beginning of quality values record not found & qual length () differs from seq length

[papori]

Hi all,
i am using the newest version of tophat.
Trying to align to Danio reiro Ensembl genome by using also gtf.
We did RNAseq using HiSEQ2000.
i am getting those errors as mention in the title....
(each for diffrent run)
Should i remove those reads?
Or , there is other problem?

My commandline is:
/tophat-2.0.4.Linux_x86_64/tophat -r 430 -G /run/media/My\ Book/2la/reference/danRef7.gtf -p 8 -o /home/Desktop/tophat_iin /run/media/My\ Book/2la/reference/danRer7 /run/media/My\ Book/2la/RNAseq_zv9_All/Sample_ii-na_1.fastq /run/media/My\ Book/2la/RNAseq_zv9_All/Sample_ii-na_2.fastq

Thanks,
Pap

[maubp]

Have you tried checking your FASTQ files are valid? Perhaps one has been truncated or otherwise corrupted?