apache.spark.repl.SparkILoop.org$apache$spark$repl$SparkILoop$$loop(SparkILoop.scala:670)
        at org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply$mcZ$sp(SparkILoop.scala:997)
        at org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
        at org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
        at scala.tools.nsc.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:135)
        at org.apache.spark.repl.SparkILoop.org$apache$spark$repl$SparkILoop$$process(SparkILoop.scala:945)
        at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:1064)
        at org.apache.spark.repl.Main$.main(Main.scala:31)
        at org.apache.spark.repl.Main.main(Main.scala)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)
        at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
        at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
        at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)


scala> val s = sc.textFile("hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam")
s: org.apache.spark.rdd.RDD[String] = hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam MapPartitionsRDD[1] at textFile at <console>:30

scala> println(s.first)
chr1    90600   91600   sequence_feature        1.0     +

Contributor

akmorrow13 commented Feb 8, 2017

scala> import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rdd.ADAMContext._

scala> val f = sc.loadFeatures("hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam")
java.io.FileNotFoundException: Couldn't find any files matching hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam
        at org.bdgenomics.adam.rdd.ADAMContext.getFsAndFilesWithFilter(ADAMContext.scala:477)
        at org.bdgenomics.adam.rdd.ADAMContext.loadAvroSequences(ADAMContext.scala:290)
        at org.bdgenomics.adam.rdd.ADAMContext.loadParquetFeatures(ADAMContext.scala:1223)
        at org.bdgenomics.adam.rdd.ADAMContext.loadFeatures(ADAMContext.scala:1372)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:30)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:35)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:37)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:39)
        at $iwC$$iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:41)
        at $iwC$$iwC$$iwC$$iwC$$iwC.<init>(<console>:43)
        at $iwC$$iwC$$iwC$$iwC.<init>(<console>:45)
        at $iwC$$iwC$$iwC.<init>(<console>:47)
        at $iwC$$iwC.<init>(<console>:49)
        at $iwC.<init>(<console>:51)
        at <init>(<console>:53)
        at .<init>(<console>:57)
        at .<clinit>(<console>)
        at .<init>(<console>:7)
        at .<clinit>(<console>)
        at $print(<console>)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.spark.repl.SparkIMain$ReadEvalPrint.call(SparkIMain.scala:1045)
        at org.apache.spark.repl.SparkIMain$Request.loadAndRun(SparkIMain.scala:1326)
        at org.apache.spark.repl.SparkIMain.loadAndRunReq$1(SparkIMain.scala:821)
        at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:852)
        at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:800)
        at org.apache.spark.repl.SparkILoop.reallyInterpret$1(SparkILoop.scala:857)
        at org.apache.spark.repl.SparkILoop.interpretStartingWith(SparkILoop.scala:902)
        at org.apache.spark.repl.SparkILoop.command(SparkILoop.scala:814)
        at org.apache.spark.repl.SparkILoop.processLine$1(SparkILoop.scala:657)
        at org.apache.spark.repl.SparkILoop.innerLoop$1(SparkILoop.scala:665)
        at org.apache.spark.repl.SparkILoop.org$apache$spark$repl$SparkILoop$$loop(SparkILoop.scala:670)
        at org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply$mcZ$sp(SparkILoop.scala:997)
        at org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
        at org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
        at scala.tools.nsc.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:135)
        at org.apache.spark.repl.SparkILoop.org$apache$spark$repl$SparkILoop$$process(SparkILoop.scala:945)
        at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:1064)
        at org.apache.spark.repl.Main$.main(Main.scala:31)
        at org.apache.spark.repl.Main.main(Main.scala)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)
        at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
        at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
        at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
        at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)


scala> val s = sc.textFile("hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam")
s: org.apache.spark.rdd.RDD[String] = hdfs://amp-bdg-master.amplab.net:8020/user/akmorrow/featuresOutput_GM12878.adam MapPartitionsRDD[1] at textFile at <console>:30

scala> println(s.first)
chr1    90600   91600   sequence_feature        1.0     +

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How are you saving that file? The short bit here is that we're somewhat lazy about autodetecting file types and we just use the file extension. So if you save reads as a SAM file but name the path "anythingnotendingindotsam.adam" or if you save features as a BED file but name the path "anythingnotendingindotbednarrowpeakgtfgffetc.adam", we'll try to load it as a Parquet file, in which case we expect to see other metadata files around.

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fnothaft commented Feb 8, 2017

How are you saving that file? The short bit here is that we're somewhat lazy about autodetecting file types and we just use the file extension. So if you save reads as a SAM file but name the path "anythingnotendingindotsam.adam" or if you save features as a BED file but name the path "anythingnotendingindotbednarrowpeakgtfgffetc.adam", we'll try to load it as a Parquet file, in which case we expect to see other metadata files around.

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        new FeatureRDD(rdd, l.sequences)
          .saveAsBed(s"featuresOutput_${cellType._1}.adam")

Lol thats it, thanks @fnothaft!

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akmorrow13 commented Feb 8, 2017

        new FeatureRDD(rdd, l.sequences)
          .saveAsBed(s"featuresOutput_${cellType._1}.adam")

Lol thats it, thanks @fnothaft!

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No sweat! I like straightforward tickets!

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fnothaft commented Feb 8, 2017

No sweat! I like straightforward tickets!

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