Error running uclust

56 views
Skip to first unread message

Olena P

unread,
Apr 8, 2016, 9:09:18 AM4/8/16
to Qiime 1 Forum

Dear all,


I have used QIIME 1.9.1 on another computer and never got this problem before:



Traceback (most recent call last):

  File "/macqiime/anaconda/bin/pick_otus.py", line 1004, in <module>

    main()

  File "/macqiime/anaconda/bin/pick_otus.py", line 924, in main

    failure_path=failure_path)

  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/pick_otus.py", line 1912, in __call__

    HALT_EXEC=HALT_EXEC)

  File "/macqiime/anaconda/lib/python2.7/site-packages/bfillings/uclust.py", line 585, in get_clusters_from_fasta_filepath

    raise ApplicationError('Error running uclust. Possible causes are '

burrito.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided


My Qiime conf: 


System information

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

         Platform: darwin

   Python version: 2.7.10 |Anaconda 2.2.0 (x86_64)| (default, May 28 2015, 17:04:42)  [GCC 4.2.1 (Apple Inc. build 5577)]

Python executable: /macqiime/anaconda/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/0.1.2


Dependency versions

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

          QIIME library version: 1.9.1

           QIIME script version: 1.9.1

qiime-default-reference version: 0.1.2

                  NumPy version: 1.9.2

                  SciPy version: 0.15.1

                 pandas version: 0.16.1

             matplotlib version: 1.4.3

            biom-format version: 2.1.4

                   h5py version: 2.4.0 (HDF5 version: 1.8.14)

                   qcli version: 0.1.1

                   pyqi version: 0.3.2

             scikit-bio version: 0.2.3

                 PyNAST version: 1.2.2

                Emperor version: 0.9.51

                burrito version: 0.9.1

       burrito-fillings version: 0.1.1

              sortmerna version: SortMeRNA version 2.0, 29/11/2014

              sumaclust version: SUMACLUST Version 1.0.00

                  swarm version: Swarm 1.2.19 [Jun  2 2015 14:40:16]

                          gdata: Installed.


QIIME config values




Could, please, help me to get it work?

Kind regards,
/Olena

Colin Brislawn

unread,
Apr 8, 2016, 12:42:12 PM4/8/16
to Qiime 1 Forum
Hello Olena,

Take a look at that initial error:

burrito.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided


Looks like there is some issue with uclust. Use the -t flag with print_qiime_config.py -t to test your qiime configuration.

Colin

Olena P

unread,
Apr 8, 2016, 1:10:19 PM4/8/16
to Qiime 1 Forum

Hi Colin!


How do I fix these problems? 

I have 4 fails and 1 error (with blast). See below


What do I do now?


Appreciate your help!


/Olena 






MacQIIME Olenas-MBP:~ $ print_qiime_config.py -tf

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

          Java version (if installed): 1.6.0_65


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: None

      pick_otus_reference_seqs_fp: /macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

                         sc_queue: all.q

      topiaryexplorer_project_dir: None

     pynast_template_alignment_fp: /macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta

                  cluster_jobs_fp: start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

                     torque_queue: friendlyq

                    jobs_to_start: 1

                       slurm_time: None

            denoiser_min_per_core: 50

assign_taxonomy_id_to_taxonomy_fp: /macqiime/anaconda/lib/python2.7/site-packages/qiime_default_reference/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 full install test results

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

..FFFE....................F

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

ERROR: test_blastall_fp (__main__.QIIMEDependencyFull)

blastall_fp is set to a valid path

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

Traceback (most recent call last):

  File "/macqiime/anaconda/bin/print_qiime_config.py", line 446, in test_blastall_fp

    blastall)

ApplicationNotFoundError: blastall_fp set to blastall, but is not in your PATH. Either use an absolute path to or put it in your PATH.


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

FAIL: test_R_supported_version (__main__.QIIMEDependencyFull)

R is in path and version is supported

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

Traceback (most recent call last):

  File "/macqiime/anaconda/bin/print_qiime_config.py", line 671, in test_R_supported_version

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

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


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

FAIL: test_ampliconnoise_install (__main__.QIIMEDependencyFull)

AmpliconNoise install looks sane.

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

Traceback (most recent call last):

  File "/macqiime/anaconda/bin/print_qiime_config.py", line 382, 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_blast_supported_version (__main__.QIIMEDependencyFull)

blast is in path and version is supported

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

Traceback (most recent call last):

  File "/macqiime/anaconda/bin/print_qiime_config.py", line 456, in test_blast_supported_version

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

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


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

FAIL: test_usearch_supported_version (__main__.QIIMEDependencyFull)

usearch is in path and version is supported

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

Traceback (most recent call last):

  File "/macqiime/anaconda/bin/print_qiime_config.py", line 650, 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 27 tests in 0.085s


FAILED (failures=4, errors=1)




Colin Brislawn

unread,
Apr 8, 2016, 1:20:40 PM4/8/16
to Qiime 1 Forum
Hello Olena,

While you are missing some software, it looks like you do have uclust installed, which is what I was checking for. (You probably don't have to worry about those other errors.) 

Maybe the issue is with your input seqs.fna file. Can you run validate_demultiplexed_fasta.py for me and to make sure you seqs.fna file is in good shape?

Thanks for working through this problem with me,
Colin 

Olena P

unread,
Apr 8, 2016, 1:33:44 PM4/8/16
to Qiime 1 Forum
Hi Colin,

here what I got:

# fasta file desktop/split_lib_qiime_1/seqs.fna validation report
Percent duplicate labels: 0.000
Percent QIIME-incompatible fasta labels: 0.000
Percent of labels that fail to map to SampleIDs: 0.000
Percent of sequences with invalid characters: 0.000
Percent of sequences with barcodes detected: 0.000
Percent of sequences with barcodes detected at the beginning of the sequence: 0.000
Percent of sequences with primers detected: 0.000
 

I used this file:

Input file paths
Sequence read filepath: qiime_joined_1/fastqjoin.join.fastq (md5: 2f1fb5ba3414831020fd32898f798b19)
Quality filter results
Total number of input sequences: 245972
Barcode not in mapping file: 0
Read too short after quality truncation: 197
Count of N characters exceeds limit: 0
Illumina quality digit = 0: 0
Barcode errors exceed max: 0

Result summary (after quality filtering)
Median sequence length: 443.00
1 245775

Total number seqs written 245775
---

/olena

Olena P

unread,
Apr 8, 2016, 3:02:34 PM4/8/16
to Qiime 1 Forum
Thanks for help!
I  fixed it by myself!

Regards,
/O

Colin Brislawn

unread,
Apr 8, 2016, 3:18:19 PM4/8/16
to Qiime 1 Forum
That's great to hear!

Would you be willing to post your solution, that way other folks with a similar problem can use the solution you discovered?

Thanks!
Colin 

Olena P

unread,
Apr 11, 2016, 2:55:18 PM4/11/16
to Qiime 1 Forum
Sure!

Embarrassing to say. I forgot  indicate -t, --taxonomy_fp
The taxonomy map [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt]

because of that I got this error "burrito.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided"
Hope, it will help someone!

Regards,
/olena

Reply all
Reply to author
Forward
0 new messages