In trying to convert a sam file to a bam file using Picard's SamFormatConverter, I get the following error:
The pos column is the fourth column, and you can see that it contains 4294967264. So why is this counted as not numeric?
Thanks.
Eric
Code:
[Tue Dec 18 12:49:04 PST 2012] net.sf.picard.sam.SamFormatConverter INPUT=AML_PAERAH_73407_RNA.sam OUTPUT=AML_PAERAH_73407_RNA.bam VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Dec 18 12:49:04 PST 2012] Executing as efoss@gizmod60 on Linux 3.2.0-24-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24 Ignoring SAM validation error: ERROR: Read name HWI-ST156_294:2:46:13125:2318:0, CIGAR M operator maps off end of reference Ignoring SAM validation error: ERROR: Read name HWI-ST156_294:2:5:11648:3249:0, CIGAR M operator maps off end of reference [Tue Dec 18 12:49:13 PST 2012] net.sf.picard.sam.SamFormatConverter done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=696385536 Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. Non-numeric value in POS column; Line 539389 Line: HWI-ST156_294:2:21:6547:4182:0 99 MT 4294967264 39 51M = 93 -176 CCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACC HHHHHHHHHHHHHHHHHFHHHHEHHGHHGHGEEFGHHDHHBGDFGDFGFFH MD:Z:51 NH:i:1 HI:i:1 NM:i:0 SM:i:39 XQ:i:40 X2:i:0
Thanks.
Eric
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