samtools picard SamFormatConverter

Bio.X2Y · 06-14-2010, 07:22 AM

Hi,

I'm trying to run SamFormatConverter to convert a BAM to a SAM, and I'm getting an error (see below).

The text suggests that samtools is trying to parse my BAM as a SAM. However, the file is definitely a BAM, has a '.bam' extension, and appears to have the necessary "magic number" at the top.

Any ideas if I might be doing something wrong?

Thanks!

Command:
java -jar <location>/SamFormatConverter.jar I=in.bam O=out.sam

Head in.bam:
BAM?@HD VN:1.0 GO:none SO:unsorted
@SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens

Exception:
Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; Line 1
Line: BAM?@HD VN:1.0 GO:none SO:unsorted
at net.sf.samtools.SAMTextReader.reportFatalErrorParsingLine(SAMTextReader.java:169)
at net.sf.samtools.SAMTextReader.access$400(SAMTextReader.java:40)
at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:261)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:224)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:196)
at net.sf.picard.sam.SamFormatConverter.doWork(SamFormatConverter.java:64)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
at net.sf.picard.sam.SamFormatConverter.main(SamFormatConverter.java:72)

bh1 · 04-26-2011, 12:16 PM

Hi,
Did you figure a solution for this problem? I'm getting exactly the same error message.
thanks.

Richard Finney · 04-26-2011, 02:19 PM

Try VALIDATION_STRINGENCY=LENIENT in the java invocation.

Example:

java-Xmx67T -jar wherever/SamTowhatevernameis.jar \
VALIDATION_STRINGENCY=LENIENT \ INPUT=uncle.sam O=nephew.sam

That might shut up the error message and get Picard to accept the input.

bw. · 07-08-2013, 08:46 AM

In this case the issue is probably the
"BAM?" on the 1st line in front of "@HD VN:1.0 GO:none SO:unsorted"
I would try deleting it.

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06-14-2010, 07:22 AM	#1
Bio.X2Y Member Location: Europe Join Date: Apr 2010 Posts: 46	samtools picard SamFormatConverter Hi, I'm trying to run SamFormatConverter to convert a BAM to a SAM, and I'm getting an error (see below). The text suggests that samtools is trying to parse my BAM as a SAM. However, the file is definitely a BAM, has a '.bam' extension, and appears to have the necessary "magic number" at the top. Any ideas if I might be doing something wrong? Thanks! Command: java -jar <location>/SamFormatConverter.jar I=in.bam O=out.sam Head in.bam: BAM?@HD VN:1.0 GO:none SO:unsorted @SQ SN:chrM LN:16571 AS:HG18 UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta M5:d2ed829b8a1628d16cbeee88e88e39eb SP:Homo sapiens Exception: Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; Line 1 Line: BAM?@HD VN:1.0 GO:none SO:unsorted at net.sf.samtools.SAMTextReader.reportFatalErrorParsingLine(SAMTextReader.java:169) at net.sf.samtools.SAMTextReader.access$400(SAMTextReader.java:40) at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:261) at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:224) at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:196) at net.sf.picard.sam.SamFormatConverter.doWork(SamFormatConverter.java:64) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150) at net.sf.picard.sam.SamFormatConverter.main(SamFormatConverter.java:72)

04-26-2011, 02:19 PM	#3
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	Validation_stringency=lenient Try VALIDATION_STRINGENCY=LENIENT in the java invocation. Example: java-Xmx67T -jar wherever/SamTowhatevernameis.jar \ VALIDATION_STRINGENCY=LENIENT \ INPUT=uncle.sam O=nephew.sam That might shut up the error message and get Picard to accept the input.

04-26-2011, 12:16 PM	#2
bh1 Junior Member Location: SF Join Date: Feb 2011 Posts: 1	Hi, Did you figure a solution for this problem? I'm getting exactly the same error message. thanks.

07-08-2013, 08:46 AM	#4
bw. Member Location: San Francisco, CA Join Date: Mar 2012 Posts: 21	In this case the issue is probably the "BAM?" on the 1st line in front of "@HD VN:1.0 GO:none SO:unsorted" I would try deleting it.