RNA STAR error: file does not contain alignment data

Hi Galaxy community,

I have a problem when running the alignment with RNA STAR. For me, it’s not clear what the error is.

the error info looks like this:
Oct 21 14:00:44 … started STAR run
Oct 21 14:00:46 … loading genome
Oct 21 14:17:51 … processing annotations GTF
Oct 21 14:18:18 … inserting junctions into the genome indices
Oct 21 14:22:34 … started 1st pass mapping
EXITING because

And when I open BAM file it looks like this:

My data set was trimmed with Cutadapt. Since it was prepared with Illumina TruSeq Kits Single Index. I used the following sequence to trim the adapter:
Read 1

Read 2

like suggested by Illumina page (TruSeq Single Indexes )

Is it the trimming that giving the issue? Because I did test run previously without trimming, it went well. But only mapped 68%.

I highly appreciate your help here.


Hi @zee_azizah,
it seems that there was a problem during the trimming, because one of the datasets is truncated:

EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length.

Please, repeat the pre-processing step with cutadapt.


Hi @gallardoalba,

Thank you for the help. I still have another question tho.

Should I use those 2 sequences to trim the adapter for all my data sets?
Or only to trim the index sequence, like 6 bp? I know the index sequence for each sample.