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'std::ios_base::failure while running STAR

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

rna-seq
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written by AP • AP

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
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written by h.mon h.mon

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.

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written by michael.ante michael.ante

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