<div dir="ltr">Dear Bio-Linux users,<br><br>I'm trying to run ChimeraSlayer using Qiime 1.3.0 on Bio-Linux.<br>The versions I have installed are:<br><br>dpkg -s qiime bio-linux-qiime chimeraslayer | grep ^Version<br>Version: 1.3.0-0ubuntu6<br>
Version: 1:1.3.0bl-6<br>Version: 20101212-1ubuntu5<br><br><div class="gmail_quote">I have ChimeraSlayer in the PATH, but for some reason I get an error when trying to call it using the qiime script as follows:<br>
<br>identify_chimeric_seqs.py -i rep_set_aligned.fna -a Silva_108_core_aligned_seqs.fna -o chimeric_seqs.txtTraceback (most recent call last):<br> File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 172, in <module><br>
main()<br> File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 169, in main<br> keep_intermediates=keep_intermediates)<br> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 148, in chimeraSlayer_identify_chimeras<br>
keep_intermediates=keep_intermediates):<br> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 133, in __call__<br> keep_intermediates=keep_intermediates)<br> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 592, in get_chimeras_from_Nast_aligned<br>
app_results = app()<br> File "/usr/lib/pymodules/python2.6/cogent/app/util.py", line 269, in __call__<br> result_paths=self._get_result_paths(data)) <br> File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py", line 405, in _get_result_paths<br>
raise ApplicationError,"Calling ChimeraSlayer failed."<br>cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.<br><br>I will be grateful for a hint if this kind of error had occurred to anyone else.<br>
I'm attaching the configuration report I get from Qiime:<br><br>root@chaysavanh-desktop:~# qiime > print_qiime_config.py -t<br>
<br>System information<br>==================<br> Platform: linux2<br> Python version: 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3]<br>Python executable: /usr/bin/python2.6<br><br>Dependency versions<br>
===================<br> PyCogent version: 1.5.1<br> NumPy version: 1.3.0<br> matplotlib version: 0.99.1.1<br> QIIME library version: 1.3.0<br>
QIIME script version: 1.3.0<br> PyNAST version (if installed): 1.1<br>RDP Classifier version (if installed): Not installed.<br><br>QIIME config values<br>===================<br> blastmat_dir: /usr/share/ncbi/data<br>
topiaryexplorer_project_dir: None<br> pynast_template_alignment_fp: None<br> cluster_jobs_fp: None<br>pynast_template_alignment_blastdb: None<br> torque_queue: friendlyq<br>
template_alignment_lanemask_fp: None<br> jobs_to_start: 1<br> cloud_environment: False<br> qiime_scripts_dir: /usr/lib/qiime/bin/<br> denoiser_min_per_core: 50<br>
working_dir: .<br> python_exe_fp: python<br> temp_dir: /tmp<br> blastall_fp: blastall<br> seconds_to_sleep: 60<br>
<br><br>running checks:<br><br>FastTree is in path and version is supported ... ok<br>INFERNAL is in path and version is supported ... ok<br>AmpliconNoise install looks sane. ... ok<br>blast is in path and version is supported ... FAIL<br>
blastall_fp is set to a valid path ... ok<br>blastmat_dir is set to a valid path. ... ok<br>cdbtools is in path and version is supported ... ok<br>cd-hit is in path and version is supported ... ok<br>no obvious problems with ChimeraSlayer install ... ok<br>
clearcut is in path and version is supported ... FAIL<br>cluster_jobs_fp is set to a valid path and is executable ... ok<br>denoiser aligner is ready to use ... ok<br>local qiime_config has no extra params ... ok<br>maptplotlib version is supported ... FAIL<br>
mothur is in path and version is supported ... ERROR<br>muscle is in path and version is supported ... FAIL<br>numpy version is supported ... ok<br>pynast version is supported ... ok<br>pynast_template_alignment_blastdb, if set, is set to a valid path ... ok<br>
pynast_template_alignment, if set, is set to a valid path ... ok<br>python_exe_fp is set to a working python env ... ok<br>python is in path and version is supported ... ok<br>qiime_scripts_dir, if set, is set to a valid path ... ok<br>
raxmlHPC is in path and version is supported ... FAIL<br>temp_dir, if set, is set to a valid path ... ok<br>template_alignment_lanemask, if set, is set to a valid path ... ok<br>uclust is in path and version is supported ... ok<br>
working_dir, if set, is set to a valid path ... ok<br><br>======================================================================<br>ERROR: mothur is in path and version is supported<br>----------------------------------------------------------------------<br>
Traceback (most recent call last):<br> File "/usr/lib/qiime/bin/print_qiime_config.py", line 472, in test_mothur_supported_version<br> version_string = stdout.strip().split(' ')[1].strip('v.')<br>
IndexError: list index out of range<br><br>======================================================================<br>FAIL: blast is in path and version is supported<br>----------------------------------------------------------------------<br>
Traceback (most recent call last):<br> File "/usr/lib/qiime/bin/print_qiime_config.py", line 374, in test_blast_supported_version<br> % ('.'.join(map(str,acceptable_version)), version_string))<br>AssertionError: Unsupported blast version. 2.2.22 is required, but running 2.2.21.<br>
<br>======================================================================<br>FAIL: clearcut is in path and version is supported<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br>
File "/usr/lib/qiime/bin/print_qiime_config.py", line 525, in test_clearcut_supported_version<br> "which components of QIIME you plan to use.")<br>AssertionError: clearcut not found. This may or may not be a problem depending on which components of QIIME you plan to use.<br>
<br>======================================================================<br>FAIL: maptplotlib version is supported<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br>
File "/usr/lib/qiime/bin/print_qiime_config.py", line 332, in test_matplotlib_suported_version<br> version_string))<br>AssertionError: Unsupported matplotlib version. Must be >= 0.98.5.3 and < 0.98.5.4 , but running 0.99.1.1.<br>
<br>======================================================================<br>FAIL: muscle is in path and version is supported<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br>
File "/usr/lib/qiime/bin/print_qiime_config.py", line 458, in test_muscle_supported_version<br> % ('.'.join(map(str,acceptable_version)), version_string))<br>AssertionError: Unsupported muscle version. 3.6 is required, but running 3.7.<br>
<br>======================================================================<br>FAIL: raxmlHPC is in path and version is supported<br>----------------------------------------------------------------------<br>Traceback (most recent call last):<br>
File "/usr/lib/qiime/bin/print_qiime_config.py", line 504, in test_raxmlHPC_supported_version<br> "which components of QIIME you plan to use.")<br>AssertionError: raxmlHPC not found. This may or may not be a problem depending on which components of QIIME you plan to use.<br>
<br>----------------------------------------------------------------------<br>Ran 28 tests in 0.048s<br><br>FAILED (failures=5, errors=1)<br><br>And my PATH value:<br><br>root@chaysavanh-desktop:~# grep -i chimera ~/.bashrc<br>
/root/.bashrc:export PATH=:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/NX/bin:/usr/lib/qiime/bin:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer<br><br>Thank you,<br>Anat<br><br><div>
<div class="h5"><div class="gmail_quote">2011/11/4 Tim Booth via RT <span dir="ltr"><<a href="mailto:website@nebc.nerc.ac.uk" target="_blank">website@nebc.nerc.ac.uk</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Anat,<br>
<br>
I think you just need to run:<br>
<br>
sudo apt-get install bio-linux-qiime<br>
<br>
This is a wrapper package that, amongst othter things, installs the<br>
uCLust clustering tool. We can't put that in the main package due to<br>
licensing restrictions.<br>
<br>
Cheers,<br>
<font color="#888888"><br>
TIM<br>
</font><div><div></div><div><br>
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