[Samtools-help] Picard 1.106 error on using /dev/stdin

[Henrikki A. <hen...@he...>]

Hi,

It seems that Picard 1.106 has problems with using /dev/stdin and 
/dev/stdout (and it now emits a stackguard warning, but will run). See 
below:

Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library 
picard/picard-tools-1.106/libIntelDeflater.so which might have disabled 
stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c 
<libfile>', or link it with '-z noexecstack'.
Exception in thread "main" net.sf.samtools.SAMFormatException: Error 
parsing text SAM file. Not enough fields; File /dev/stdin; Line 1
Line: Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library 
picard/picard-tools-1.106/libIntelDeflater.so which might have disabled 
stack guard. The VM will try to fix the stack guard now.
         at 
net.sf.samtools.SAMLineParser.reportFatalErrorParsingLine(SAMLineParser.java:420)
         at net.sf.samtools.SAMLineParser.parseLine(SAMLineParser.java:210)
         at 
net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:242)
         at 
net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:230)
         at 
net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:206)
         at 
net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:768)
         at 
net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:746)
         at net.sf.picard.sam.CleanSam.doWork(CleanSam.java:81)
         at 
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
         at 
net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:120)
         at net.sf.picard.sam.CleanSam.main(CleanSam.java:56)


The command that I'm trying to run is:

java -Xmx5g -jar picard/picard-tools-1.106/MergeSamFiles.jar 
INPUT=alignment-paired.sam INPUT=alignment-single.sam OUTPUT=/dev/stdout 
USE_THREADING=true VALIDATION_STRINGENCY=SILENT QUIET=true 
VERBOSITY=WARNING COMPRESSION_LEVEL=0 TMP_DIR=tmp | java -Xmx5g -jar 
picard/picard-tools-1.106/CleanSam.jar INPUT=/dev/stdin OUTPUT=foo.bam 
VALIDATION_STRINGENCY=SILENT QUIET=true VERBOSITY=WARNING TMP_DIR=tmp

If I run just the merge so that it prints out bam file normally, it 
completes normally. I have used version 1.90 with the stdin and stdout.

-- 
Henrikki Almusa