bowtie2-align died with signal 6 (ABRT) (core dumped)
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2.4 years ago
Ric ▴ 350

I do not know why I got the below error:

bowtie2 -x tdna -U s21.fq -S sample5.sam 
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

Thank you in advance.

RNA-Seq alignment • 1.3k views
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Please share first few lines of s21.fq

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Also, are you using some very old version of bowtie2. Please specify the bowtie2 version.

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1
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Check validity of your fastq files

Checking fastq is valid

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Thank you all, my fastq file was broken.

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How did you discover that ?

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I opened the file and saw that accidentally during the trimming stage I converted it to a FASTA file.

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