'std::ios_base::failure while running STAR

Question

[AP]

Hello everyone,

I was trying to align RNAseq reads to a reference genome using STAR . My script looks like this:

STAR --runThreadN 4 --genomeDir /home/aubayp/rnaseq/star/genome --runMode genomeGenerate --genomeFastaFiles /home/aubayp/rnaseq/star/genome/Fov89-1A_65_contigs.fasta --sjdbGTFfile /home/aubayp/rnaseq/star/annotation_file  --readFilesIn SL264821_1_paired.fastq.gz SL264821_2_paired.fastq.gz --readFilesCommand gzip -c --outFilterType BySJout --outFileNamePrefix /home/aubayp/rnaseq/star/SL264821_out --outSAMtype SAM

and the error that I got is:

terminate called after throwing an instance of 'std::ios_base::failure'

  what():  basic_filebuf::underflow error reading the file

This error is coming after my script tries to process GTF file. Any suggestions on what might be going on.Many thanks in advance.

Ambika

[michael.ante]

According to your script, you run index generation and alignment simultaneously. This will not work. Please read the manual, compute the index first and run afterwards the alignment.

[h.mon]

This error is coming after my script tries to process GTF file.

Could you show us the GTF then?

head /home/aubayp/rnaseq/star/annotation_file