Chimera Slayer issue

[Jen Underwood]

Hello all, 

I'm having a Chimera Slayer problem.  I've searched the forum and the fixes don't seem to help

*here I have my files in the same directory

identify_chimeric_seqs.py -m ChimeraSlayer -i pynast_aligned/rep_set_aligned.fasta -a pynast_aligned/Silva_108_core_aligned_seqs.fasta -o chimeric_seqs.txt

*error

Traceback (most recent call last):

  File "/macqiime/QIIME/bin/identify_chimeric_seqs.py", line 324, in <module>

    main()

  File "/macqiime/QIIME/bin/identify_chimeric_seqs.py", line 299, in main

    keep_intermediates=keep_intermediates)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 154, in chimeraSlayer_identify_chimeras

    keep_intermediates=keep_intermediates):

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 139, in __call__

    keep_intermediates=keep_intermediates)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 616, in get_chimeras_from_Nast_aligned

    app_results = app()

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 274, in __call__

    out,err,exit_status,self._get_result_paths(data))

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 411, in _get_result_paths

    raise ApplicationError,"Calling ChimeraSlayer failed."

cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.

print_qiime_config.py -t

System information

==================

         Platform: darwin

   Python version: 2.7.3 (default, Dec 19 2012, 09:12:08)  [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]

Python executable: /macqiime/bin/python

Dependency versions

===================

                     PyCogent version: 1.5.3

                        NumPy version: 1.5.1

                   matplotlib version: 1.1.0

                  biom-format version: 1.1.2

                QIIME library version: 1.7.0

                 QIIME script version: 1.7.0

        PyNAST version (if installed): 1.2

RDP Classifier version (if installed): rdp_classifier-2.2.jar

          Java version (if installed): 1.6.0_45

QIIME config values

===================

                     blastmat_dir: None

                         sc_queue: all.q

      topiaryexplorer_project_dir: None

     pynast_template_alignment_fp: /macqiime/greengenes/core_set_aligned.fasta.imputed

                  cluster_jobs_fp: /macqiime/QIIME/bin/start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /macqiime/greengenes/gg_12_10_otus/rep_set/97_otus.fasta

                     torque_queue: friendlyq

   template_alignment_lanemask_fp: /macqiime/greengenes/lanemask_in_1s_and_0s

                    jobs_to_start: 1

                cloud_environment: False

                qiime_scripts_dir: /macqiime/QIIME/bin/

            denoiser_min_per_core: 50

                      working_dir: None

                    python_exe_fp: /macqiime/bin/python

                         temp_dir: /tmp/

                      blastall_fp: blastall

                 seconds_to_sleep: 60

assign_taxonomy_id_to_taxonomy_fp: /macqiime/greengenes/gg_12_10_otus/taxonomy/97_otu_taxonomy.txt

running checks:

test_FastTree_supported_version (__main__.Qiime_config)

FastTree is in path and version is supported ... ok

test_INFERNAL_supported_version (__main__.Qiime_config)

INFERNAL is in path and version is supported ... ok

test_ParsInsert_supported_version (__main__.Qiime_config)

ParsInsert is in path and version is supported ... ok

test_R_supported_version (__main__.Qiime_config)

R is in path and version is supported ... ok

test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane. ... FAIL

test_blast_supported_version (__main__.Qiime_config)

blast is in path and version is supported ... ok

test_blastall_fp (__main__.Qiime_config)

blastall_fp is set to a valid path ... ok

test_blastmat_dir (__main__.Qiime_config)

blastmat_dir is set to a valid path. ... ok

test_cdbtools_supported_version (__main__.Qiime_config)

cdbtools is in path and version is supported ... ok

test_cdhit_supported_version (__main__.Qiime_config)

cd-hit is in path and version is supported ... ok

test_chimeraSlayer_install (__main__.Qiime_config)

no obvious problems with ChimeraSlayer install ... ok

test_clearcut_supported_version (__main__.Qiime_config)

clearcut is in path and version is supported ... ok

test_cluster_jobs_fp (__main__.Qiime_config)

cluster_jobs_fp is set to a valid path and is executable ... ok

test_denoiser_supported_version (__main__.Qiime_config)

denoiser aligner is ready to use ... ok

test_for_obsolete_values (__main__.Qiime_config)

local qiime_config has no extra params ... ok

test_gdata_install (__main__.Qiime_config)

gdata is installed ... ok

test_matplotlib_suported_version (__main__.Qiime_config)

maptplotlib version is supported ... ok

test_mothur_supported_version (__main__.Qiime_config)

mothur is in path and version is supported ... ok

test_muscle_supported_version (__main__.Qiime_config)

muscle is in path and version is supported ... ok

test_numpy_suported_version (__main__.Qiime_config)

numpy version is supported ... ok

test_pplacer_supported_version (__main__.Qiime_config)

pplacer is in path and version is supported ... ok

test_pynast_suported_version (__main__.Qiime_config)

pynast version is supported ... ok

test_pynast_template_alignment_blastdb_fp (__main__.Qiime_config)

pynast_template_alignment_blastdb, if set, is set to a valid path ... ok

test_pynast_template_alignment_fp (__main__.Qiime_config)

pynast_template_alignment, if set, is set to a valid path ... ok

test_python_exe_fp (__main__.Qiime_config)

python_exe_fp is set to a working python env ... ok

test_python_supported_version (__main__.Qiime_config)

python is in path and version is supported ... ok

test_qiime_scripts_dir (__main__.Qiime_config)

qiime_scripts_dir, if set, is set to a valid path ... ok

test_raxmlHPC_supported_version (__main__.Qiime_config)

raxmlHPC is in path and version is supported ... ok

test_rtax_supported_version (__main__.Qiime_config)

rtax is in path and version is supported ... ok

test_sourcetracker_installed (__main__.Qiime_config)

sourcetracker is installed ... FAIL

test_temp_dir (__main__.Qiime_config)

temp_dir, if set, is set to a valid path ... ok

test_template_alignment_lanemask_fp (__main__.Qiime_config)

template_alignment_lanemask, if set, is set to a valid path ... ok

test_uclust_supported_version (__main__.Qiime_config)

uclust is in path and version is supported ... ok

test_usearch_supported_version (__main__.Qiime_config)

usearch is in path and version is supported ... FAIL

test_working_dir (__main__.Qiime_config)

working_dir, if set, is set to a valid path ... ok

======================================================================

FAIL: test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane.

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/bin/print_qiime_config.py", line 144, in test_ampliconnoise_install

    "$PYRO_LOOKUP_FILE variable is not set. See %s for help." % url)

AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://qiime.org/install/install.html#ampliconnoise-install-notes for help.

======================================================================

FAIL: test_sourcetracker_installed (__main__.Qiime_config)

sourcetracker is installed

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/bin/print_qiime_config.py", line 245, in test_sourcetracker_installed

    ("SOURCETRACKER_PATH is not set. This is "

  File "/macqiime/lib/python2.7/site-packages/cogent/util/unit_test.py", line 332, in failIfEqual

    % (`observed`, `expected`))

AssertionError: SOURCETRACKER_PATH is not set. This is only important if you plan to use SourceTracker.

======================================================================

FAIL: test_usearch_supported_version (__main__.Qiime_config)

usearch is in path and version is supported

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/bin/print_qiime_config.py", line 678, in test_usearch_supported_version

    "which components of QIIME you plan to use.")

AssertionError: usearch not found. This may or may not be a problem depending on which components of QIIME you plan to use.

----------------------------------------------------------------------

Ran 35 tests in 1.859s

FAILED (failures=3)

[Tony Walters]

Hello Jen,

Can you run the unit test (test_identify_chimeric_seqs.py) and see if it passes the ChimeraSlayer tests?

Also, did you generate the aligned_seqs representative file using the Silva template or the default Greengenes template file?

Finally, can you change to the pynast_aligned/ folder and run the command there:

identify_chimeric_seqs.py -m ChimeraSlayer -i rep_set_aligned.fasta -a Silva_108_core_aligned_seqs.fasta -o chimeric_seqs.txt

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[Jen Underwood]

When I run test_identify script it shows command not found: 

MacQIIME igskdghwwsqiime:Split_Libraries $ test_identify_chimeric_seqs.py

bash: test_identify_chimeric_seqs.py: command not found

When I ran it all under my pynast aligned file I got the same error: 

MacQIIME igskdghwwsqiime:pynast_aligned $ identify_chimeric_seqs.py -m ChimeraSlayer -i rep_set_aligned.fasta -a Silva_108_core_aligned_seqs.fasta -o chimeric_seqs.txt

Traceback (most recent call last):

  File "/macqiime/QIIME/bin/identify_chimeric_seqs.py", line 324, in <module>

    main()

  File "/macqiime/QIIME/bin/identify_chimeric_seqs.py", line 299, in main

    keep_intermediates=keep_intermediates)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 154, in chimeraSlayer_identify_chimeras

    keep_intermediates=keep_intermediates):

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 139, in __call__

    keep_intermediates=keep_intermediates)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 616, in get_chimeras_from_Nast_aligned

    app_results = app()

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 274, in __call__

    out,err,exit_status,self._get_result_paths(data))

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 411, in _get_result_paths

    raise ApplicationError,"Calling ChimeraSlayer failed."

cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.

On Monday, June 17, 2013 4:52:27 PM UTC-6, TonyWalters wrote:

Hello Jen,

Can you run the unit test (test_identify_chimeric_seqs.py) and see if it passes the ChimeraSlayer tests?

Also, did you generate the aligned_seqs representative file using the Silva template or the default Greengenes template file?

Finally, can you change to the pynast_aligned/ folder and run the command there:

identify_chimeric_seqs.py -m ChimeraSlayer -i rep_set_aligned.fasta -a Silva_108_core_aligned_seqs.fasta -o chimeric_seqs.txt

My aligned seqs command: 

align_seqs.py -i split_libraries_491/rep_set -t Silva_108/core_aligned/Silva_108_core_aligned_seqs.fasta -o split_libraries_491/pynast_aligned 

[Tony Walters]

Jen,

I think this is the path to run the unit test on macqiime, although it might be slightly different on your system (and you may have to search the file test_identify_chimeric_seqs.py):

python /macqiime/QIIME/tests/test_identify_chimeric_seqs.py

Can you post a few lines from your rep_set_aligned.fasta as well?

-Tony

[Jen Underwood]

Hi Tony, 

Ok, I think that worked for the test_identify_chimeric...::, thanks!  

A couple of lines from rep_set_aligned.fasta:

>0 MP_3854 1..434

--------------------------------------------A-GCA--TA-TG-CT--TGTCTC-AAAG-ATTAAGCCATGCATGTCTAAA-GT-----------A-TAA--C-CA-A---------------------------------------------------------------------------CATTAT-AC-----------------------------------------------------------------------T-G----G--GA------AA-CTGCGTACAGCTCATTATATCAGTAATT-ATTTATTTGATG-G-T-A----------------CCTTAC----------TA-CA-TGGATAACCGTAGTAATTCTAGAG-CTAATACATGC--G----TAA-AA--TCC--C---G--------------A--C--T-----------------------------G-CA-A--------------------------GG---------------AA----GGGA-T-GTATTTATTAG-ATA---AAA-AAT-CAATG-------C-AG----------------------T-

Result of test_identify_chimeric_seqs.py

MacQIIME igskdghwwsqiime:pynast_aligned $ python /macqiime/QIIME/tests/test_identify_chimeric_seqs.py

E..EE...........EE.EEEE

======================================================================

ERROR: test_call (__main__.BlastFragmentsChimeraCheckerTests)

BlastFragmentsChimeraChecker: correct assignments on known results

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 241, in test_call

    actual = list(self.bcc(self.input_seqs_fp))

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 248, in getResult

    [self._get_taxonomy(fragment) for fragment in fragments]

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 311, in _get_taxonomy

    r = self._taxon_assigner(seqs=[('fragment',fragment)])['fragment']

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 206, in __call__

    current_seqs,blast_db,id_to_taxonomy_map))

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 249, in _seqs_to_taxonomy

    blast_hits = self._get_blast_hits(blast_db,seqs)

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 297, in _get_blast_hits

    add_seq_names=False)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 665, in blast_seqs

    HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 402, in __init__

    HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 167, in __init__

    raise RuntimeError, blastmat_error_message

RuntimeError: BLAST cannot run if the BLASTMAT environment variable is not set.

Usually, the BLASTMAT environment variable points to the NCBI data directory,

which contains matrices like PAM30 and PAM70, etc.

Alternatively, you may create a .ncbirc file to define these variables.

From help file:

2) Create a .ncbirc file. In order for Standalone BLAST to operate, you

have will need to have a .ncbirc file that contains the following lines:

[NCBI] 

Data="path/data/"

Where "path/data/" is the path to the location of the Standalone BLAST

"data" subdirectory. For Example: 

Data=/root/blast/data

The data subdirectory should automatically appear in the directory where

the downloaded file was extracted. Please note that in many cases it may

be necessary to delimit the entire path including the machine name and

or the net work you are located on. Your systems administrator can help

you if you do not know the entire path to the data subdirectory.

Make sure that your .ncbirc file is either in the directory that you

call the Standalone BLAST program from or in your root directory.

======================================================================

ERROR: test_function_w_preexisting_blastdb (__main__.BlastFragmentsChimeraCheckerTests)

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 95, in test_function_w_preexisting_blastdb

    actual = list(self.bcc(self.input_seqs_fp))

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 248, in getResult

    [self._get_taxonomy(fragment) for fragment in fragments]

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 311, in _get_taxonomy

    r = self._taxon_assigner(seqs=[('fragment',fragment)])['fragment']

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 206, in __call__

    current_seqs,blast_db,id_to_taxonomy_map))

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 249, in _seqs_to_taxonomy

    blast_hits = self._get_blast_hits(blast_db,seqs)

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 297, in _get_blast_hits

    add_seq_names=False)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 665, in blast_seqs

    HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 402, in __init__

    HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 167, in __init__

    raise RuntimeError, blastmat_error_message

RuntimeError: BLAST cannot run if the BLASTMAT environment variable is not set.

Usually, the BLASTMAT environment variable points to the NCBI data directory,

which contains matrices like PAM30 and PAM70, etc.

Alternatively, you may create a .ncbirc file to define these variables.

From help file:

2) Create a .ncbirc file. In order for Standalone BLAST to operate, you

have will need to have a .ncbirc file that contains the following lines:

[NCBI] 

Data="path/data/"

Where "path/data/" is the path to the location of the Standalone BLAST

"data" subdirectory. For Example: 

Data=/root/blast/data

The data subdirectory should automatically appear in the directory where

the downloaded file was extracted. Please note that in many cases it may

be necessary to delimit the entire path including the machine name and

or the net work you are located on. Your systems administrator can help

you if you do not know the entire path to the data subdirectory.

Make sure that your .ncbirc file is either in the directory that you

call the Standalone BLAST program from or in your root directory.

======================================================================

ERROR: test_get_taxonomy (__main__.BlastFragmentsChimeraCheckerTests)

BlastFragmentsChimeraChecker: getTaxonomy functions with full-length sequence

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 229, in test_get_taxonomy

    actual = self.bcc._get_taxonomy(str(s1))

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 311, in _get_taxonomy

    r = self._taxon_assigner(seqs=[('fragment',fragment)])['fragment']

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 206, in __call__

    current_seqs,blast_db,id_to_taxonomy_map))

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 249, in _seqs_to_taxonomy

    blast_hits = self._get_blast_hits(blast_db,seqs)

  File "/macqiime/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 297, in _get_blast_hits

    add_seq_names=False)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 665, in blast_seqs

    HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 402, in __init__

    HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/blast.py", line 167, in __init__

    raise RuntimeError, blastmat_error_message

RuntimeError: BLAST cannot run if the BLASTMAT environment variable is not set.

Usually, the BLASTMAT environment variable points to the NCBI data directory,

which contains matrices like PAM30 and PAM70, etc.

Alternatively, you may create a .ncbirc file to define these variables.

From help file:

2) Create a .ncbirc file. In order for Standalone BLAST to operate, you

have will need to have a .ncbirc file that contains the following lines:

[NCBI] 

Data="path/data/"

Where "path/data/" is the path to the location of the Standalone BLAST

"data" subdirectory. For Example: 

Data=/root/blast/data

The data subdirectory should automatically appear in the directory where

the downloaded file was extracted. Please note that in many cases it may

be necessary to delimit the entire path including the machine name and

or the net work you are located on. Your systems administrator can help

you if you do not know the entire path to the data subdirectory.

Make sure that your .ncbirc file is either in the directory that you

call the Standalone BLAST program from or in your root directory.

======================================================================

ERROR: test_identify_chimeras_usearch61_intersection (__main__.Usearch61Tests)

Properly returns intersection results

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 615, in test_identify_chimeras_usearch61_intersection

    log_lines = log_lines)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/macqiime/lib/python2.7/site-packages/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_identify_chimeras_usearch61_union (__main__.Usearch61Tests)

Properly returns union results

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 587, in test_identify_chimeras_usearch61_union

    log_lines = log_lines)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/macqiime/lib/python2.7/site-packages/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check (__main__.Usearch61Tests)

Overall usearch61 functionality test with default params

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 473, in test_usearch61_chimera_check

    self.ref_seqs_fp)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 750, in usearch61_chimera_check

    log_lines, verbose)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/macqiime/lib/python2.7/site-packages/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check_no_denovo (__main__.Usearch61Tests)

Overall usearch61 functionality test, no denovo detection

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 500, in test_usearch61_chimera_check_no_denovo

    suppress_usearch61_denovo=True)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 750, in usearch61_chimera_check

    log_lines, verbose)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/macqiime/lib/python2.7/site-packages/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check_no_ref (__main__.Usearch61Tests)

Overall usearch61 functionality test, no ref detection

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 526, in test_usearch61_chimera_check_no_ref

    suppress_usearch61_ref=True)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 750, in usearch61_chimera_check

    log_lines, verbose)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/macqiime/lib/python2.7/site-packages/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check_split_on_id (__main__.Usearch61Tests)

Overall usearch61 functionality test, splits on SampleID

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/macqiime/QIIME/tests/test_identify_chimeric_seqs.py", line 553, in test_usearch61_chimera_check_split_on_id

    split_by_sampleid = True)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 735, in usearch61_chimera_check

    log_lines, verbose)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/macqiime/lib/python2.7/site-packages/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

----------------------------------------------------------------------

Ran 23 tests in 71.915s

FAILED (errors=9)

[Tony Walters]

Okay, it looks like it's a problem with the BLAST install (you can ignore the usearch61 errors, they aren't related).

 Can you follow the instructions on this page: http://www.wernerlab.org/software/macqiime/macqiime-installation/installing-blast-in-os-x

Once this is installed, you should be able to run the unit test without the BLASTMAT errors.

[Jen Underwood]

Ok, I did the Blast Install but still same problem.  This time I only of usearch61 errors: 

MacQIIME igskdghwwsqiime:pynast_aligned $ identify_chimeric_seqs.py -m ChimeraSlayer -i rep_set_aligned.fasta -a Silva_108_core_aligned_seqs.fasta -o chimeric_seqs.txt

Traceback (most recent call last):

  File "/macqiime/QIIME/bin/identify_chimeric_seqs.py", line 324, in <module>

    main()

  File "/macqiime/QIIME/bin/identify_chimeric_seqs.py", line 299, in main

    keep_intermediates=keep_intermediates)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 154, in chimeraSlayer_identify_chimeras

    keep_intermediates=keep_intermediates):

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 139, in __call__

    keep_intermediates=keep_intermediates)

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 616, in get_chimeras_from_Nast_aligned

    app_results = app()

  File "/macqiime/lib/python2.7/site-packages/cogent/app/util.py", line 274, in __call__

    out,err,exit_status,self._get_result_paths(data))

  File "/macqiime/lib/python2.7/site-packages/qiime/identify_chimeric_seqs.py", line 411, in _get_result_paths

    raise ApplicationError,"Calling ChimeraSlayer failed."

cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.

MacQIIME igskdghwwsqiime:pynast_aligned $ python /macqiime/QIIME/tests/test_identify_chimeric_seqs.py

................EE.EEEE

Ran 23 tests in 70.746s

FAILED (errors=6)

[Tony Walters]

Jen,

Can you reopen the terminal and try the command again?

If it's still failing, can you send me a subset of your sequences (william(dot)a(dot)walters(at)gmail(dot)com:

head rep_set_aligned.fasta > sample_seqs_aligned.fasta

-Tony

[Tony Walters]

Hello,

I'm just posting the solution to this issue-the directory structure was too long to be handled properly.

Steps to troubleshoot ChimeraSlayer:

1. Make sure ChimeraSlayer is running (should be able to type ChimeraSlayer.pl in the terminal and get a response)

2. Make sure BLAST is installed (should be able to type blastall and get a response).

3. Check the unit test to see if it runs (test_identify_chimeric_seqs.py).

4. copy the reference alignment and input aligned sequences to the directory you are running identify_chimeric_seqs.py in.

5. Make sure the directory isn't very long or has spaces in it, if so, create another directory and copy the files over to run identify_chimeric_seqs.py in.

-Tony

[Ivy Yang]

Hi Tony, 

I ran into similar situation. I'm using QIIME1.7 in virtual box on my PC.

I followed your instructions above, as well as the chimera notes on http://qiime.org/install/install.html. 

Here is what I have done in QIIME.

First I ran 

qiime@qiime-VirtualBox:~/Desktop/Shared_Folder/fpnor4truncatewithnewversion$ ChimeraSlayer.pl

It returned:

##########################################################################################

#

#  Required:

#

#    --query_NAST      multi-fasta file containing query sequences in alignment format

#

#  Common opts:

#

#    --db_NAST        db in NAST format (default: /home/qiime/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta)

#    --db_FASTA       db in fasta format (megablast formatted) (default: /home/qiime/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer/../RESOURCES/rRNA16S.gold.fasta)

#

#

#    -n       number of top matching database sequences to compare to (default 15)

#    -R       min divergence ratio default: 1.007

#    -P       min percent identity among matching sequences (default: 90)

#

#  ## parameters to tune ChimeraParentSelector:

#   

#  Scoring parameters:

#   -M match score   (default: +5)

#   -N mismatch penalty  (default: -4)

#   -Q min query coverage by matching database sequence (default: 70)

#   -T maximum traverses of the multiple alignment  (default: 1)

#

#  ## parameters to tune ChimeraPhyloChecker:

#

#

#    --windowSize                default 50

#    --windowStep                default 5

#    --minBS      minimum bootstrap support for calling chimera (default: 90)

#    -S           percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10)

#    --num_parents_test       number of potential parents to test for chimeras (default: 3)

#    --MAX_CHIMERA_PARENT_PER_ID    Chimera/Parent alignments with perID above this are considered non-chimeras (default 100; turned off) 

#

#  ## misc opts

#

#   --printFinalAlignments          shows alignment between query sequence and pair of candidate chimera parents

#   --printCSalignments             print ChimeraSlayer alignments in ChimeraSlayer output

#   --exec_dir                      chdir to here before running

#

#########################################################################################

Then I ran:

qiime@qiime-VirtualBox:~/Desktop/Shared_Folder/fpnor4truncatewithnewversion$ print_qiime_config.py -t

It returned:

System information

==================

         Platform: linux2

   Python version: 2.7.3 (default, May 14 2013, 14:35:10)  [GCC 4.6.3]

Python executable: /home/qiime/qiime_software/python-2.7.3-release/bin/python

Dependency versions

===================

                     PyCogent version: 1.5.3

                        NumPy version: 1.5.1

                   matplotlib version: 1.1.0

                  biom-format version: 1.1.2

                QIIME library version: 1.7.0

                 QIIME script version: 1.7.0

        PyNAST version (if installed): 1.2

RDP Classifier version (if installed): rdp_classifier-2.2.jar

          Java version (if installed): 1.6.0_27

QIIME config values

===================

                     blastmat_dir: /home/qiime/qiime_software/blast-2.2.22-release/data

                         sc_queue: all.q

      topiaryexplorer_project_dir: None

     pynast_template_alignment_fp: /home/qiime/qiime_software/core_set_aligned.fasta.imputed

                  cluster_jobs_fp: /home/qiime/qiime_software/qiime-1.7.0-release/bin/start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /home/qiime/qiime_software/gg_otus-12_10-release/rep_set/97_otus.fasta

                     torque_queue: friendlyq

   template_alignment_lanemask_fp: /home/qiime/qiime_software/lanemask_in_1s_and_0s

                    jobs_to_start: 1

                cloud_environment: False

                qiime_scripts_dir: /home/qiime/qiime_software/qiime-1.7.0-release/bin

            denoiser_min_per_core: 50

                      working_dir: /tmp/

                    python_exe_fp: /home/qiime/qiime_software/python-2.7.3-release/bin/python

                         temp_dir: /tmp/

                      blastall_fp: /home/qiime/qiime_software/blast-2.2.22-release/bin/blastall

                 seconds_to_sleep: 60

assign_taxonomy_id_to_taxonomy_fp: /home/qiime/qiime_software/gg_otus-12_10-release/taxonomy/97_otu_taxonomy.txt

running checks:

test_FastTree_supported_version (__main__.Qiime_config)

FastTree is in path and version is supported ... ok

test_INFERNAL_supported_version (__main__.Qiime_config)

INFERNAL is in path and version is supported ... ok

test_ParsInsert_supported_version (__main__.Qiime_config)

ParsInsert is in path and version is supported ... ok

test_R_supported_version (__main__.Qiime_config)

R is in path and version is supported ... ok

test_ampliconnoise_install (__main__.Qiime_config)

AmpliconNoise install looks sane. ... ok

sourcetracker is installed ... ok

test_temp_dir (__main__.Qiime_config)

temp_dir, if set, is set to a valid path ... ok

test_template_alignment_lanemask_fp (__main__.Qiime_config)

template_alignment_lanemask, if set, is set to a valid path ... ok

test_uclust_supported_version (__main__.Qiime_config)

uclust is in path and version is supported ... ok

test_usearch_supported_version (__main__.Qiime_config)

usearch is in path and version is supported ... FAIL

test_working_dir (__main__.Qiime_config)

working_dir, if set, is set to a valid path ... ok

======================================================================

FAIL: test_usearch_supported_version (__main__.Qiime_config)

usearch is in path and version is supported

----------------------------------------------------------------------

Traceback (most recent call last):

  File "/home/qiime/qiime_software/qiime-1.7.0-release/bin/print_qiime_config.py", line 678, in test_usearch_supported_version

    "which components of QIIME you plan to use.")

AssertionError: usearch not found. This may or may not be a problem depending on which components of QIIME you plan to use.

----------------------------------------------------------------------

It did say blast-2.2.22 was installed and no obvious problems with chimeraSlayer was found, although at the end it said usearch not found and I don't know if that's related to my chmeraSlayer issue. 

Then I tried to run 

qiime@qiime-VirtualBox:~/Desktop/Shared_Folder/fpnor4truncatewithnewversion$ test_identify_chimeric_seqs.py

An message returned saying test_identify_chimeric_seqs.py: command not found

. 

So what should I do to fix this problem? 

Thank you. 

Regards, 

Ivy

[Tony Walters]

Hello,

usearch should not impact ChimeraSlayer. usearch61, if it's not installed, will cause some of the test_identify_chimeric_seqs.py unit tests to fail, but should not cause any of the ChimeraSlayer tests to fail.

Open a terminal, and type:

find . -name  test_identify_chimeric_seqs.py

and see if you get the location of the test_identify_chimeric_seqs.py file.

Then type:

python X

where X is the full filepath to the unit test file.

You might have to use:

find / -name  test_identify_chimeric_seqs.py

instead, but there will be a lot "permissions denied" lines to sift through.

-Tony

[Ivy Yang]

Hi Tony, 

I just did what you told me:

for find . -name  test_identify_chimeric_seqs.py,

it returned:

./qiime_software/qiime-1.7.0-release/tests/test_parallel/test_identify_chimeric_seqs.py

./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py

Then when I ran python, python qiime_software/qiime-1.7.0-release/tests/test_parallel/test_identify_chimeric_seqs.py

it returned

-----------------------------

 Ran 2 tests in 39.867s

OK

-----------------------------

the 'find / -name  test_identify_chimeric_seqs.py' revealed the same location for test_identify_chimeric_seqs.p as shown above. 

So how should I proceed now?

Thanks.

Ivy

[Tony Walters]

Can you run this file too:

python ./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py

[Ivy Yang]

Here is the returned message:

................EE.EEEE

======================================================================

ERROR: test_identify_chimeras_usearch61_intersection (__main__.Usearch61Tests)

Properly returns intersection results

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py", line 615, in test_identify_chimeras_usearch61_intersection

    log_lines = log_lines)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_identify_chimeras_usearch61_union (__main__.Usearch61Tests)

Properly returns union results

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py", line 587, in test_identify_chimeras_usearch61_union

    log_lines = log_lines)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check (__main__.Usearch61Tests)

Overall usearch61 functionality test with default params

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py", line 473, in test_usearch61_chimera_check

    self.ref_seqs_fp)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 750, in usearch61_chimera_check

    log_lines, verbose)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check_no_denovo (__main__.Usearch61Tests)

Overall usearch61 functionality test, no denovo detection

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py", line 500, in test_usearch61_chimera_check_no_denovo

    suppress_usearch61_denovo=True)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 750, in usearch61_chimera_check

    log_lines, verbose)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check_no_ref (__main__.Usearch61Tests)

Overall usearch61 functionality test, no ref detection

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py", line 526, in test_usearch61_chimera_check_no_ref

    suppress_usearch61_ref=True)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 750, in usearch61_chimera_check

    log_lines, verbose)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

======================================================================

ERROR: test_usearch61_chimera_check_split_on_id (__main__.Usearch61Tests)

Overall usearch61 functionality test, splits on SampleID

----------------------------------------------------------------------

Traceback (most recent call last):

  File "./qiime_software/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py", line 553, in test_usearch61_chimera_check_split_on_id

    split_by_sampleid = True)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 735, in usearch61_chimera_check

    log_lines, verbose)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py", line 865, in identify_chimeras_usearch61

    consout_filepath=output_consensus_fp)

  File "/home/qiime/qiime_software/qiime-1.7.0-release/lib/qiime/pycogent_backports/usearch.py", line 2243, in usearch61_smallmem_cluster

    app = Usearch61(params, WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 165, in __init__

    self._error_on_missing_application(params)

  File "/home/qiime/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/app/util.py", line 434, in _error_on_missing_application

    % command

ApplicationNotFoundError: Cannot find usearch61. Is it installed? Is it in your path?

----------------------------------------------------------------------

Ran 23 tests in 42.153s

FAILED (errors=6)

Ivy

[Tony Walters]

Okay, so the ChimeraSlayer software seems to be working and QIIME can see it. It probably is an issue with your input sequences then.

Have you tried the steps 4 and 5 from the previous post:

4. copy the reference alignment and input aligned sequences to the directory you are running identify_chimeric_seqs.py in.

5. Make sure the directory isn't very long or has spaces in it, if so, create another directory and copy the files over to run identify_chimeric_seqs.py in.

Can you also post the exact command you are using for identify_chimeric_seqs.py, and the output of the command?

[Ivy Yang]

This is what I typed in:

~/Desktop/Shared_Folder/chicheck$ identify_chimeric_seqs.py -m ChimeraSlayer -i seqs.fna -a chicore.fasta -o chioutput.txt

It has been almost 15 minutes. Is it normal to run such a long time?

Ivy

[Ivy Yang]

sorry, just realized I got the wrong input file. I'm going to run it again with rep_set_aligned.fasta.

Ivy

AssertionError: $PYRO_LOOKUP_FILE variable is not set. See <a href="http://qiime.org/install/install.ht

...

[Tony Walters]

Hello Ivy,

Yes, it can take some time to run. Just saw your update about using the aligned seqs file which might be part of the long time to run (it looks like the original file was the unclustered demultiplexed file, at least based on its name).

[Ivy Yang]

Hi Tony, 

I got it to work, I guessed there was nothing wrong with my QIIME. Just the run took much longer than I expected, roughly 1.5 hours. 

My co-worker did ask me to pass a question regarding to the chimera check. He was wondering why QIMME did not have a super script that covered the chimera check step in the  pick_de_novo_otus.py?

Thanks.

Ivy

...

[Tony Walters]

Hello Ivy,

You might put in a request for added options for chimera checking for the de novo OTU picking workflow scripts (https://github.com/qiime/qiime/issues?state=open). We often use closed-reference OTU picking (discarding reads that do not match the reference) as a way to avoid doing an explicit chimera checking-this does have a risk of matching chimeras that may be floating around in the Greengenes/Silva database and potentially discards novel, but real reads, but also runs faster than the de novo approach.

-Tony

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