Could you post the lines (including few lines before and after too) in which you are getting the error (i.e., line 25640-25650) in your sam file to see what makes that error.

Thanks for your reply.. below is the lines 25640-25650

HWI-ST365_0135:2:1101:17649:2719#TACTAG-1 16 gnl|Cflo_3.3|scaffold1656 205450 42 28M66N22M * 00 GGAAGCTACGGCTGCTAATATTATGAAGGCCATCGTTTTGATAACTGGCG `\c_Ybb_be\gggggggggggggggggggggggggfggggggggggggg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17674:2720#TACTAG-2 16 gnl|Cflo_3.3|scaffold469 269161 42 19M495N31M * 00 TGATACCAAAGGCTACAAGGAAGGGGTGCGGCTGGTACCCTTCTCCGATG dbed^eeggegegegegggggegeeeagggeeeegf[eeeg[fdgggggg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17612:2739#TACTAG-1 0 gnl|Cflo_3.3|scaffold863 85331 42 28M2886N22M * 00 GTTGTCGATTATCAAATCCCTTGAACTTCTTCTAGTATGCATCCTTATCG gfggfgcgfafbcfffggeggggefcgefggggfggdgdggefggeabgd AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17910:2521#TACTAG-1 0 gnl|Cflo_3.3|scaffold643 113193 42 47M452N3M * 00 CGCATTTTTTGCCTTCGTAGTCGCTTGTTTAGCAGTAGCCGTTCATGGCT gffgggggggfggfgffUefafffffceedVXcc``^a`d`_``BBBBBB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17910:2521#TACTAG-2 16 gnl|Cflo_3.3|scaffold643 113812 42 31M162N19M * 00 CTGTTCTCACTGCCGCTCATTGTTTAGCAGATATGGTCAACAATCCCGTG bbacc`ad]egggegdgegggfgeggggdgggggefeffbgggefggggg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17777:2540#TACTAG-1 16 gnl|Cflo_3.3|scaffold284 403867 42 15.5M90N34.5M * 00 TCAACTACTGGTGTGAAAGGAGTGATAAGATTGTAAAAGAAATACATAAA eggggggggggggggggggggggggggggggggggggggggggggggggg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17848:2632#TACTAG-1 16 gnl|Cflo_3.3|scaffold2377 112017 42 22M313N28M * 00 GCATAGCCGCTAAATCATCATTCTGTATATTTTCAGAATTTGTAGTTAAA a[Ocegeegggggeaeggggggeggggegggegggggggggggggggggg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17763:2636#TACTAG-2 16 gnl|Cflo_3.3|scaffold1702 27973 42 9M441N41M * 00 TGACATCAGCTATTTTTTGGGGTTTGCATGCTGTTTGATTTAAAAGAGGG eedde]ee\edfcffdc_eeefeedffffaahfcfggeggggggdgffgg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:17782:2739#TACTAG-2 0 gnl|Cflo_3.3|scaffold28 211904 42 28M92N22M * 0 0AAGATTTTGACTAAATGCGCCAAGCAAGACGGCGCGGATGTTTGCGATAA gggggggggggggggggggfdggcgggggggeggggegefbggdgedeed AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:18146:2514#TACTAG-1 16 gnl|Cflo_3.3|scaffold866 37971 42 8M114N42M * 00 GGCGAAATCTGTTCCACTCTGGCGATCGCGATCTTGTCATCCAATTGCCG gggdgggggggggggcggggggggggggggggbgggeggegggggggggg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

HWI-ST365_0135:2:1101:18053:2519#TACTAG-1 0 gnl|Cflo_3.3|scaffold232 533726 42 15M367N35M * 00 CCTTTGCCCAAGATGACGAAGGGTACATCCAGTTTTGGTAAACGGCGTAA gggggggggggggggggggggggdggggggggegggggggggeegggdgg AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

As you can see in the CIGAR value of 6th line in your output, 15.5M90N34.5M is not a valid CIGAR value. From the output format, I believe this is a TopHat output. Normal alignment CIGAR value and TopHat alignment CIGAR value are bit different. But as far as I know, decimal values can't be there in alignment CIGAR value. It means half of the base aligned in one position and the remaining half aligned after an intron. Funny huh??

One possible solution is to remove these kind of lines. If you feel like loosing so many reads like this, then you can try with different versions of TopHat.

Thanks again. I used Tophat2 in my work. Could you share any script or any one-liner by which I can identify all such bad CIGAR value and remove them?

Try using something like this:

samtools view -bS output.sam > output.bam