Problems with OTU Picking 18S - qiime.util.EmptyBIOMTableError: Attempting to write an empty BIOM ta
Rodrigo Vargas
Pick Reference OTUs
pick_otus.py -i /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/combined_fasta/combined_seqs.fna -o /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus -r /Users/rvargas/Downloads/gb203_pr2_all_10_28_99p_clean.fasta -m sortmerna --sortmerna_coverage 0.8 --threads 4 --similarity 0.98 --suppress_new_clusters
sh: line 1: 9647 Abort trap: 6 indexdb_rna --ref "/Users/rvargas/Downloads/gb203_pr2_all_10_28_99p_clean.fasta,/Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering/step1_otus/gb203_pr2_all_10_28_99p_clean" --max_pos 10000 --tmpdir "/var/folders/9n/25vpydl55fbf1751y7qv9jx00000gn/T" > "/var/folders/9n/25vpydl55fbf1751y7qv9jx00000gn/T/tmpdBrN4pmZDeDr8UeW4E3h.txt" 2> "/var/folders/9n/25vpydl55fbf1751y7qv9jx00000gn/T/tmpEWv6Up3rLRKZhXKmjla9.txt"
Generate full failures fasta file
filter_fasta.py -f /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/combined_fasta/combined_seqs.fna -s /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus/combined_seqs_failures.txt -o /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus/failures.fasta
Pick rep set
pick_rep_set.py -i /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus/combined_seqs_otus.txt -o /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus/step1_rep_set.fna -f /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/combined_fasta/combined_seqs.fna
Pick de novo OTUs on step1 failures
pick_otus.py -i /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus/failures.fasta -o /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step4_otus/ -m sumaclust --sortmerna_coverage 0.8 --threads 4 --denovo_otu_id_prefix New.CleanUp.ReferenceOTU --similarity 0.98
Merge OTU maps
cat /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus/combined_seqs_otus.txt /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step4_otus//failures_otus.txt > /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//final_otu_map.txt
Pick representative set for subsampled failures
pick_rep_set.py -i /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step4_otus//failures_otus.txt -o /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step4_otus//step4_rep_set.fna -f /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//step1_otus/failures.fasta
Make the otu table
make_otu_table.py -i /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//final_otu_map_mc1.txt -o /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//otu_table_mc1.biom
Traceback (most recent call last):
File "/Users/rvargas/miniconda3/envs/qiime1/bin/pick_open_reference_otus.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'pick_open_reference_otus.py')
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 748, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
exec(code, namespace, namespace)
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/pick_open_reference_otus.py", line 453, in <module>
main()
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/pick_open_reference_otus.py", line 432, in main
minimum_failure_threshold=minimum_failure_threshold)
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/pick_open_reference_otus.py", line 966, in pick_subsampled_open_reference_otus
close_logger_on_success=False)
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/util.py", line 122, in call_commands_serially
raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:
*** ERROR RAISED DURING STEP: Make the otu table
Command run was:
make_otu_table.py -i /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//final_otu_map_mc1.txt -o /Users/rvargas/Desktop/MetagenomicUruguay/FungiO/clustering//otu_table_mc1.biom
Command returned exit status: 1
Stdout:
Stderr
Traceback (most recent call last):
File "/Users/rvargas/miniconda3/envs/qiime1/bin/make_otu_table.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.1', 'make_otu_table.py')
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 748, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
exec(code, namespace, namespace)
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/make_otu_table.py", line 119, in <module>
main()
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/make_otu_table.py", line 115, in main
write_biom_table(biom_otu_table, opts.output_biom_fp)
File "/Users/rvargas/miniconda3/envs/qiime1/lib/python2.7/site-packages/qiime/util.py", line 569, in write_biom_table
"Attempting to write an empty BIOM table to disk. "
qiime.util.EmptyBIOMTableError: Attempting to write an empty BIOM table to disk. QIIME doesn't support writing empty BIOM output files.
zech xu
It basically means you don't have any OTU clustered after OTU picking. Could you check your input fasta file are ok?