Logging started at 09:28:37 on 14 May 2018
QIIME version: 1.8.0

qiime_config values:
blastmat_dir	/home/worker/software/qiime-1.8/blast-2.2.22-release/data
sc_queue	all.q
pynast_template_alignment_fp	/home/worker/software/qiime-1.8/core_set_aligned.fasta.imputed
cluster_jobs_fp	/home/worker/software/qiime-1.8/qiime-1.8.0-release/bin/start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/home/worker/software/qiime-1.8/gg_otus-13_8-release/rep_set/97_otus.fasta
torque_queue	friendlyq
template_alignment_lanemask_fp	/home/worker/software/qiime-1.8/lanemask_in_1s_and_0s
jobs_to_start	1
cloud_environment	False
qiime_scripts_dir	/home/worker/software/qiime-1.8/qiime-1.8.0-release/bin
denoiser_min_per_core	50
working_dir	/tmp/
python_exe_fp	/home/worker/software/qiime-1.8/python-2.7.3-release/bin/python
temp_dir	/tmp/
blastall_fp	/home/worker/software/qiime-1.8/blast-2.2.22-release/bin/blastall
seconds_to_sleep	60
assign_taxonomy_id_to_taxonomy_fp	/home/worker/software/qiime-1.8/gg_otus-13_8-release/taxonomy/97_otu_taxonomy.txt

parameter file values:
parallel:jobs_to_start	8

Input file md5 sums:
output/seqs.fna: 9aad767dfa1ef5cdfecd059de54e698f
/home/worker/software/qiime-1.8/gg_otus-13_8-release/rep_set/97_otus.fasta: 50b2269712b3738afb41892bed936c29

Overridding similiary with 0.600.
Executing commands.

# Pick Reference OTUs (prefilter) command 
parallel_pick_otus_uclust_ref.py -i output/seqs.fna -o otus//prefilter_otus/ -r /home/worker/software/qiime-1.8/gg_otus-13_8-release/rep_set/97_otus.fasta -T --jobs_to_start 8 --similarity 0.6

Stdout:

Stderr:

# Filter prefilter failures from input command 
filter_fasta.py -f output/seqs.fna -o otus//prefilter_otus//prefiltered_seqs.fna -s otus//prefilter_otus//seqs_failures.txt -n

Stdout:

Stderr:

Executing commands.

# Pick Reference OTUs command 
parallel_pick_otus_uclust_ref.py -i otus//prefilter_otus//prefiltered_seqs.fna -o otus//step1_otus -r /home/worker/software/qiime-1.8/gg_otus-13_8-release/rep_set/97_otus.fasta -T --jobs_to_start 8 

Stdout:

Stderr:

# Generate full failures fasta file command 
filter_fasta.py -f otus//prefilter_otus//prefiltered_seqs.fna -s otus//step1_otus/prefiltered_seqs_failures.txt -o otus//step1_otus/failures.fasta

Stdout:

Stderr:

Executing commands.

# Pick rep set command 
pick_rep_set.py -i otus//step1_otus/prefiltered_seqs_otus.txt -o otus//step1_otus/step1_rep_set.fna -f otus//prefilter_otus//prefiltered_seqs.fna

Stdout:

Stderr:

# Subsample the failures fasta file using API 
python -c "import qiime; qiime.util.subsample_fasta('/home/worker/analysis/Auto-Analysen/2018-05-14__16s_new__Spindelboeck_KinderUro_v3/Combined_V8/otus/step1_otus/failures.fasta', '/home/worker/analysis/Auto-Analysen/2018-05-14__16s_new__Spindelboeck_KinderUro_v3/Combined_V8/otus/step1_otus/subsampled_failures.fasta', '0.001000')

"Executing commands.

# Pick de novo OTUs for new clusters command 
pick_otus.py -i otus//step1_otus/subsampled_failures.fasta -o otus//step2_otus/ -m uclust  --uclust_otu_id_prefix New.ReferenceOTU

Stdout:

Stderr:

# Pick representative set for subsampled failures command 
pick_rep_set.py -i otus//step2_otus//subsampled_failures_otus.txt -o otus//step2_otus//step2_rep_set.fna -f otus//step1_otus/subsampled_failures.fasta

Stdout:

Stderr:

# Pick reference OTUs using de novo rep set command 
parallel_pick_otus_uclust_ref.py -i otus//step1_otus/failures.fasta -o otus//step3_otus/ -r otus//step2_otus//step2_rep_set.fna -T --jobs_to_start 8 

Stdout:

Stderr:

# Create fasta file of step3 failures command 
filter_fasta.py -f otus//step1_otus/failures.fasta -s otus//step3_otus//failures_failures.txt -o otus//step3_otus//failures_failures.fasta

Stdout:

Stderr:

# Pick de novo OTUs on step3 failures command 
pick_otus.py -i otus//step3_otus//failures_failures.fasta -o otus//step4_otus/ -m uclust  --uclust_otu_id_prefix New.CleanUp.ReferenceOTU

Stdout:

Stderr:

# Merge OTU maps command 
cat otus//step1_otus/prefiltered_seqs_otus.txt otus//step3_otus//failures_otus.txt otus//step4_otus//failures_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_failures_otus.txt -o otus//step4_otus//step4_rep_set.fna -f otus//step3_otus//failures_failures.fasta

Stdout:

Stderr:

# Filter singletons from the otu map using API 
python -c "import qiime; qiime.filter.filter_otus_from_otu_map('/home/worker/analysis/Auto-Analysen/2018-05-14__16s_new__Spindelboeck_KinderUro_v3/Combined_V8/otus/final_otu_map.txt', '/home/worker/analysis/Auto-Analysen/2018-05-14__16s_new__Spindelboeck_KinderUro_v3/Combined_V8/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 /home/worker/software/qiime-1.8/gg_otus-13_8-release/rep_set/97_otus.fasta otus//new_refseqs.fna

# Write non-singleton otus representative sequences from step 2 and 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_uclust.py -i otus//rep_set.fna -o otus//uclust_assigned_taxonomy -T --jobs_to_start 8 

Stdout:

Stderr:

Executing commands.

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

Stdout:

Stderr:
/home/worker/software/qiime-1.8/pyqi-0.3.1-release/bin/pyqi:4: UserWarning: Module pkg_resources was already imported from /home/worker/software/qiime-1.8/setuptools-0.6c11-release/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py, but /home/worker/software/qiime-1.8/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg is being added to sys.path
  import pkg_resources
/home/worker/software/qiime-1.8/pyqi-0.3.1-release/bin/pyqi:4: UserWarning: Module site was already imported from /home/worker/software/qiime-1.8/python-2.7.3-release/lib/python2.7/site.pyc, but /home/worker/software/qiime-1.8/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg is being added to sys.path
  import pkg_resources

Executing commands.

# Align sequences command 
parallel_align_seqs_pynast.py -i otus//rep_set.fna -o otus//pynast_aligned_seqs -T --jobs_to_start 8 

Stdout:

Stderr:

# Filter alignment command 
filter_alignment.py -o otus//pynast_aligned_seqs -i otus//pynast_aligned_seqs/rep_set_aligned.fasta 

Stdout:

Stderr:

# Build phylogenetic tree command 
make_phylogeny.py -i otus//pynast_aligned_seqs/rep_set_aligned_pfiltered.fasta -o otus//rep_set.tre 

Stdout:

Stderr:

Executing commands.


Logging stopped at 10:05:31 on 14 May 2018
