UClust Issues

[Samuel Major]

Hello,

I've been trying to run my sequences through SILVA_123 and I have gotten 2 different types of errors depending on which data set I use.

the first code I send through

 pick_open_reference_otus.py -i F16_16S/1_qlab/combined_seqs.fna -o F16_16S/5_SILVA_usearch/silva123_otus -r SILVA123_QIIME_release/rep_set/rep_set_16S_only/97/97_otus_16S.fasta -p F16_16S/silva-123-params.txt

and this results in

*** ERROR RAISED DURING STEP: Pick Reference OTUs

Command run was:

 pick_otus.py -i F16_16S/1_qlab/combined_seqs.fna -o F16_16S/5_SILVA_usearch/silva123_otus/step1_otus -r SILVA123_QIIME_release/rep_set/rep_set_16S_only/97/97_otus_16S.fasta -m uclust_ref --enable_rev_strand_match --suppress_new_clusters

Command returned exit status: 137

Stdout:

Stderr

Killed

The error I'm getting on a different set of data is:

 pick_open_reference_otus.py -i 3_mock/combined_seqs.fna  -o tmp_MSC_SILVA_opref_otus -r ~/SILVA123_QIIME_release/rep_set/rep_set_16S_only/97/97_otus_16S.fasta -p ~/F16_16S/silva-123-params.txt

 burrito.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided

I literally ran these at the same time, so I'm not sure what the real underlying issue is here. The last code ran fine when it was just the defaults for pick_open_reference_otus.py. So I'm not sure it's UClust that is the issue. 

I've read the previous posts about similar issues and I've attached my parameters file. 

Can anyone help me decipher what the issue might be?

Thank you

Sam

[Greg Caporaso]

Hi Sam,

For the first error, I think it's possible that you're running out of memory. Is it possible to increase the memory that is available for that job? If you're working in VirtualBox, this might involve increasing the amount of memory that the virtual machine has access to. uclust can use a lot of memory, and the enable-rev-strand-match doubles the amount of memory that is use. 

For the second error, can you try replacing the ~ with /home/qiime (assuming that /home/qiime is your home directory, which seems to be the case based on your parameters file)?