Fatal Error - input contains amino acid sequences


I’m trying to run identify_chimeric_seqs.py script using the usearch61 option.

My script is as following:

identify_chimeric_seqs.py -i seqs.fna -m usearch61 -o usearch_checked_chimeras -r gg_13_8_otus/rep_set/97_otus.fasta

And I’m getting the following error:

Traceback (most recent call last):

File “/usr/local/bin/identify_chimeric_seqs.py”, line 354, in


File “/usr/local/bin/identify_chimeric_seqs.py”, line 350, in main


File “/usr/local/lib/python2.7/dist-packages/qiime/identify_chimeric_seqs.py”, line 774, in usearch61_chimera_check

log_lines, verbose, threads)

File “/usr/local/lib/python2.7/dist-packages/qiime/identify_chimeric_seqs.py”, line 928, in identify_chimeras_usearch61


File “/usr/local/lib/python2.7/dist-packages/bfillings/usearch.py”, line 2345, in usearch61_chimera_check_denovo

app_result = app()

File “/usr/local/lib/python2.7/dist-packages/burrito/util.py”, line 285, in call

'StdErr:\n%s\n' % open(errfile).read())

burrito.util.ApplicationError: Unacceptable application exit status: 1


cd “/home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/”; usearch61 --mindiffs 3 --uchime_denovo “/home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/seqs.fna_consensus_fixed.fasta” --minh 0.28 --xn 8.0 --minseqlength 64 --mindiv 0.8 --abskew 2.0 --uchimeout “/home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/seqs.fna_chimeras_denovo.uchime” --dn 1.4 --log “/home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/seqs.fna_chimeras_denovo.log” > “/tmp/tmpFpk8iSqlajiIeUl6KKhY.txt” 2> “/tmp/tmp70Tv8qmFRTOBLxjQcGFZ.txt”


usearch_i86linux32 v6.1.544, 4.0Gb RAM (65.9Gb total), 24 cores

© Copyright 2010-12 Robert C. Edgar, all rights reserved.



00:00 2.0Mb Reading /home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/seqs.fna_consensus_fixed.fasta (empty file)

usearch61 --mindiffs 3 --uchime_denovo /home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/seqs.fna_consensus_fixed.fasta --minh 0.28 --xn 8.0 --minseqlength 64 --mindiv 0.8 --abskew 2.0 --uchimeout /home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/seqs.fna_chimeras_denovo.uchime --dn 1.4 --log /home/juanitahsolano/Documents/Sequenciamento/usearch_checked_chimeras/seqs.fna_chimeras_denovo.log

**—Fatal error—**

Input contains amino acid sequences

About this error, what can I do?


Hi @jhsolano! This is the QIIME 2 forum, which is focused on user support and discussion centered around the QIIME 2 project. Can you please post your question on the QIIME 1 forum? Thanks!

1 Like

Hi again! @thermokarst pointed out that you already posted your question to the QIIME 1 forum. Please avoid posting the same question on the QIIME 1 and QIIME 2 forums, as that will only slow us down in helping you. The QIIME 1 forum is monitored by developers and power users, and you’ll typically receive a response within 24 hours.