[HTCondor-users] issue with java(possibly) - cannot find non-existent file

[Karin Lagesen <karin.lagesen@xxxxxxxxxx>]

First, I am completely new at condor, so I am sorry if I have stumbled 
on a faq.

I have a master.dag condor script that looks like this:

JOB    A 
/condor_sh/projects/project_twinsamples/separate_samples/mapping_2013-03-22_113332//aln1.condor
JOB    B 
/condor_sh/projects/project_twinsamples/separate_samples/mapping_2013-03-22_113332//samse.condor
JOB    C 
/condor_sh/projects/project_twinsamples/separate_samples/mapping_2013-03-22_113332//picard_sort.condor
JOB    d 
/condor_sh/projects/project_twinsamples/separate_samples/mapping_2013-03-22_113332//picard_casm.condor
SCRIPT POST d 
/condor_sh/projects/project_twinsamples/separate_samples/mapping_2013-03-22_113332//createReport
PARENT A CHILD B
PARENT B CHILD C
RETRY  A 3
RETRY  B 3
RETRY  C 3


This fails on picard_sort.condor:

universe   = java
executable = /tools/Picard/picard/SortSam.jar
arguments  = net.sf.picard.sam.SortSam INPUT=twinsample.sam 
OUTPUT=twinsample.posiSrt.bam SORT_ORDER=coordinate
jar_files  = /tools/Picard/picard/SortSam.jar, 
/tools/Picard/snappy-java-1.0.3-rc3.jar
Log        = /data/condor/submit_logs/twinsample.log
Error      = 
/condor_sh/projects/project_twinsamples/separate_samples/mapping_2013-03-22_113332/logs//twinsample.posiSrt.bam.out

notification=never
should_transfer_files=YES
when_to_transfer_output = ON_EXIT
Requirements   =  (OpSys == "OSX" || OpSys == "LINUX")
request_cpus=1
request_memory = 2 * 1024
request_disk = 2 * 1024
get_env = true
java_vm_args = -Xmx4g -Djava.io.tmpdir=/condor_sh//java_tmp

queue

with the following error message:

$cat twinsample.posiSrt.bam.out
[Fri Mar 22 12:07:20 CET 2013] net.sf.picard.sam.SortSam 
INPUT=twinsample.sam OUTPUT=twinsample.posiSrt.bam SORT_ORDER=coordinate 
   VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT 
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false 
CREATE_MD5_FILE=false
[Fri Mar 22 12:07:20 CET 2013] Executing as nobody@tor on Linux 
2.6.32-279.11.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; 
Picard version: 1.62(1113)
[Fri Mar 22 12:07:20 CET 2013] net.sf.picard.sam.SortSam done. Elapsed 
time: 0.00 minutes.
Runtime.totalMemory()=504168448
net.sf.picard.PicardException: Cannot read non-existent file: 
/data/condor/condor_scratch/execute/dir_17280/twinsample.sam
	at net.sf.picard.io.IoUtil.assertFileIsReadable(IoUtil.java:55)
	at net.sf.picard.sam.SortSam.doWork(SortSam.java:59)
	at 
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
	at 
net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
	at net.sf.picard.sam.SortSam.main(SortSam.java:79)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	at CondorJavaWrapper.main(CondorJavaWrapper.java:106)



I see that the missing file is actually created, but in the specified 
directory that the previous condor script specified with its output 
parameter.

Due to my fairly new aquaintance with condor, I am unable to figure out 
where to start solving this issue.

Thanks for your help!


Karin
--
Karin Lagesen, Ph.D.
Department of Medical Genetics
and Norwegian High-Throughput Sequencing Centre (NSC)
Oslo University Hospital