identify_chimeric_seqs.py ERROR
Juanita H. Solano
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 <module>
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
(C) 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
What this means?
When I did: print_qiime_config.py -t, I’d the following printed out:
System information
==================
Platform: linux2
Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2]
Python executable: /usr/bin/python
QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3
Dependency versions
===================
QIIME library version: 1.9.1
QIIME script version: 1.9.1
qiime-default-reference version: 0.1.3
NumPy version: 1.8.2
SciPy version: 0.18.1
pandas version: 0.19.1
matplotlib version: 1.3.1
biom-format version: 2.1.5
h5py version: 2.2.1 (HDF5 version: 1.8.11)
qcli version: 0.1.1
pyqi version: 0.3.2
scikit-bio version: 0.2.3
PyNAST version: 1.2.2
Emperor version: 0.9.60
burrito version: 0.9.1
burrito-fillings version: 0.1.1
sortmerna version: SortMeRNA version 2.0, 29/11/2014
sumaclust version: SUMACLUST Version 1.0.01
swarm version: Swarm 1.2.19 [Dec 14 2016 15:48:25]
gdata: Installed.
QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:
http://qiime.org/install/qiime_config.html
http://qiime.org/tutorials/parallel_qiime.html
blastmat_dir: /usr/share/ncbi/data
pick_otus_reference_seqs_fp: /usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
python_exe_fp: python
sc_queue: all.q
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: /usr/share/qiime/data/core_set_aligned.fasta.imputed
cluster_jobs_fp: None
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue: friendlyq
jobs_to_start: 1
slurm_time: None
qiime_scripts_dir: /usr/lib/qiime/bin/
denoiser_min_per_core: 50
working_dir: .
assign_taxonomy_id_to_taxonomy_fp: # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir: /tmp/
slurm_memory: None
slurm_queue: None
blastall_fp: blastall
seconds_to_sleep: 60
QIIME base install test results
===============================
...F.....
======================================================================
FAIL: test_for_unrecognized_values (__main__.QIIMEDependencyBase)
qiime_config has no extra values
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 301, in test_for_unrecognized_values
error_msg_fragment % ", ".join(extra_vals))
AssertionError: The QIIME config file set via the QIIME_CONFIG_FP environment variable contains unrecognized values:
python_exe_fp, qiime_scripts_dir, working_dir
Once this is done (identify chimeras) I should be using filter_fasta.py script.
Thanks!
Stefan Janssen
it says that "Input contains amino acid sequences". Could it be that your fasta sequences contain non nucleotide characters. Search for anything but A C G U T N. Can you post the first four lines of your input file?
Juanita H. Solano
Stefan Janssen
Juanita H. Solano
Thanks