Command exit status 137

[Bibaswan]

Hi al,,

I am trying to run my samples though the pick_otus_through_otu_table.py workflow and I am continuously getting a error message saying that the process has been killed with an exit status of 137. I have increased the memory as well, but still it won't work.

Here is the detailed error message

# Align sequences command 

/home/qiime/qiime_software/python-2.7.1-release/bin/python /home/qiime/qiime_software/qiime-1.5.0-release/bin/align_seqs.py -i otus/rep_set//all_seqs_rep_set.fasta -o otus

/pynast_aligned_seqs --template_fp /home/qiime/data/biba_16S_rRNA_RFI/gg_12_10_aligned.fasta --alignment_method pynast --pairwise_alignment_method uclust --min_percent_id 

0.75 --min_length 150

*** ERROR RAISED DURING STEP: Align sequences

Command run was:

 /home/qiime/qiime_software/python-2.7.1-release/bin/python /home/qiime/qiime_software/qiime-1.5.0-release/bin/align_seqs.py -i otus/rep_set//all_seqs_rep_set.fasta -o otu

s/pynast_aligned_seqs --template_fp /home/qiime/data/biba_16S_rRNA_RFI/gg_12_10_aligned.fasta --alignment_method pynast --pairwise_alignment_method uclust --min_percent_id

 0.75 --min_length 150

Command returned exit status: 137

Stdout:

Stderr

Killed

Here is the QIIME config details for the system

System information

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

         Platform: linux2

   Python version: 2.7.3 (default, Apr 20 2012, 23:04:22)  [GCC 4.6.3]

Python executable: /home/qiime/qiime_software/python-2.7.1-release/bin/python

Dependency versions

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

                     PyCogent version: 1.5.1

                        NumPy version: 1.5.1

                   matplotlib version: 1.1.0

                  biom-format version: 0.9.3

                QIIME library version: 1.5.0

                 QIIME script version: 1.5.0

        PyNAST version (if installed): 1.1

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

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-1.5.0-release/bin/start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: /home/qiime/qiime_software/gg_otus-4feb2011-release/rep_set/gg_97_otus_4feb2011.fasta

                     torque_queue: friendlyq

              qiime_test_data_dir: None

   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-1.5.0-release/bin

            denoiser_min_per_core: 50

                      working_dir: /tmp/

                    python_exe_fp: /home/qiime/qiime_software/python-2.7.1-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-4feb2011-release/taxonomies/greengenes_tax_rdp_train.txt

Help would be really appreciated.

Thanks,

Bibaswan

[Will Van Treuren]

Hi Bibaswan,

I have seen this error before on a variety of different scripts. It has always been a memory issue in the past. How much memory does your system (or virtual box) have?

Here is a related post  where memory was the issue:

https://groups.google.com/forum/?fromgroups=#!searchin/qiime-forum/137/qiime-forum/zYKzu0ljSEg/jEa_sFd0sSQJ

Will 

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[Jose Navas]

Hi Bibaswan,

This error code means that your process have been killed due to your machine doesn't have enough memory. Looking at your command, the template file that you're using (/home/qiime/data/biba_16S_rRNA_RFI/gg_12_10_aligned.fasta) is a big file wich is consuming your memory. In order to be able to perform this step, you should use the greengenes core set data file (if you do not have it, you can download it from this link).

For the alignment step (if you perform it) you can use this alignment lanemask file.

Cheers,

2012/11/19 Bibaswan <bibaswan...@gmail.com>

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Jose Navas

[Bibaswan]

Hi Jose,

I am trying that step right now. Will update you if that works. But my question is will it be okay to use this file with the latest greengenes taxonomy file.

Thanks,

Bibaswan

[Jose Navas]

Yes, it shouldn't be any problem

2012/11/19 Bibaswan <bibaswan...@gmail.com>

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Jose Navas