bam to sam coversion and flagstat

[questioner]

Try GUI tool SAMMate. It allows one to convert SAM to BAM and vice versa.

http://sammate.sourceforge.net/

[volks]

Usage: samtools flagstat <in.bam>

flagstat needs BAM as input. why do you want to convert to SAM in the first place?

[badhikari]

Hi Everybody,

I converted the Tophat result accepted_hits.bam to .sam using
samtools view accepted_hits.bam > accepted_hits.sam

and now my sam file looks like
SOLEXA1_0001:7:53:1361:1750#0 163 pcu_contig_1 78 255 84M = 139 0 GTTCGCGTATTTTGGTCGAAATGCTAAAAGCTCAACAGCCTTTGCGATACATGCGTCGTCACTAGGGTACAATGCCAGCCATGCHHHHHIHHHHDHHHHGHHHHHHHGHHHHHHHHGHHEHHHGHHFHDHGHHHHHHGHBHHGHHHHHHHHDHHHDGHBHGHGHHEFG NM:i:0 NH:i:1
SOLEXA1_0001:7:26:430:480#0 99 pcu_contig_1 117 255 84M = 195 0 CTTTGCGATACATGCGTCGTCACTAGGGTACAATGCCAGCCATGCTATTGAGCAAGTTAACAGTTGACATGAAGCTAGATCGCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHDHHFHHHHEHHHHHHHHHFHIHHGEFHHHHIIGHHFIHAGH?GGBGFB NM:i:0 NH:i:1
Now when i try to run flagstat, it shows following;

[bam_header_read] EOF marker is absent.
[bam_flagstat_core] Truncated file? Continue anyway.

and the flaststat is

0 in total
0 QC failure
0 duplicates
0 mapped (nan%)
0 paired in sequencing
0 read1
0 read2
0 properly paired (nan%)
0 with itself and mate mapped
0 singletons (nan%)
0 with mate mapped to a different chr
0 with mate mapped to a different chr (mapQ>=5)

I do not know what i am doing wrong. It could be the way i converted my bam file to sam or something else.