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bedtools bamtofastq: Segmentation fault (core dumped)

I want to get all the reads from a bam file in a single fastq file. I am getting the message "Segmentation fault (core dumped)" while running 

bedtools bamtofastq -i in.name.sorted.bam -fq out.fq

However, it works for the PE mode

bedtools bamtofastq -i in.name.sorted.bam -fq out.R1.fq -fq2 out.R2.fq

Bedtools version: v2.29.0

Any suggestion would be very helpful.

bedtools bamtofastq bam rna-seq
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updated by h.mon h.mon • written by Rashedul Islam Rashedul Islam

It might be because your directory doesn't have enough space/memory or your program is trying to write in a file that is read only.

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written by Fatima Fatima

1 answer

an alternative would be to try

samtools fastq

the bedtools bamtofastq also recommends that:

If you want to create a single, interleaved FASTQ file for paired-end data, you can just write both to /dev/stdout:

   bedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq

Also, the samtools fastq command has more fucntionality and is a useful alternative.
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written by Istvan Albert Istvan Albert

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