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hisat2 error

I have paired end data and am running a hisat2 alignment. It ran ok the first time but when I tried it with another paired end sample,

This is the command used to run-

hisat2 -p 8 \
 -x /path_to_/genome_index/hg38_index \
 -1 sample1_1.fastq.gz \
 -2 sample1_2.fastq.gz \
 -S sample1.sam

am getting this error-

Error while flushing and closing output libc++abi: terminating due to uncaught exception of type int (ERR): hisat2-align died with signal 6 (ABRT)

alignment hisat2
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updated by Arup Ghosh Arup Ghosh • written by aj123 aj123

If the program install and index are "known" to have worked before then you should investigate if your fastq files are corrupt or truncated and/or if the reads are synchronized in paired-end files.

You could run them through repair.sh from BBMap suite (https://bbmap.org/tools/repair ) and check on the above possibility.

• 0 views • link
written by GenoMax GenoMax

1 answer

Check the validity of the .gz files with the following command. Make sure the system has sufficient free memory and storage to run the alignment. Also, check the files against the MD5 checksums.

gzip -v -t sample1_1.fastq.gz

You had reported a similar error earlier. hisat2 error-Paired end reads not equal or lack of RAM/disk space?

• 0 views • link
written by Arup Ghosh Arup Ghosh

Thank you, Im not sure if it is a memory issue this time as well. Could lack of memory potentially cause this issue when you run alignment in general?

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written by aj123 aj123

Yes, the aligner will fail in that situation.

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written by Arup Ghosh Arup Ghosh

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