Fragment insertion tree error

[ad2459 (Alison D)]

Hello, I'm watching along on youtube as a 'free' viewer. I am using virtual box on a Mac.

I had a plugin error occur when doing the phylogenetic tree generation in the Parkinson's Mouse Tutorial.

Could you help if you get a chance so that I can continue to follow hands-on portion?

Here's the error:

(qiime2-2019.10) qiime2@qiime2core2019-10:~/mouse_tutorial$ qiime fragment-insertion sepp \

--i-representative-sequences ./dada2_rep_set.qza
--i-reference-database sepp-refs-gg-13-8.qza
--o-tree ./tree.qza
--o-placements ./tree_placements.qza
--p-threads 1
libgcc_s.so.1 must be installed for pthread_cancel to work
Plugin error from fragment-insertion:

Command '['run-sepp.sh', '/tmp/qiime2-archive-0qsxq9q5/38a1b22d-589c-4685-9f1f-f5c376efdb91/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-litqw7na/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-litqw7na/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk', '-r', '/tmp/qiime2-archive-litqw7na/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt']' returned non-zero exit status 134.

Debug info has been saved to /tmp/qiime2-q2cli-err-kpcc0as_.log

Thanks,
Alison

[Mehrbod_Estaki]

Sorry but providing support for these is going to be very difficult for all of us who are attending the workshop, your best bet is to try and recruit help after or simply grab the output files for problematic steps from here:
https://docs.qiime2.org/2020.8/tutorials/pd-mice/
that way you can continue along

[ad2459 (Alison D)]

Ok, will do, thanks Bod! I appreciate your swift reply.

[ChrisKeefe]

@ad2459, like @Mehrbod_Estaki suggested, probably best to just download the output files so you can keep up.

When you have time to troubleshoot this later, though, you might look at what resources you have allocated to your VM. You may be running out of memory (RAM).

A forum search will turn up other questions that troubleshoot out of memory (OOM) errors in VMs - you may find useful resources there.

[ad2459 (Alison D)]

Thanks Chris, I appreciate your help. I will look into the VM settings.

[Stefan (Stefan Janssen)]

Exit code 134 refers to memory allocation issues. I am pretty sure you have to increase the amount of RAM assigned to the VM in order to get this computation done.

[DRALABU_SAVIOUR]

@Stefan, @ChrisKeefe, @Mehrbod_Estaki et al, thanks for this topic I faced the same problem.
I am viewing the livestream form Uganda