Logging started at 00:20:09 on 17 Nov 2016
QIIME version: 1.9.1

qiime_config values:
blastmat_dir	/usr/share/ncbi/data
pick_otus_reference_seqs_fp	/usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
pynast_template_alignment_fp	/usr/share/qiime/data/core_set_aligned.fasta.imputed
assign_taxonomy_reference_seqs_fp	/usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
jobs_to_start	1
assign_taxonomy_id_to_taxonomy_fp	/usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
qiime_scripts_dir	/usr/lib/qiime/bin/
working_dir	.
python_exe_fp	python
temp_dir	/tmp/
seconds_to_sleep	60
blastall_fp	blastall

parameter file values:
assign_taxonomy:reference_seqs_fp	/usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
assign_taxonomy:id_to_taxonomy_fp	/usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
assign_taxonomy:assignment_method	rdp
assign_taxonomy:confidence	0.8
parallel:jobs_to_start	20

Input file md5 sums:
seqs_chimera_filtered: 23425d67494d0a3861cb76694f10fe7b
/usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta: 50b2269712b3738afb41892bed936c29

Executing commands.

# Pick Reference OTUs command 
parallel_pick_otus_uclust_ref.py -i seqs_chimera_filtered -o otus/step1_otus -r /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta -T --jobs_to_start 20 

Stdout:

Stderr:

# Generate full failures fasta file command 
filter_fasta.py -f seqs_chimera_filtered -s otus/step1_otus/seqs_chimera_filtered_failures.txt -o otus/step1_otus/failures.fasta

Stdout:

Stderr:

Executing commands.

# Pick rep set command 
pick_rep_set.py -i otus/step1_otus/seqs_chimera_filtered_otus.txt -o otus/step1_otus/step1_rep_set.fna -f seqs_chimera_filtered

Stdout:

Stderr:

Executing commands.

# Pick de novo OTUs on step1 failures command 
pick_otus.py -i otus/step1_otus/failures.fasta -o otus/step4_otus/ -m uclust  --denovo_otu_id_prefix New.CleanUp.ReferenceOTU

Stdout:

Stderr:

# Merge OTU maps command 
cat otus/step1_otus/seqs_chimera_filtered_otus.txt  otus/step4_otus//failures_otus.txt > otus/final_otu_map.txt

Stdout:

Stderr:

# Pick representative set for subsampled failures command 
pick_rep_set.py -i otus/step4_otus//failures_otus.txt -o otus/step4_otus//step4_rep_set.fna -f otus/step1_otus/failures.fasta

Stdout:

Stderr:

# Filter singletons from the otu map using API 
python -c "import qiime; qiime.filter.filter_otus_from_otu_map('/home/mcampa/BP_Cosm11/Com8/split_lib_q20/otus/final_otu_map.txt', '/home/mcampa/BP_Cosm11/Com8/split_lib_q20/otus/final_otu_map_mc2.txt', '2')"

# Write non-singleton otus representative sequences from step1 to the final rep set file: otus/rep_set.fna

# Copy the full input refseqs file to the new refseq file
cp /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta otus/new_refseqs.fna

# Write non-singleton otus representative sequences from step 4 to the final representative set and the new reference set (otus/rep_set.fna and otus/new_refseqs.fna respectively)

Executing commands.

# Make the otu table command 
make_otu_table.py -i otus/final_otu_map_mc2.txt -o otus/otu_table_mc2.biom

Stdout:

Stderr:

Executing commands.

# Assign taxonomy command 
parallel_assign_taxonomy_rdp.py -i otus/rep_set.fna -o otus/rdp_assigned_taxonomy -T --jobs_to_start 20 --reference_seqs_fp /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta --id_to_taxonomy_fp /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt --confidence 0.8

Stdout:

Stderr:

Executing commands.

# Add taxa to OTU table command 
biom add-metadata -i otus/otu_table_mc2.biom --observation-metadata-fp otus/rdp_assigned_taxonomy/rep_set_tax_assignments.txt -o otus/otu_table_mc2_w_tax.biom --sc-separated taxonomy --observation-header OTUID,taxonomy



*** ERROR RAISED DURING STEP: Add taxa to OTU table
Command run was:
 biom add-metadata -i otus/otu_table_mc2.biom --observation-metadata-fp otus/rdp_assigned_taxonomy/rep_set_tax_assignments.txt -o otus/otu_table_mc2_w_tax.biom --sc-separated taxonomy --observation-header OTUID,taxonomy
Command returned exit status: 2
Stdout:

Stderr
/usr/bin/biom: 22: export: 4.0/dist-packages: bad variable name


Logging stopped at 00:25:23 on 17 Nov 2016