ADAM to BAM conversion fails using relative path

[jpdna]

Using local filesystem ( I didn't try on HDFS) I observed the ADAM to BAM conversion using a relative path to the output BAM file attempted with:

adam-submit transform /mypath/mydataset.adam bam_limit_proj_marked/limit_proj_marked_v2.bam -single -sort_reads
to fail with error
java.io.FileNotFoundException: File bam_limit_proj_marked/limit_proj_marked_v2.bam_head does not exist

the same error also occurs if only the name of the intended output bam file (with no path) is provided

however, this will succed when specifying the absolute path to the output bam file like

adam-submit -- transform /mypath/mydataset.adam /mypath/bam_limit_proj_marked_v2/limit_proj_marked.bam -single -sort_reads

[fnothaft]

That's odd! What line is causing this error to throw? Can you post the full stack trace?

[jpdna]

Here you go:

Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using SPARK_SUBMIT=/home/jp/Apps/Spark/1.6_on_scala_2.11/spark-1.6.1/bin/spark-submit
2016-04-24 08:20:17 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2016-04-24 08:21:26 WARN  TaskSetManager:70 - Lost task 11.0 in stage 2.0 (TID 493, localhost.localdomain): java.io.FileNotFoundException: File try2.bam_head does not exist
    at org.apache.hadoop.fs.RawLocalFileSystem.deprecatedGetFileStatus(RawLocalFileSystem.java:511)
    at org.apache.hadoop.fs.RawLocalFileSystem.getFileLinkStatusInternal(RawLocalFileSystem.java:724)
    at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:501)
    at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:397)
    at org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker.<init>(ChecksumFileSystem.java:137)
    at org.apache.hadoop.fs.ChecksumFileSystem.open(ChecksumFileSystem.java:339)
    at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:764)
    at org.seqdoop.hadoop_bam.util.SAMHeaderReader.readSAMHeaderFrom(SAMHeaderReader.java:46)
    at org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat.readSAMHeaderFrom(KeyIgnoringBAMOutputFormat.java:66)
    at org.bdgenomics.adam.rdd.read.ADAMBAMOutputFormatHeaderLess.getRecordWriter(ADAMBAMOutputFormat.scala:94)
    at org.apache.spark.rdd.InstrumentedOutputFormat.getRecordWriter(InstrumentedOutputFormat.scala:35)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1107)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1091)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
    at org.apache.spark.scheduler.Task.run(Task.scala:89)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

[fnothaft]

Closing as we haven't been able to reproduce.