I have a very strange behavior of tophat v1.2.0 tool where it generate a blank sequence name on the stub_header.sam file.

@HD VN:1.0  SO:sorted
@SQ SN: LN:29893408
@SQ SN: LN:15549267
@SQ SN: LN:13234341
@SQ SN: LN:12718334
@SQ SN: LN:12965953
@SQ SN: LN:14726556
@SQ SN: LN:11902654
@SQ SN: LN:10288499
@SQ SN: LN:10253655
@SQ SN: LN:10167229
@SQ SN: LN:7207165
@SQ SN:Group5   LN:14363272
@SQ SN:Group6   LN:18472937
@SQ SN:Group7   LN:13219345
@SQ SN:Group8   LN:13546544
@SQ SN:Group9   LN:11120453

Is there away to identify if this issue come from gff file or the fastq file?