Problem runnign STAR from bin.tar.gz

[nickholz]

I have obtained the following error while trying to run the halvade RNA. Looks there is an issue when the program tries to run STAR from the bin.tar.gz file on the HDFS

[2017/11/29 21:12:26 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /tmp/halvade/m_000000_0-star1/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory

[ddcap]

Could you give me the arguments you used to start Halvade?

[sdhutchins]

@ddcap did you figure this out? I'm having the same issue.

[ddcap]

Not really, since I didn't have all the information to figure things out.
Could you send me the command you used (i.e. which arguments) and the logs of the failed task.
That should help me narrow down the problem.

[sdhutchins]

I used the exact workflow at https://github.com/biointec/halvade/wiki/Recipe:-RNA-seq-with-Halvade-on-a-local-Hadoop-cluster

[sdhutchins]

Here is the halvade.stderr file.

Here is my example configuration.

#----------------------------------
# required Halvade arguments
#----------------------------------
N=1
M=128
C=24
B="/home/shutchins2/halvade/bin.tar.gz"
D="/home/shutchins2/halvade/ref/dbsnp/dbsnp_138.hg19.vcf"
R="/home/shutchins2/halvade/ref/ucsc.hg19.fasta"
S="/home/shutchins2/halvade/ref/STAR_ref"
I="/home/shutchins2/halvade/in/"
O="/home/shutchins2/halvade/out3/"
smt
rna

[sdhutchins]

That text file was ugly...

18/05/31 14:38:24 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
[2018/05/31 14:38:24 - DEBUG] reference file not found on a distributed fs (HDFS)
[2018/05/31 14:38:24 - DEBUG] reference file is on local disk
[2018/05/31 14:38:24 - DEBUG] requires star genome 2 upload? false
[2018/05/31 14:38:24 - DEBUG] pass 2 UID: 310518023824.895
[2018/05/31 14:38:24 - DEBUG] All reference files are available
[2018/05/31 14:38:24 - DEBUG] pmem check disabled, using less memory for STAR because of shared memory
[2018/05/31 14:38:24 - DEBUG] set # map containers: 21
[2018/05/31 14:38:24 - DEBUG] resources set to 21 maps [2 cpu , 6144 mb] per node and 2 reducers [11 cpu, 32768 mb] per node
[2018/05/31 14:38:24 - DEBUG] parsing dictionary /home/shutchins2/halvade/ref/ucsc.hg19.dict
[2018/05/31 14:38:24 - DEBUG] requested # reducers: 36
[2018/05/31 14:38:25 - DEBUG] final # reducers: 35
[2018/05/31 14:38:25 - DEBUG] Started Halvade pass 1 Job
18/05/31 14:38:25 INFO Configuration.deprecation: session.id is deprecated. Instead, use dfs.metrics.session-id
18/05/31 14:38:25 INFO jvm.JvmMetrics: Initializing JVM Metrics with processName=JobTracker, sessionId=
18/05/31 14:38:25 INFO input.FileInputFormat: Total input files to process : 8
18/05/31 14:38:25 INFO mapreduce.JobSubmitter: number of splits:8
18/05/31 14:38:25 INFO mapreduce.JobSubmitter: Submitting tokens for job: job_local406084068_0001
18/05/31 14:38:28 INFO mapred.LocalDistributedCacheManager: Localized hdfs://localhost:9000/home/shutchins2/halvade/bin.tar.gz as file:/tmp/hadoop-shutchins2/mapred/local/1527795505390/bin.tar.gz
18/05/31 14:38:28 INFO mapreduce.Job: The url to track the job: http://localhost:8080/
18/05/31 14:38:28 INFO mapreduce.Job: Running job: job_local406084068_0001
18/05/31 14:38:28 INFO mapred.LocalJobRunner: OutputCommitter set in config null
18/05/31 14:38:28 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:28 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:28 INFO mapred.LocalJobRunner: OutputCommitter is org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Waiting for map tasks
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000000_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_0_0.fq.gz:0+28657878
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000000_0
[2018/05/31 14:38:29 - DEBUG] task = 0
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] STAR instance type: 1
18/05/31 14:38:29 INFO Configuration.deprecation: mapred.map.tasks is deprecated. Instead, use mapreduce.job.maps
[2018/05/31 14:38:29 - DEBUG] containers left: 8
[2018/05/31 14:38:29 - DEBUG] paired? true
[2018/05/31 14:38:29 - DEBUG] ref: /home/shutchins2/halvade/ref/STAR_ref/
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000001_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_6_0.fq.gz:0+28656471
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000001_0
[2018/05/31 14:38:29 - DEBUG] task = 1
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000002_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_3_0.fq.gz:0+28630703
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000002_0
[2018/05/31 14:38:29 - DEBUG] task = 2
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000003_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_7_0.fq.gz:0+28601002
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000003_0
[2018/05/31 14:38:29 - DEBUG] task = 3
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000004_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_5_0.fq.gz:0+28324989
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000004_0
[2018/05/31 14:38:29 - DEBUG] task = 4
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000005_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_4_0.fq.gz:0+27663011
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000005_0
[2018/05/31 14:38:29 - DEBUG] task = 5
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000006_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_2_0.fq.gz:0+27636390
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000006_0
[2018/05/31 14:38:29 - DEBUG] task = 6
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: Starting task: attempt_local406084068_0001_m_000007_0
18/05/31 14:38:29 INFO output.FileOutputCommitter: File Output Committer Algorithm version is 1
18/05/31 14:38:29 INFO output.FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: false
18/05/31 14:38:29 INFO mapred.Task:  Using ResourceCalculatorProcessTree : [ ]
18/05/31 14:38:29 INFO mapred.MapTask: Processing split: hdfs://localhost:9000/home/shutchins2/halvade/in/halvade_1_0.fq.gz:0+27600220
18/05/31 14:38:29 INFO mapred.MapTask: (EQUATOR) 0 kvi 26214396(104857584)
18/05/31 14:38:29 INFO mapred.MapTask: mapreduce.task.io.sort.mb: 100
18/05/31 14:38:29 INFO mapred.MapTask: soft limit at 83886080
18/05/31 14:38:29 INFO mapred.MapTask: bufstart = 0; bufvoid = 104857600
18/05/31 14:38:29 INFO mapred.MapTask: kvstart = 26214396; length = 6553600
18/05/31 14:38:29 INFO mapred.MapTask: Map output collector class = org.apache.hadoop.mapred.MapTask$MapOutputBuffer
18/05/31 14:38:29 INFO compress.CodecPool: Got brand-new decompressor [.gz]
[2018/05/31 14:38:29 - DEBUG] taskId = attempt_local406084068_0001_m_000007_0
[2018/05/31 14:38:29 - DEBUG] task = 7
[2018/05/31 14:38:29 - DEBUG] file lock: /tmp/halvade/ load_sh_mem.lock
[2018/05/31 14:38:29 - DEBUG] Checking for binaries...
[2018/05/31 14:38:29 - DEBUG] empty directory ./bin.tar.gz/bin
[2018/05/31 14:38:29 - DEBUG] Started STAR
[2018/05/31 14:38:29 - DEBUG] Load ref [/home/shutchins2/halvade/ref/STAR_ref/] to shared memory
[2018/05/31 14:38:29 - DEBUG] running command [./bin.tar.gz/bin/STAR, --genomeDir, /home/shutchins2/halvade/ref/STAR_ref/, --genomeLoad, LoadAndExit]
[EXCEPTION] Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
java.io.IOException: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:116)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.IOException: error=20, Not a directory
	at java.lang.UNIXProcess.forkAndExec(Native Method)
	at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
	at java.lang.ProcessImpl.start(ProcessImpl.java:134)
	at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
	... 13 more
18/05/31 14:38:29 INFO mapred.MapTask: Starting flush of map output
18/05/31 14:38:29 INFO mapred.LocalJobRunner: map task executor complete.
18/05/31 14:38:29 WARN mapred.LocalJobRunner: job_local406084068_0001
java.lang.Exception: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory exited with code -1
	at org.apache.hadoop.mapred.LocalJobRunner$Job.runTasks(LocalJobRunner.java:491)
	at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:551)
Caused by: Cannot run program "./bin.tar.gz/bin/STAR": error=20, Not a directory exited with code -1
	at be.ugent.intec.halvade.utils.ProcessBuilderWrapper.startProcess(ProcessBuilderWrapper.java:132)
	at be.ugent.intec.halvade.tools.STARInstance.loadSharedMemoryReference(STARInstance.java:248)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.loadReference(StarAlignPassXMapper.java:98)
	at be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.setup(StarAlignPassXMapper.java:68)
	at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:143)
	at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:793)
	at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
	at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:270)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
18/05/31 14:38:29 INFO mapreduce.Job: Job job_local406084068_0001 running in uber mode : false
18/05/31 14:38:29 INFO mapreduce.Job:  map 0% reduce 0%
18/05/31 14:38:29 INFO mapreduce.Job: Job job_local406084068_0001 failed with state FAILED due to: NA
18/05/31 14:38:29 INFO mapreduce.Job: Counters: 0
[2018/05/31 14:38:29 - DEBUG] Finished Halvade pass 1 Job [runtime: 4s 923ms ]
[2018/05/31 14:38:29 - DEBUG] Halvade pass 1 job failed.

[ddcap]

Ye thats fine, I'm trying to test it now.
If you can find them can you find the stderr of the individual map tasks? They should show more information as to whats wrong.

[sdhutchins]

I'll look around for it. I also get this error? Seems the directory is "creating" at an odd location...

[INFO] The output directory '/home/shutchins2/halvade/out//pass1' already exists.

[ddcap]

I think that is caused by the first error, it creates a directory pass1 to store the information of the first pass of STAR alignment, which is then used in the second step.
But since the first job failed but created the directory now Hadoop MapReduce detects the directory and stops the job.
If you delete the /home/shutchins2/halvade/out directory this error should go away.

[sdhutchins]

Currently having some hadoop issues on my server, but once I figure that out, I'll try to recreate this.