밤파일 만들때 레퍼런스랑 지금 돌리는 레퍼런스랑 다를 경우 발생되는 에러이다.


<에러메세지>
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Invalid sequence number 24
 at org.broadinstitute.sting.gatk.datasources.reads.GATKBAMIndex.<init>(GATKBAMIndex.java:100)
 at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.<init>(BAMSchedule.java:105)
 at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:205)
 at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.advance(BAMScheduler.java:108)
 at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.next(BAMScheduler.java:79)
 at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.next(BAMScheduler.java:47)
 at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
 at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
 at org.broadinstitute.sting.gatk.datasources.reads.LowMemoryIntervalSharder.next(LowMemoryIntervalSharder.java:61)
 at org.broadinstitute.sting.gatk.datasources.reads.LowMemoryIntervalSharder.next(LowMemoryIntervalSharder.java:36)
 at org.broadinstitute.sting.gatk.datasources.reads.LocusShardStrategy.next(LocusShardStrategy.java:142)
 at org.broadinstitute.sting.gatk.datasources.reads.LocusShardStrategy.next(LocusShardStrategy.java:42)
 at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:258)
 at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator$1.doBody(GenomeLocProcessingTracker.java:250)
 at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$WithLock.run(GenomeLocProcessingTracker.java:423)
 at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:250)
 at org.broadinstitute.sting.utils.threading.GenomeLocProcessingTracker$OwnershipIterator.next(GenomeLocProcessingTracker.java:213)
 at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:53)
 at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:235)
 at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:117)
 at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
 at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)

==>

This is a terrible error message with what I suspect is a fairly simple cause: I think you're running with a different reference (or different version of the same reference) than the reference to which your BAMs were initially aligned. Can you check to make sure that the version of the reference you're using matches the BAMs exactly?
(http://getsatisfaction.com/gsa/topics/unifiedgenotyper_problem_with_nt_option)

> vi /etc/exports

root_squash, no_root_squash : NFS 서버에도 root 사용자가 있을 것이고, NFS 클라이언트에도 root가 있을 것이다. 그러나 두 root가 같은 root가 될 순 없다. NFS 클라이언트의 root가 NFS 서버의 root 권한을 가질 수 없다. 따라서 기본값은 root_squash로 클라이언트 root는 nobody와 같은 사용자로 맵핑되어 버린다. 서버와 클라언트의 root 사용자를 일치하도록 하려면 no_root_squash라고 적으면 된다.

all_squash, no_all_squash : 기본값은 no_all_squash로서 root를 제외한 일반 사용자 ID에 대해서는 서버와 클라이언트 UID가 동일한 사용자이며 동일한 권한을 갖는다고 생각한다. 이는 root에 대한 기본 처리값과 반대이다. 그러나 all_squash를 해버리면 모든 UID, GID를 무조건 익명 사용자 ID로 매핑해 버린다.

> nfs restart


======================

[Rocks-Discuss]Cannot write to user home on compute node

Tim Carlson tim.carlson at pnl.gov
Thu Feb 16 11:47:40 PST 2006

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---

On Thu, 16 Feb 2006, Chuming Chen wrote:

Add no_root_squash to the options in /etc/exports and then restart the NFS 
services on the frontend.

Tim

Tim Carlson
Voice: (509) 376 3423
Email: Tim.Carlson at pnl.gov
Pacific Northwest National Laboratory
HPCaNS: High Performance Computing and Networking Services

> Hi,
>
> On the compute node, as the user, I can create file in my home. But as
> root, I failed. What would be wrong here?
>
> [chen at compute-0-0 ~]$ pwd
> /home/chen
> [chen at compute-0-0 ~]$ ls -l test
> ls: test: No such file or directory
> [chen at compute-0-0 ~]$ touch test
> [chen at compute-0-0 ~]$ ls -l test
> -rw-rw-r--  1 chen chen 0 Feb 16 13:50 test
>
> [root at compute-0-0 chen]# pwd
> /home/chen
> [root at compute-0-0 chen]# touch test
> touch: cannot touch `test': Permission denied
>
> Thanks a lot.
>
> Chuming Chen
>