Empty sequence dictionary

[aquleaf]

Hi.

When I used picardtools ValidateSamFile, it reported the empty sequence dictionary error in sam file. What does this error mean?

Wish help! Thanks very much in advance!

[maubp]

Are there no @SQ lines in the SAM header?

[DNASpeaks]

trouble converting sam to bam, ValidateSamFile output "empty seq group"

Are there no @SQ lines in the SAM header?

Hello Everyone,
I am having trouble converting the sam files to bam using samtools. I used this cmd to convert my sam to bam -

samtools view -bT hg19.fa s_chip2.sam > s_chip2.bam
I got this error.
Parse error at line 7707082: sequence and quality are inconsistent
Aborted


I ran ValidateSamFile.jar, a picard tool and got the following error, hundreds of them -

WARNING: Read name HWI-ST798R:82: D18MUACXX:2:1101:2025:1987, A record is missing a read group
ERROR: Record 5, Read name HWI-ST798R:82: D18MUACXX:2:1101:8625:1992, Empty sequence dictionary.

I am not sure how to fix this, any help is appreciated.