Kmc might cause iva autopkgtest fail on arm64

[Andreas Tille <andreas@an3as.eu>]

Hi folks,

I stumbled upon the autopkgtests log of iva[1] which possibly uncovers
an issue in kmc since the log says:

...
The following command failed with exit code 1
/usr/bin/iva --threads 1 --trimmomatic /usr/share/java/trimmomatic.jar --pcr_primers hiv_pcr_primers.fa -f reads_1.fq.gz -r reads_2.fq.gz iva.out

The output was:

The following command failed with exit code 139
bash run_kmc.sh

The output was:

run_kmc.sh: line 2:  5046 Segmentation fault      kmc -fa -m4 -k95 -sf1 -ci25 -cs1000000 -cx1000000 /tmp/tmp.GkQzyocbDU/test/iva.out/tmp.common_kmers.8oo5afnl/reads.fa kmc_out $PWD > /dev/null


Running iva in test mode...
...

There are more Segmentation faults in connection with kmc later.
I think a Segmentation fault is just not good.  Is anybody up for
this issue?

Kind regards

    Andreas.


[1] https://ci.debian.net/data/autopkgtest/unstable/arm64/i/iva/8016157/log.gz

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