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.
This is how I use to pick OTUs using the open reference method.
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:
EDIT: More information required: