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error with bowtie2

I use this command to filter the chrM RNA.

$bowtie2 -x ./chrM/chrM_index ./S1_R1.fastq --un ./S1_R1_nochrM.fastq

And got this error after quite a long time of running:

libc++abi.dylib: terminate called throwing an exception (ERR): bowtie2-align died with signal 6 (ABRT)

It still gave me the output file.

My question is that, is the output file is complete and how to fix this error.

Thanks a lot~~

rna-seq
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written by jolin0701-dy jolin0701-dy

Dose someone can help me with it?

Thanks!!

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written by jolin0701-dy jolin0701-dy

If you want to "bump" a question then edit your original post. There is no need to post a new answer (that isn't a real answer).

That said, have you tried to capture stdout/stderr to files to see if that can give you any additional information?

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written by GenoMax GenoMax

Thanks for your suggestions, and I'll try it…..

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written by jolin0701-dy jolin0701-dy

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