Question: 'std::ios_base::failure while running STAR
0
gravatar for Ambika
2.9 years ago by
Ambika30
United States
Ambika30 wrote:

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 • 1.3k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Ambika30
1

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.

ADD REPLYlink written 2.9 years ago by michael.ante3.6k

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
ADD REPLYlink written 2.9 years ago by h.mon31k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1217 users visited in the last hour