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Old 06-11-2014, 10:49 PM   #1
wbb1813
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Location: China Shanghai

Join Date: May 2014
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Default Sam error when use cufflinks

Hi everyone ,when I use cufflinks to deal with a bem file,I get some errors.
like this :SAM error on line 451162: CIGAR op has zero length

[tuser@bioiserver1 ~/binwang/project1]$ cufflinks -p 8 -o 1v2 wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2.bam
cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.2.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
Warning: BAM header has 0 length or is corrupted. Try using 'samtools reheader'.
File wgEncodeCaltechRnaSeqH1hescR2x75Il200AlignsRep1V2.bam doesn't appear to be a valid BAM file, trying SAM...
[10:59:58] Inspecting reads and determining fragment length distribution.
SAM error on line 6782: CIGAR op has zero length
SAM error on line 42019: CIGAR op has zero length
SAM error on line 42988: CIGAR op has zero length
SAM error on line 144697: CIGAR op has zero length
SAM error on line 161350: invalid CIGAR operation
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Old 06-19-2014, 05:37 AM   #2
TiborNagy
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Use TopHat to align reads. This create a proper BAM file.
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Old 06-19-2014, 11:56 PM   #3
WhatsOEver
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The error message is quite clear, though there are a lot of informations missing to provide a solution.

The cigar string is not properly read or hasn't been properly set by the mapper. What program are you using for mapping? How do the lines 6782, 42019, 42988, etc look like in your sam file? Are the cigar fields (6th column) really empty? What is the invalid operation in line 161350?
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