Bowtie2 ABRT error

Question

[a.hayat20]

Hi all,

I have aligned my data using Bowtie2 for a number of samples over the last couple of days but I am suddenly getting this error:

Error while flushing and closing output libc++abi.dylib: terminating with uncaught exception of type int (ERR): bowtie2-align died with signal 6 (ABRT)

The command seems to run but then comes up with the above error at the end.

I am using the below command to aligned my paired-end data: bowtie2 -x Reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index -1 1.fastq -2 2.fastq -S file.sam

Thanks a lot in advance!

Answer 1

[ATpoint]

http://seqanswers.com/forums/showthread.php?t=15599 => Your disk is probably full.

Given that you use GRCh38 you do not seem to be aware that bowtie2 is not a splice-aware aligner. STAR, hisat2 or Rsubread is usually used for splice-aware alignment of RNA-seq data. Alternatively a lightweight franework such as salmon to directly quantify reads against a transcriptome.