Error: assigin taxonomy, pick_open_reference_otus.py
0
0
Entering edit mode
7.6 years ago

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.

Qiime • 3.6k views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1333 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6