Hi,
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
main()
File “/usr/local/bin/identify_chimeric_seqs.py”, line 350, in main
threads=threads)
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
HALT_EXEC=HALT_EXEC)
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
Command:
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”
StdOut:
usearch_i86linux32 v6.1.544, 4.0Gb RAM (65.9Gb total), 24 cores
© Copyright 2010-12 Robert C. Edgar, all rights reserved.
StdErr:
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?
Thanks.