Error: assigin taxonomy, pick_open_reference_otus.py

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Manil

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May 18, 2017, 10:40:22 AM5/18/17
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Hello everyone, 

I am using qiime 1.9.1 trough virtual box. After split libraries,I used the command "pick_open_reference_otus.py -i SEQ/seqs.fna -o SEQ/OTU -p SEQ/ otu_settings.txt in my otu_settings.txt file i have pick_otu: enable_rev_strand_match True. After that the program runs and I got these files: final_otu_map.txt , final_otu_map_mc2.txt, new_refseqs.fna, rep_set.fna, otu_table_mc2.biom, but it crashed with an error msg :

*** 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:
 I have checked in some forums but I could not really resolve it !

S.O.S

Jai Ram Rideout

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May 18, 2017, 6:11:14 PM5/18/17
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Hello,

uclust exit code 137 usually indicates that your system ran out of memory (during execution of assign_taxonomy.py). How much memory do you have on your host system, and how much memory did you allocate to the VirtualBox? If possible, try increasing the amount of memory allocated to the VirtualBox and rerun the command.

Unrelated note: your otu_settings.txt file has:

pick_otu: enable_rev_strand_match True

If you want this option enabled, change it to:

pick_otus:enable_rev_strand_match True

Note that this will roughly double the amount of required memory.

Best,
Jai

Manil

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May 19, 2017, 8:46:11 AM5/19/17
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Hello Jai Ram,

Thank you fr your reply indeed it was a problem of memory I increased it in my virtual box from 2024Mo to 4042Mo (I have 8Go in my host system) and it works. 


Cheers!!

Manil
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