Question: Error: assigin taxonomy, pick_open_reference_otus.py
0
gravatar for ericleelionking
2.2 years ago by
ericleelionking0 wrote:

Dear expert in qiime,

Hello. I am a qiime newbie. I am using qiime trough virtual box. After split libraries,I used a script "pick_open_reference_otus.py -i seqs.fna -o pickopenref/". And then, I got these files: final_otu_map.txt , final_otu_map_mc2.txt, new_refseqs.fna, rep_set.fna, otu_table_mc2.biom.

But two important files (Either "otu_table_mc2_w_tax.biom" or "otu_table_mc_w_tax_no_pynast_failures.biom" and rep_set.tre) were not created . I understand those files are required for the downstream proceedings and beta-diversity analysis.

I checked a log and found an error:

*** ERROR RAISED DURING STEP: Assign taxonomy
 Command run was:
 assign_taxonomy.py -o PickOpenRef//uclust_assigned_taxonomy -i PickOpenRef//rep_set.fna 
 Command returned exit status: 1
 Stdout:

Stderr
Traceback (most recent call last):
  File "/usr/local/bin/assign_taxonomy.py", line 417, in <module>
    main()
  File "/usr/local/bin/assign_taxonomy.py", line 394, in main
    log_path=log_path)
  File "/usr/local/lib/python2.7/dist-packages/qiime/assign_taxonomy.py", line 1304, in __call__
    '--uc': uc_path})
  File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 285, in __call__
    'StdErr:\n%s\n' % open(errfile).read())
burrito.util.ApplicationError: Unacceptable application exit status: 137
Command:
cd "/home/qiime/Desktop/Catfish/SplitLibraries/OutputSplitLibraries/"; uclust --input "PickOpenRef//rep_set.fna" --id 0.9 --rev --maxaccepts 3 --allhits --libonly --lib "/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta" --uc "/tmp/UclustConsensusTaxonAssigner_XLWUKJ.uc" > "/tmp/tmpG40Sjf8Fh9nnIucNMeAO.txt" 2> "/tmp/tmpogzde1pgyC9F854vl4Hl.txt"
StdOut:

How can I create the two files? Could someone please help me solve this problem?

Thank you very much.

ADD COMMENTlink modified 2.2 years ago by genomax62k • written 2.2 years ago by ericleelionking0

This is how I use to pick OTUs using the open reference method.

pick_open_reference_otus.py -i seqs.fna  -r 99_otus.fasta -o OTUS_Open_ref --suppress_taxonomy_assignment --suppress_align_and_tree

Notice that I had suppressed "taxonomy_assignment" and "align_and_tree". However, in your case you haven't used the -r option (where is your reference?). What files and folders did you get by running your script?

I usually get these:

-rw-rw-r-- 1 qiime root 111179830 Dec 21 01:33 final_otu_map_mc2.txt
-rw-rw-r-- 1 qiime root 118901518 Dec 21 01:33 final_otu_map.txt
-rw-rw-r-- 1 qiime root      5789 Dec 21 01:34 log_20161217130128.txt
-rw-r--r-- 1 qiime root 315347261 Dec 21 01:34 new_refseqs.fna
-rw-rw-r-- 1 qiime root   4536840 Dec 21 01:34 otu_table_mc2.biom
drwxrwxr-x 1 qiime root      4096 Dec 19 05:57 prefilter_otus/
-rw-rw-r-- 1 qiime root  25644853 Dec 21 01:34 rep_set.fna
drwxrwxr-x 1 qiime root      4096 Dec 20 19:28 step1_otus/
drwxrwxr-x 1 qiime root      4096 Dec 20 19:29 step2_otus/
drwxrwxr-x 1 qiime root      4096 Dec 20 19:59 step3_otus/
drwxrwxr-x 1 qiime root      4096 Dec 21 01:33 step4_otus/

EDIT: More information required:

  1. How many samples do you have?
  2. Picking OTUs by open reference method is super time and memory consuming.
ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Vijay Lakhujani3.6k
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