I’ve being trying to use cutadapt Read output as input in a paired-en alignment with RNA STAR. The thing is that some kind of error is happening, and I think I cannot handle it. The STAR output says:
Apr 23 14:04:29 … started STAR run
Apr 23 14:04:29 … loading genome
Apr 23 14:07:30 … processing annotations GTF
Apr 23 14:07:46 … inserting junctions into the genome indices
Apr 23 14:09:50 … started mapping
EXITING because of FATAL
No more information is given.
I’ve tried to run the same alignment using the raw FASTQ files, and setting the same exact parameters as before. Everything worked fine, a in less than 30 minutes STAR finished its job.
So the problem seems to be related with the cuatadapt output. I checked the file format and it says fastq.gz, which seems correct to me. I opened the viewer to see the file, and it looked perfect. The only thing that changed after the trimming process is that I trimmed 5 bp from the 3’ end. Nothing else.
Any idea about what can be happening?