Taxonomy; Error segmentation fault (core dumped)

[karina_F]

Hi, I am trying to generate my taxonomy.qza file and after a while running the command: qiime feature-classifier classify-sklearn --i-classifier silva-138-99-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
I get the following error: Segmentation fault (core dumped)

I have tried to free space and also to make the file go to another new directory, I can't think what else to do, could you help me?

Thanks!

[SoilRotifer (Mike Robeson)]

Hi @karina_F,

This usually implies that you are running out of memory. Typically, anywhere from ~24 - 64 GB or RAM is required for full length Small-Sub-Unit (SSU) rRNA gene sequences.

You can save memory usage by trimming your SILVA reference sequences such that it only spans your amplicon region. I've been able to get away with 16 - 32 GB of RAM, depending on the marker gene. You can use RESCRIPt to help make your own SILVA amplicon reference database. You can look through these tutorials:

• General RESCRIPt Tutorial
• Alternative approach to extract amplicon regions with RESCRIPt

If you still observe Segmentation faults, then you'll need to find a machine with more memory.

-Good luck!
-Mike