Last command failed (134/SIGABRT)

Marco Sollitto

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Jul 5, 2021, 9:06:48 AM7/5/21

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Dear all,

I am using the following command with 2.55 Stacks version.

denovo_map.pl -M 5 -T 1 -o ./stacks --popmap ./statistics/popmap.txt --samples ./trimmed_reads/subset

I obtain the following error:

"""

Merging secondary stacks (max. dist. N=7 from consensus)...

free(): invalid next size (fast)

Command terminated by signal 6

4.67user 0.03system 0:05.57elapsed 84%CPU (0avgtext+0avgdata 11052maxresident)k

0inputs+0outputs (0major+3013minor)pagefaults 0swaps

denovo_map.pl: Aborted because the last command failed (134/SIGABRT). """

What could be the problem?

Thanks for the reply!

Marco

Giulia Trauzzi

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Jul 6, 2021, 4:35:31 AM7/6/21

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Sometimes I got this error message because I hadn't allocated enough memory for the slurm job to run. So I solved it increasing the memory.

Cheers,

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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Marco Sollitto

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Jul 6, 2021, 7:27:51 AM7/6/21

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Thank you Giulia for the support.

I am quite new in the Perl scripting, how could I modify the script for allocating more memory?

Marco

Giulia Trauzzi

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Jul 6, 2021, 1:58:26 PM7/6/21

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Hi Marco,

are you using some kind of high performance computer (or cluster) to run Stacks? Or are you running it locally?

I am submitting my slurm jobs that look like the screenshot attached.

and at #SBATCH --mem= XG it is how I can allocate more memory for the job to run.

In particular for the core module "gstacks", I found it requires more memory than the other modules.

I hope this helps.

Best,

Giulia

To view this discussion on the web visit https://groups.google.com/d/msgid/stacks-users/05b02201-869c-4cf6-a963-32e5535c2adfn%40googlegroups.com.

Screenshot_2021-07-07-05-54-13-049_com.android.chrome.jpg

Marco Sollitto

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Jul 7, 2021, 8:22:00 AM7/7/21

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It's not a cluster.

Thanks for your support,

Marco

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