Denoiser.py error

[cricket]

Greetings. I am trying to denoise my 454 data using the denoiser.py
program.

I am using this command:

denoiser.py -i qiime/SFF/454Reads.13.sff.txt --num_cpus 16 -f qiime/
split_library_output/seqs.fna --primer GAGTTTGATCNTGGCTCAG -o qiime/
Outdir --force -v

I am receiving this error:

AttributeError: 'NoneType' object has no attribute 'group'

A bit of info...

1. The .sff.txt file was produced using mothur from the orginal .sff
file
2. The seqs.fna file was produced during the split_library filtering
process

Is this error a result of not incorporating a mapping file? I saw a
few posts where people were mapping to a text file using -m. Looking
at the documentation for denoise_wrapper.py this seems to work, but
for denoiser.py, -m pertains to "Maximal number of iterations in phase
II". I did add a -m just to verify this and the I get an error that I
was using an invalid integer value.

Any suggestions are warmly appreciated.

[Jose Carlos Clemente]

Hi,

just to confirm, you tried using denoise_wrapper as:

denoise_wrapper.py -i qiime/SFF/454Reads.13.sff.txt -f
qiime/split_library_output/seqs.fna -m mapping_file.txt -o
qiime/Outdir -v

and that return an error. Could you please post the exact error, the
output of split_library_log.txt and the output of
print_qiime_config.py -t? I assume you didn't use -m with some integer
value in denoise_wrapper.py: in denoise.py this parameter is for the
number of iterations, but in denoise_wrapper.py it is used for the
mapping file.

Additionally, could you try to obtain the flowgram file (.sff.txt)
using process_sff.py instead of mothur and see whether that fixes the
problem?

Jose

[cricket]

Thank you for your quick response Jose.

No no - I am using denoise.py.

denoiser.py -i qiime/SFF/454Reads.13.sff.txt --num_cpus 16 -f qiime/
split_library_output/seqs.fna --primer GAGTTTGATCNTGGCTCAG -o qiime/
Outdir --force -v

Here is the information you requested (plus some you did not).

The -v output is:

Denoising data....
Traceback (most recent call last):
File "/usr/local/bin/denoiser.py", line 259, in <module>
main()
File "/usr/local/bin/denoiser.py", line 256, in main
opts.checkpoint_fp)
File "/usr/local/lib/python2.6/site-packages/qiime/denoiser/
flowgram_clustering.py", line 612, in denoise_seqs
verbose=verbose, squeeze=squeeze, primer=primer)
File "/usr/local/lib/python2.6/site-packages/qiime/denoiser/
preprocess.py", line 202, in preprocess
barcode_mapping = extract_barcodes_from_mapping(labels)
File "/usr/local/lib/python2.6/site-packages/qiime/denoiser/
flowgram_filter.py", line 253, in extract_barcodes_from_mapping
flowgram_id = tmatch.group(2)

AttributeError: 'NoneType' object has no attribute 'group'

print_qiime_config.py -t: I see that there are some errors - most
noticeably the python error.


System information
==================
Platform: linux2
Python version: 2.6 (r26:66714, Feb 21 2009, 02:16:04) [GCC 4.3.2
[gcc-4_3-branch revision 141291]]
Python executable: /usr/bin/python

Dependency versions
===================
PyCogent version: 1.5.1
NumPy version: 1.5.1
matplotlib version: 1.0.1
QIIME library version: 1.3.0-dev
QIIME script version: 1.3.0-dev
PyNAST version (if installed): 1.1
RDP Classifier version (if installed): rdp_classifier-2.2.jar

QIIME config values
===================
blastmat_dir: None
topiaryexplorer_project_dir: None
pynast_template_alignment_fp: None
cluster_jobs_fp: None
pynast_template_alignment_blastdb: None
assign_taxonomy_reference_seqs_fp: None
torque_queue: friendlyq
template_alignment_lanemask_fp: None
jobs_to_start: 1
cloud_environment: False
qiime_scripts_dir: None
denoiser_min_per_core: 50
working_dir: None
python_exe_fp: python
temp_dir: None
blastall_fp: blastall
seconds_to_sleep: 60
assign_taxonomy_id_to_taxonomy_fp: None


running checks:

FastTree is in path and version is supported ... ok
INFERNAL is in path and version is supported ... ok
AmpliconNoise install looks sane. ... ok
blast is in path and version is supported ... ok
blastall_fp is set to a valid path ... ok
blastmat_dir is set to a valid path. ... ok
cdbtools is in path and version is supported ... ok
cd-hit is in path and version is supported ... ok
no obvious problems with ChimeraSlayer install ... ok
clearcut is in path and version is supported ... ok
cluster_jobs_fp is set to a valid path and is executable ... ok
denoiser aligner is ready to use ... ok
local qiime_config has no extra params ... ok
maptplotlib version is supported ... FAIL
mothur is in path and version is supported ... ok
muscle is in path and version is supported ... ok
numpy version is supported ... FAIL
pynast version is supported ... ok
pynast_template_alignment_blastdb, if set, is set to a valid path ...
ok
pynast_template_alignment, if set, is set to a valid path ... ok
python_exe_fp is set to a working python env ... ok
python is in path and version is supported ... ERROR
qiime_scripts_dir, if set, is set to a valid path ... ok
raxmlHPC is in path and version is supported ... FAIL
temp_dir, if set, is set to a valid path ... ok
template_alignment_lanemask, if set, is set to a valid path ... ok
uclust is in path and version is supported ... ok
working_dir, if set, is set to a valid path ... ok

======================================================================
ERROR: python is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 287, in
test_python_supported_version
version = tuple(version[0],version[1],0)
TypeError: tuple() takes at most 1 argument (3 given)

======================================================================
FAIL: maptplotlib version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 332, in
test_matplotlib_suported_version
version_string))
AssertionError: Unsupported matplotlib version. Must be >= 0.98.5.3
and < 0.98.5.4 , but running 1.0.1.

======================================================================
FAIL: numpy version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 314, in
test_numpy_suported_version
version_string))
AssertionError: Unsupported numpy version. Must be >= 1.3.0 and <
1.5.1 , but running 1.5.1.

======================================================================
FAIL: raxmlHPC is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/print_qiime_config.py", line 518, in
test_raxmlHPC_supported_version
% ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported raxmlHPC version. 7.0.3 is required, but
running 7.2.8.

----------------------------------------------------------------------
Ran 28 tests in 0.254s

FAILED (failures=3, errors=1)


split_library_log.txt*


Num Samples 36
Sample ct min/max/mean: 752 / 11700 / 3772.22
Sample Sequence Count Barcode
48.6132011 11700 AAAAAAGC
.
.
.
27.1192011 752 AAAAATAC

Total number seqs written 135800
"split_library_log.txt" [noeol] 62L, 1925C

*removed all but two files names and altered the ones seen to remove
pt. initials.



Denoiser version: 1.3.0-dev
SFF file: qiime/SFF/454Reads.13.11.10.2010.sff.txt
Fasta file: qiime/split_library_output/seqs.fna
Preprocess dir: None
Primer sequence: GAGTTTGATCNTGGCTCAG
Running on cluster: False
Num CPUs: 16
Squeeze Seqs: False
tmpdir: qiime/Outdir/
percent_id threshold: 0.97
Minimal sequence coverage for first phase: 1
Low cut-off: 3.75
High cut-off: 4.50
Error profile: /usr/local/lib/python2.6/site-packages/qiime/
support_files/denoiser/Data/FLX_error_profile.dat
Maximal number of iteration: None



On Oct 26, 3:04 pm, Jose Carlos Clemente <jose.cleme...@gmail.com>
wrote:

[Jose Carlos Clemente]

Ok so first of all try to run denoise_wrapper.py with the command I
sent in the previous email, and see whether that works. If you check
the denoising tutorial
(http://qiime.org/tutorials/denoising_454_data.html), you will see we
now use denoise_wrapper.py instead of denoiser.py. If that doesn't
work, you can try to post a few sequences from seqs.fna (for instance,
do head -n 20 seqs.fna) so we can see whether there is an issue there.

[cricket]

Jose,

Thank you again for the response.

I used the following command:

denoise_wrapper.py -i qiime/SFF/454Reads.13.11.10.2010.sff.txt -n 16 -
f qiime/split_library_output/seqs.fna -m map.txt -p
GAGTTTGATCNTGGCTCAG -o qiime/Outdir --force_overwrite -v

...and now I get a new error (cluster_jobs_fp not set in config
file!). Before you respond, let me search around on this forum and the
web to see what I can find. Thanks again.



On Oct 26, 3:40 pm, Jose Carlos Clemente <jose.cleme...@gmail.com>
wrote:

[Jose Carlos Clemente]

No worries; however, notice you don't need to specify -p since the
primer is directly extracted from the mapping file. Let me know if you
have further problems.

[cricket]

Jose,

(removing -p ...) Ok...the previous error (cluster_jobs_fp not set in
config file!) pertains to running multiple CPUs and I think it can be
fixed by adding the following to the qiime_config.txt file:
cluster_jobs_fp /usr/local/bin/start_parallel_jobs.py

This will hopefully be confirmed when someone of more privilege
changes the file (I am dangerous in UNIX).

For the present, I removed the -n 16 from the command and when I ran
the script - the old error returned.

Hoping that it may have just been an issue with the sff.txt file, I
used process_sff.py to create a new txt file on the smallest .sff
file. I did a side-side comparison and there were some subtle
differences (indents) so I used the latter file in the command.

denoise_wrapper.py -i qiime/SFF/454Reads.27-1.19.2011.txt -f qiime/
split_library_output/seqs.fna -m map.txt -o qiime/Outdir --
force_overwrite -v

Same error (AttributeError: 'NoneType' object has no attribute
'group'):

File "/usr/local/bin/denoise_wrapper.py", line 159, in <module>
main()
File "/usr/local/bin/denoise_wrapper.py", line 145, in main
titanium=opts.titanium)
File "/usr/local/lib/python2.6/site-packages/qiime/
denoise_wrapper.py", line 37, in fast_denoiser
verbose=verbose, titanium=titanium)

File "/usr/local/lib/python2.6/site-packages/qiime/denoiser/
flowgram_clustering.py", line 612, in denoise_seqs
verbose=verbose, squeeze=squeeze, primer=primer)
File "/usr/local/lib/python2.6/site-packages/qiime/denoiser/
preprocess.py", line 202, in preprocess
barcode_mapping = extract_barcodes_from_mapping(labels)
File "/usr/local/lib/python2.6/site-packages/qiime/denoiser/
flowgram_filter.py", line 253, in extract_barcodes_from_mapping
flowgram_id = tmatch.group(2)
AttributeError: 'NoneType' object has no attribute 'group'

Here is a peek into the seqs.fna file.

>13.11102010_1 13.11102010::G9NMJ1U04JYR3Y orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAGCATGGTCTTAGCTTGCTAAGGCTGATGGCGACCGGCGCACGGGTGAGTAACATGTATCCAACCTGCCGTCTACTCTTGGCCAGCCTTCTGAAAGGAAGATTAATCCAGGATGGCATCATGAGTTCACATGTCCGCATGATTAAAGGTATTTTCCGGTAGACGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGCCCACCTAGTCAACGATGGATAGGGGTTCTGAGAGGAAC
>13.11102010_2 13.11102010::G9NMJ1U04JOJ62 orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGGCAGCATAATGGATAGCAATATCTATGGTGGCGACCGGCGCGACGGGTGCGTAACGCGTATGCAACCTACCTTTAACAGGGGGATAACACTGAGAAATTGGTACTAATACCCCATAATATCATAGAAGGCATCTTTATGGTTGAAATTCCGATGGTTAGAGATGGGCATGCGTTGTATTAGCTAGTTGGTGGGGTAACGGCTC
>13.11102010_3 13.11102010::G9NMJ1U04JJNC1 orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
ATCTCAGAGCCCTTGGCTGCTGCAGACATCCCAGCCTACTACATCAGTACTTTCAAGTTTGATCATGCACTTGTGAGTGTCCAGCGCCAGACCCCTCCAGGGCAGGGCCGGGGTGGGGAAGCAGGTTCCTGGGCTCACGGGCAGGCATCTGCCTCCTCTACCCCTGCACAGGTCCCCGAAGAGAACATCAATGGTGTCATCAGTGCCCTGAAGGTCAGCCAAGCAGAGAAGCACTAGAAGGGTCTCTTCTGCTCCTCCAGCCGCCGCGGTAAC
>13.11102010_4 13.11102010::G9NMJ1U04JFVC1 orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGCAGCATAATGGATAGCAATATCTATGGTGGCGACCGGCGCACGGGTGCGTAACGCGTATGCAACCTACCTTTAACAGGGGGATAACACTGAGAAATTGGTACTAATACCCCATAATATCATAGAAGGCATCTTTTATGGTTGAAAATTCCGATGGTTAGAGATGGGCATGCGTTGTATTAGCTAGTTGGTGGGGTAACGGCTCACCAAGGCGACGATACA
>13.11102010_5 13.11102010::G9NMJ1U04JRE6Y orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGATATTTAGAATGAGAGCTTCGGCAGGATTTTTATCTATCTTAGTGGCGGACGGGTGAGTAACGTGTGGGCAACCTGCCCTGTACTGTGGAATAATCATTGGAAACGATGACTAATACCGCATGTGGTCCTCGGAAGGCATCTTCTGAGGAAGAAAGGATTTATTCGGTACAGGATGGGCCCGCATCTGATTAGCTAGTTGGTGAGATAACAGCCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTAC
>13.11102010_6 13.11102010::G9NMJ1U04JRT3T orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCACAGGTAGCAATACCGGGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTGCCTATCAGAGGGGGATAACCCGGCGAAAGTCGGACTAATACCGCATGAAGCAGGGATCCCGCATGGGAATATTTGCTAAAGATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACC
>13.11102010_7 13.11102010::G9NMJ1U04JO6QJ orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAAAGACGGAAAGAGCTTGCTCTTTTCAGAATTGAGTGGCAAACGGGTGAGTAACACGTAAACAACCTGCCTTCAGGATGGGGACAACAGACGGAAACGACTGCTAATACCGAATAAGTTCCAAGAGCCGCATGGCCCATGGAAGAAAAGGTGGCCTCTACCTGTAAGCTATCGCCTGAAGAGGGGTTTGCGTCTGATTAGCTGGTTGGAGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCCGGTCTGAGAGGATGAACGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGACGGCCT
>13.11102010_8 13.11102010::G9NMJ1U04JWK0I orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCACAGGTAGCAATACCGGGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTGCCTATCAGAGGGGGATAACCCGCGAAAGTCGGACTAATACCGCATGAAGCAGGGATCCCGCATGGGAATATTTGCTAAAGATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGG
>13.11102010_9 13.11102010::G9NMJ1U04JUS4G orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGAAGCACTTTGGTTGATTCTTCGGATGAAGACCTTTGTGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTCATACAGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGACCACGGTACCGCATGGTACAGTGGTAAAAACTACCGGTGGTATGAGATGG
>13.11102010_10 13.11102010::G9NMJ1U04JXV5M orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAAAGACGGAAAGAGCTTGCTCTTTTCAGAATTGAGTGGCAAACGGGTGAGTAACACGTAAACAACCTGCCTTCAGGATGGGGACAACAGACGGAAACGACTGCTAATACCGAATAAGTTCCAAGAGCCGCATGGCCCATGGAAGAAAAGGTGGCCTCTACCTGTAAGCTATCGCCTGAAGAGGGGTTTGCGTCTGATTAGCTGGTTGGAGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCCGGTCTGAGAGGATGAACGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGACGGCCTT




On Oct 26, 4:04 pm, Jose Carlos Clemente <jose.cleme...@gmail.com>
wrote:

> ...
>
> read more »

[cricket]

P.S.

As stated previously, the initials have been removed from the post but
do exist in seqs.fna and 454*.txt (i.e. XX13.11102010...,
454Reads.XY27....).

> GATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAGCATGGTCTTAGCTTGCTAAGGCTGATGGCG ACCGGCGCACGGGTGAGTAACATGTATCCAACCTGCCGTCTACTCTTGGCCAGCCTTCTGAAAGGAAGATTAATC CAGGATGGCATCATGAGTTCACATGTCCGCATGATTAAAGGTATTTTCCGGTAGACGATGGGGATGCGTTCCATT AGATAGTAGGCGGGGTAACGCCCACCTAGTCAACGATGGATAGGGGTTCTGAGAGGAAC>13.11102010_2 13.11102010::G9NMJ1U04JOJ62 orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> GATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGGCAGCATAATGGATAGCAATATCTATGGTGGCGA CCGGCGCGACGGGTGCGTAACGCGTATGCAACCTACCTTTAACAGGGGGATAACACTGAGAAATTGGTACTAATA CCCCATAATATCATAGAAGGCATCTTTATGGTTGAAATTCCGATGGTTAGAGATGGGCATGCGTTGTATTAGCTA GTTGGTGGGGTAACGGCTC>13.11102010_3 13.11102010::G9NMJ1U04JJNC1 orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> ATCTCAGAGCCCTTGGCTGCTGCAGACATCCCAGCCTACTACATCAGTACTTTCAAGTTTGATCATGCACTTGTG AGTGTCCAGCGCCAGACCCCTCCAGGGCAGGGCCGGGGTGGGGAAGCAGGTTCCTGGGCTCACGGGCAGGCATCT GCCTCCTCTACCCCTGCACAGGTCCCCGAAGAGAACATCAATGGTGTCATCAGTGCCCTGAAGGTCAGCCAAGCA GAGAAGCACTAGAAGGGTCTCTTCTGCTCCTCCAGCCGCCGCGGTAAC>13.11102010_4 13.11102010::G9NMJ1U04JFVC1 orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> GATGAACGCTAGCGGCAGGCTTAACACATGCAAGTCGAGGGCAGCATAATGGATAGCAATATCTATGGTGGCGAC CGGCGCACGGGTGCGTAACGCGTATGCAACCTACCTTTAACAGGGGGATAACACTGAGAAATTGGTACTAATACC CCATAATATCATAGAAGGCATCTTTTATGGTTGAAAATTCCGATGGTTAGAGATGGGCATGCGTTGTATTAGCTA GTTGGTGGGGTAACGGCTCACCAAGGCGACGATACA>13.11102010_5 13.11102010::G9NMJ1U04JRE6Y orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> GATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGATATTTAGAATGAGAGCTTCGGCAGGATTTT TATCTATCTTAGTGGCGGACGGGTGAGTAACGTGTGGGCAACCTGCCCTGTACTGTGGAATAATCATTGGAAACG ATGACTAATACCGCATGTGGTCCTCGGAAGGCATCTTCTGAGGAAGAAAGGATTTATTCGGTACAGGATGGGCCC GCATCTGATTAGCTAGTTGGTGAGATAACAGCCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGATCGG CCACATTGGGACTGAGACACGGCCCAAACTCCTAC>13.11102010_6 13.11102010::G9NMJ1U04JRT3T orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> GATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCACAGGTAGCAATACCGGGTGGCGACCGGC GCACGGGTGAGTAACGCGTATGCAACTTGCCTATCAGAGGGGGATAACCCGGCGAAAGTCGGACTAATACCGCAT GAAGCAGGGATCCCGCATGGGAATATTTGCTAAAGATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGT TGGCGGGGTAACGGCCCACC>13.11102010_7 13.11102010::G9NMJ1U04JO6QJ orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAAAGACGGAAAGAGCTTGCTCTTTTCAGAATTG AGTGGCAAACGGGTGAGTAACACGTAAACAACCTGCCTTCAGGATGGGGACAACAGACGGAAACGACTGCTAATA CCGAATAAGTTCCAAGAGCCGCATGGCCCATGGAAGAAAAGGTGGCCTCTACCTGTAAGCTATCGCCTGAAGAGG GGTTTGCGTCTGATTAGCTGGTTGGAGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCCGGTCTGAGAGGATG AACGGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTCCGCAATGGGCG AAAGCCTGACGGAGCAACGCCGCGTGAGTGATGACGGCCT>13.11102010_8 13.11102010::G9NMJ1U04JWK0I orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> GATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCACAGGTAGCAATACCGGGTGGCGACCGGC GCACGGGTGAGTAACGCGTATGCAACTTGCCTATCAGAGGGGGATAACCCGCGAAAGTCGGACTAATACCGCATG AAGCAGGGATCCCGCATGGGAATATTTGCTAAAGATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTT GG>13.11102010_9 13.11102010::G9NMJ1U04JUS4G orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0
>
> GATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAGCGAAGCACTTTGGTTGATTCTTCGGATGAAGACCTT TGTGACTGAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTCATACAGGGGGATAACAGTTAGAAATGAC TGCTAATACCGCATAAGACCACGGTACCGCATGGTACAGTGGTAAAAACTACCGGTGGTATGAGATGG>13.11102010_10 13.11102010::G9NMJ1U04JXV5M orig_bc=AAAAAAAC new_bc=AAAAAAAC bc_diffs=0

> > >> >                    jobs_to_start:      1...
>
> read more »

[Jens Reeder]

Hi,

There are two things in your fasta file that cause the error:

1.  The flowgram identifier G9NMJ1U04JYR3Y is preceded by your sample name, which is not qiime compatible
>13.11102010_1 13.11102010::G9NMJ1U04JYR3Y
See here for someone with the same problem.
You might want to make sure that your input fasta to split_libraries follows the qiime rules strictly.
This site specifies exactly how the split_library file has to look.

2. Contrary to the rest of qiime (which allows dots), this script expects the sample names to be a combination of a-z, A-Z, or _ (underscore)
   You do have a . (dot) in your samples names, which break the code. This will be fixed in the next release of qiime.

Jens

[cricket]

It is back to the drawing board, but with an increased chance of
success. Thank you very much Jens (and Jose).

On Oct 26, 5:59 pm, Jens Reeder <jens.ree...@gmail.com> wrote:
> Hi,
>
> There are two things in your fasta file that cause the error:
>
> 1.  The flowgram identifier G9NMJ1U04JYR3Y is preceded by your sample name,
> which is not qiime compatible>13.11102010_1 13.11102010::G9NMJ1U04JYR3Y
>

> See here<http://groups.google.com/group/qiime-forum/browse_thread/thread/2f049...>for

> someone with the same problem.
> You might want to make sure that your input fasta to split_libraries follows
> the qiime rules strictly.

> This site<http://qiime.org/documentation/file_formats.html#post-split-libraries...>specifies

> ...
>
> read more »

[Greg Caporaso]

Hi,
Could you run:

python --version

and post the output?

Thanks!
Greg

[Greg Caporaso]

Oops, nevermind - I see that you're running 2.6.

Greg