Logging started at 18:10:58 on 17 Mar 2016 QIIME version: 1.8.0 qiime_config values: sc_queue all.q torque_queue friendlyq jobs_to_start 1 cloud_environment False denoiser_min_per_core 50 python_exe_fp python temp_dir /tmp/ blastall_fp blastall seconds_to_sleep 2 parameter file values: parallel:jobs_to_start 16 Input file md5 sums: /home/liutong/glob/illumina_project_1/test/splited/seqs.fna: af296260f969f16fc753fc895c20c9dc /home/liutong/glob/illumina_project_1/97_otus.fasta: 50b2269712b3738afb41892bed936c29 Executing commands. # Pick Reference OTUs command parallel_pick_otus_uclust_ref.py -i /home/liutong/glob/illumina_project_1/test/splited/seqs.fna -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus -r /home/liutong/glob/illumina_project_1/97_otus.fasta -T --jobs_to_start 16 Stdout: Stderr: # Generate full failures fasta file command filter_fasta.py -f /home/liutong/glob/illumina_project_1/test/splited/seqs.fna -s /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/seqs_failures.txt -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/failures.fasta Stdout: Stderr: Executing commands. # Pick rep set command pick_rep_set.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/seqs_otus.txt -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/step1_rep_set.fna -f /home/liutong/glob/illumina_project_1/test/splited/seqs.fna Stdout: Stderr: # Subsample the failures fasta file using API python -c "import qiime; qiime.util.subsample_fasta('/home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/failures.fasta', '/home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/subsampled_failures.fasta', '0.100000') "Executing commands. # Pick de novo OTUs for new clusters command pick_otus.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/subsampled_failures.fasta -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step2_otus/ -m uclust --uclust_otu_id_prefix New.ReferenceOTU Stdout: Stderr: # Pick representative set for subsampled failures command pick_rep_set.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step2_otus//subsampled_failures_otus.txt -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step2_otus//step2_rep_set.fna -f /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/subsampled_failures.fasta Stdout: Stderr: # Pick reference OTUs using de novo rep set command parallel_pick_otus_uclust_ref.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/failures.fasta -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step3_otus/ -r /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step2_otus//step2_rep_set.fna -T --jobs_to_start 16 Stdout: Stderr: # Create fasta file of step3 failures command filter_fasta.py -f /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/failures.fasta -s /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step3_otus//failures_failures.txt -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step3_otus//failures_failures.fasta Stdout: Stderr: # Pick de novo OTUs on step3 failures command pick_otus.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step3_otus//failures_failures.fasta -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step4_otus/ -m uclust --uclust_otu_id_prefix New.CleanUp.ReferenceOTU Stdout: Stderr: # Merge OTU maps command cat /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step1_otus/seqs_otus.txt /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step3_otus//failures_otus.txt /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step4_otus//failures_failures_otus.txt > /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/final_otu_map.txt Stdout: Stderr: # Pick representative set for subsampled failures command pick_rep_set.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step4_otus//failures_failures_otus.txt -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/step4_otus//step4_rep_set.fna -f /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/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/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/final_otu_map.txt', '/home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/final_otu_map_mc3.txt', '3')" # Write non-singleton otus representative sequences from step1 to the final rep set file: /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/rep_set.fna # Copy the full input refseqs file to the new refseq file cp /home/liutong/glob/illumina_project_1/97_otus.fasta /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/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 (/home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/rep_set.fna and /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/new_refseqs.fna respectively) Executing commands. # Make the otu table command make_otu_table.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/final_otu_map_mc3.txt -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/otu_table_mc3.biom Stdout: Stderr: Executing commands. # Assign taxonomy command parallel_assign_taxonomy_uclust.py -i /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/rep_set.fna -o /home/liutong/glob/illumina_project_1/test/splited/open_otu_pick/uclust_97/uclust_assigned_taxonomy -T --jobs_to_start 16