Due to lack of memory on my personal computer I have run the latest AMI version (ami-19118ff72) of qiime in the Amazon EC2.
I want to perform the “chimera checking sequences” with usearch61 algorithm.
After installing the correct version of usearch61 in the server, copying the seqs.fna coming from the split_library_output script and downloading the reference database gg_13_5.fasta I ran:
identify_chimeric_seqs.py -i seqs.fna -m usearch61 -o usearch_checked_chimeras/ -r gg_13_5.fasta
For my surprise there was only two files:
No “.txt” extension file, so I continue with the pipeline using the “.uc”:
filter_fasta.py -f seqs.fna -o seqs_chimeras_filtered.fna -s usearch_checked_chimeras/ seqs.fna_consensus_with_abundance.uc -n
the output file was:
when I try to run the last step of the pipeline:
pick_otus.py -m usearch61 -i seqs_chimeras_filtered.fna -o usearch61_picked_otus/
I get the following error:
cogent.app.util.ApplicationError: Error running usearch61. Possible causes are unsupported version (current supported version is usearch v6.1.544) is installed or improperly formatted input file was provided
why there is not a “.txt” file in the identify_chimeric_seqs.py output? could I use.uc file to continue with the pipeline o I have to switch to uclust algorithm to pick the OTUs? I am not sure what the .uc kind of file is, I find searching in the tutorial that is an intermediate uclust(.uc) files.
I attached 20 lines of the input files and the log file.
Thanks in advanced for the help