I'm using the latest samtools (1.1) and picard (1.128). If I make a bam using the -u option of eg. calmd, it now creates a raw uncompressed bam (as opposed to a bgzip bam with compression level 0, which is what samtools v0 did).
Picard falls over given such a bam: $ java -jar /.../picard-1.128.jar ValidateSamFile I=/.../my.bam [Wed Feb 11 13:07:17 GMT 2015] picard.sam.ValidateSamFile INPUT=/.../my.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Wed Feb 11 13:07:17 GMT 2015] Executing as [...] on Linux 2.6.32-44-server amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_20-b02; Picard version: 1.128(bce9562c1b163bc6007e76eabc0ab990a516450b_1421251575) JdkDeflater ERROR: Read groups is empty SAMFormatException on record 01 [Wed Feb 11 13:07:17 GMT 2015] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1267007488 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: SAMFormatException on record 01 at htsjdk.samtools.SamFileValidator.validateSamRecordsAndQualityFormat(SamFileValidator.java:308) at htsjdk.samtools.SamFileValidator.validateSamFile(SamFileValidator.java:199) at htsjdk.samtools.SamFileValidator.validateSamFileVerbose(SamFileValidator.java:159) at picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:166) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105) Caused by: htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /lustre/scratch105/vrpipe_testing/sb10/pipelines_test_output/smalt_mapping_with_improvement/9/d/d/e/2/8_sam_to_fixed_bam/2822_7.pe.3.bam; Line 1 Line: BAM�@HD VN:1.3 SO:coordinate at htsjdk.samtools.SAMLineParser.reportFatalErrorParsingLine(SAMLineParser.java:427) at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:217) at htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:248) at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:236) at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:212) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:515) at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:489) at htsjdk.samtools.SamFileValidator.validateSamRecordsAndQualityFormat(SamFileValidator.java:263) ... 6 more samtools is fine with it: $ samtools view -H /.../my.bam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. @HD VN:1.3 SO:coordinate @SQ SN:fake_chr1 LN:290640 @SQ SN:fake_chr2 LN:1716851 @PG [...] Can compatibility be expected in the future, or should I develop a work-around? -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
