Hi,
I am running picard to sort sam file generated from bwa mem. But I got errors as the following lines show. Could you please help me in solving this problem?
Thank you very much.
Hui Liu
java -jar /home/liuhui/bin/picard-tools-2.4.1/picard.jar SortSam \
INPUT=lib_1.sam \
OUTPUT=lib_1_corSort.bam \
SORT_ORDER=coordinate
[Fri Jun 17 21:12:47 CST 2016] picard.sam.SortSam INPUT=lib_1.sam OUTPUT=lib_1_corSort.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 GA4GH_CLIENT_SECRETS=client_secrets.json
[Fri Jun 17 21:12:47 CST 2016] Executing as liuhui@ginkgo on Linux 3.8.0-44-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: 2.4.1(7c4d36e011df1aec4689b51efcada44e92d1817f_1464389670) JdkDeflater
[Fri Jun 17 21:12:47 CST 2016] picard.sam.SortSam done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Insert size out of range; File lib_1.sam; Line 10072
Line: HWI-ST1283:245:C4K2TACXX:6:1101:8926:2934 65 Scaffold_1000 77285907 0 100M = 657067308 579781402 CTCATACCTTGAAACATGGGAGGGCTAGCACCATTTTCAGTGCCCTCAATGTTGGAGCAGAATTAGACATTCACACCACCAGGACACCCATGAGCCCCAT CCCFFFFFHHHHHJJIJJJJJJIIIJJJJIJJIJJJJJIIGJJJHEHEHGGGEHICGGIIDGIGGGEFFHGHF<@CB???AA???=?58??A@C3:2529 NM:i:11 MD:Z:12G14A0A5C4A1T7A0A12C20G9A5 AS:i:45 XS:i:41 RG:Z:lib1 XA:Z:Scaffold_1000,+129324137,61M39S,4;Scaffold_920,+15157804,6S51M43S,2;Scaffold_1000,-653898065,37S50M13S,2;
at htsjdk.samtools.SAMLineParser.reportErrorParsingLine(SAMLineParser.java:439)
at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:341)
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:545)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:519)
at picard.sam.SortSam.doWork(SortSam.java:91)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)