how to change tmp directory if I want to use pick_otus.py -m mothur

[Isiah]

Hi,

I want to use pick_otus.py -i out/seqs.fna -o mothur_picked_otus/ -m mothur but it kept saying no space on device.

I know it might be the problem of the /tmp directory which I don't have enough space. I faced the same problem when I  ran pick_otus_through_otu_table.py -i out/seqs.fna -o otus .

After I modified the temp_dir to my local directory (I don't have root access) as /home/lc178/tmp/ which I got enough space, pick_otus_through_otu_table.py -i out/seqs.fna -o otus  works.

However, when I attempted to use pick_otus.py -i out/seqs.fna -o mothur, the following is the error message:

[lc178@dav-dd-l0151 merge]$ pick_otus.py -i out/seqs.fna -o mothur_picked_otus/ -m mothur

Traceback (most recent call last):

  File "/home/lc178/install/QIIME1.6/bin/pick_otus.py", line 591, in <module>

    main()

  File "/home/lc178/install/QIIME1.6/bin/pick_otus.py", line 565, in main

    result_path=result_path, log_path=log_path)

  File "/home/lc178/install/QIIME1.6/lib/python2.7/site-packages/qiime/pick_otus.py", line 1393, in __call__

    results = app(seq_path)

  File "/home/lc178/install/QIIME1.6/src/PyCogent/cogent/app/mothur.py", line 119, in __call__

    getattr(self, self.InputHandler)(data)

  File "/home/lc178/install/QIIME1.6/src/PyCogent/cogent/app/mothur.py", line 314, in _input_as_path

    copyfile(data, self._input_filename)

  File "/home/lc178/install/QIIME1.6/lib/python2.7/shutil.py", line 84, in copyfile

    copyfileobj(fsrc, fdst)

  File "/home/lc178/install/QIIME1.6/lib/python2.7/shutil.py", line 52, in copyfileobj

    fdst.write(buf)

IOError: [Errno 28] No space left on device

I checked the /tmp and /home/lc178/tmp, and the temporary file is still created in /tmp instead of /home/lc178/tmp.

I think this might be the problem. But I don't know how to change it.

I've tried modify the parameter in these files,

 /home/lc178/install/QIIME1.6/lib/python2.7/site-packages/cogent/app/mothur.py

 /home/lc178/install/QIIME1.6/src/PyCogent-1.5.3/cogent/app/mothur.py 

 /home/lc178/install/QIIME1.6/src/PyCogent-1.5.3/build/lib.linux-x86_64-2.7/cogent/app/mothur.py

changing TmpDir='/tmp' to /home/lc178/tmp/ in def __init__(self, params=None, InputHandler=None, SuppressStderr=None,

                 SuppressStdout=None, WorkingDir=None, TmpDir='/tmp',

But it still failed. And I also added environment variables of $TMPDIR, $TMP, $TEMP, but still no use.

I don't know how to change it.

Here's my config:

[lc178@dav-dd-l0151 merge]$ print_qiime_config.py -t

System information

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

         Platform: linux2

   Python version: 2.7.3 (default, Mar 15 2013, 11:25:05)  [GCC 4.4.6 20110731 (Red Hat 4.4.6-3)]

Python executable: /home/lc178/install/QIIME1.6/bin/python

 

Dependency versions

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

                     PyCogent version: 1.5.3

                        NumPy version: 1.5.1

                   matplotlib version: 1.1.0

                  biom-format version: 1.1.1

                QIIME library version: 1.6.0

                 QIIME script version: 1.6.0

        PyNAST version (if installed): 1.2

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

          Java version (if installed): 1.6.0_43

 

QIIME config values

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

                     blastmat_dir: /home/lc178/install/QIIME1.6/src/blast/data

                         sc_queue: all.q

      topiaryexplorer_project_dir: None

     pynast_template_alignment_fp: /home/lc178/install/QIIME1.6/data/core_set_aligned.fasta.imputed

                  cluster_jobs_fp: /home/lc178/install/QIIME1.6/bin/start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /home/lc178/install/QIIME1.6/data/gg_12_10_otus/rep_set/97_otus.fasta

                     torque_queue: friendlyq

              qiime_test_data_dir: None

   template_alignment_lanemask_fp: /home/lc178/install/QIIME1.6/data/lanemask_in_1s_and_0s

                    jobs_to_start: 1

                cloud_environment: False

                qiime_scripts_dir: /home/lc178/install/QIIME1.6/src/qiime/scripts/

            denoiser_min_per_core: 50

                      working_dir: /home/lc178/tmp/

                    python_exe_fp: python

                         temp_dir: /home/lc178/tmp/

                      blastall_fp: blastall

                 seconds_to_sleep: 2

assign_taxonomy_id_to_taxonomy_fp: /home/lc178/install/QIIME1.6/data/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. ... ok

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_qiime_test_data_dir (__main__.Qiime_config)

qiime_test_data_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_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 ... ok

test_working_dir (__main__.Qiime_config)

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

 

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

Ran 35 tests in 0.314s

 

OK

Please help me. Thanks.

[Tony Walters]

Hello Isiah,

In this case, I think the only way to change the tmp directory used by mothur would be to modify the pycogent app controller:

cogent/app/mother.py

on line 52 (after making a copy of the file):

    def __init__(self, params=None, InputHandler=None, SuppressStderr=None,

                 SuppressStdout=None, WorkingDir=None, TmpDir='/tmp',

                 TmpNameLen=20, HALT_EXEC=False)

Change the TmpDir setting here to the location you want it.

-Tony

--
 
---
You received this message because you are subscribed to the Google Groups "Qiime Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to qiime-forum...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Isiah]

Hi Tony,

Thanks for your reply. After I changed all the /tmp in the files of cogent/app/mother.py and /cogent/app/util.py to my local directories. It works.

Thanks,

Isiah