error while Alignment

[mehwish wahid]

Hello , 

I want to do RNAseq analysis, while doing the alignment using STAR  of multiple samples , some were successfully aligned while for some I got this error.

Can somebody please guide me how to remove this error and complete the alignment step 

EXITING because of FATAL ERROR in reads input: short read sequence line: 0

Read Name=@K00363
Read Sequence====
DEF_readNameLengthMax=50000
DEF_readSeqLengthMax=650

thanks in anticipation

[Alexander Dobin]

Hi,

it seems like your FASTQ file has empty sequences. If you trimmed the reads, please make sure that empty sequences are dropped from both Read1 and Read2 files.