Logging started at 14:16:06 on 24 May 2016 QIIME version: 1.9.1 qiime_config values: pick_otus_reference_seqs_fp /home/obrett/my_env/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta sc_queue all.q pynast_template_alignment_fp /home/obrett/my_env/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta cluster_jobs_fp start_parallel_jobs.py assign_taxonomy_reference_seqs_fp /home/obrett/my_env/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta torque_queue friendlyq jobs_to_start 1 denoiser_min_per_core 50 assign_taxonomy_id_to_taxonomy_fp /home/obrett/my_env/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt temp_dir /tmp/ blastall_fp blastall seconds_to_sleep 1 parameter file values: assign_taxonomy:reference_seqs_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta assign_taxonomy:id_to_taxonomy_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_taxonomy_qiime_ver7_97_s_31.01.2016.txt pick_open_reference_otus:suppress_align_and_tree True pick_open_reference_otus:otu_picking_method usearch61 pick_open_reference_otus:enable_rev_strand_match True pick_open_reference_otus:reference_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta pick_open_reference_otus:prefilter_refseqs_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta pick_open_reference_otus:prefilter_percent_id 0.6 pick_open_reference_otus:id_to_taxonomy_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_taxonomy_qiime_ver7_97_s_31.01.2016.txt parallel:jobs_to_start 1 Input file md5 sums: filtered_R1.fasta: 5235176b0afb03fb24d78b5d84635e7f /home/obrett/my_env/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta: 50b2269712b3738afb41892bed936c29 Forcing --suppress_new_clusters as this is reference-based OTU picking. Executing commands. # Pick Reference OTUs command pick_otus.py -i filtered_R1.fasta -o open_reference_otus2//step1_otus -r /home/obrett/my_env/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta -m uclust_ref --suppress_new_clusters Stdout: Stderr: # Generate full failures fasta file command filter_fasta.py -f filtered_R1.fasta -s open_reference_otus2//step1_otus/filtered_R1_failures.txt -o open_reference_otus2//step1_otus/failures.fasta Stdout: Stderr: Executing commands. # Pick rep set command pick_rep_set.py -i open_reference_otus2//step1_otus/filtered_R1_otus.txt -o open_reference_otus2//step1_otus/step1_rep_set.fna -f filtered_R1.fasta Stdout: Stderr: # Subsample the failures fasta file using API python -c "import qiime; qiime.util.subsample_fasta('/workspace/scratch/obrett/processing/open_reference_otus2/step1_otus/failures.fasta', '/workspace/scratch/obrett/processing/open_reference_otus2/step2_otus/subsampled_failures.fasta', '0.001000') "Forcing --suppress_new_clusters as this is reference-based OTU picking. Executing commands. # Pick de novo OTUs for new clusters command pick_otus.py -i open_reference_otus2//step2_otus//subsampled_failures.fasta -o open_reference_otus2//step2_otus/ -m uclust --denovo_otu_id_prefix New.ReferenceOTU Stdout: Stderr: # Pick representative set for subsampled failures command pick_rep_set.py -i open_reference_otus2//step2_otus//subsampled_failures_otus.txt -o open_reference_otus2//step2_otus//step2_rep_set.fna -f open_reference_otus2//step2_otus//subsampled_failures.fasta Stdout: Stderr: # Pick reference OTUs using de novo rep set command pick_otus.py -i open_reference_otus2//step1_otus/failures.fasta -o open_reference_otus2//step3_otus/ -r open_reference_otus2//step2_otus//step2_rep_set.fna -m uclust_ref --suppress_new_clusters Stdout: Stderr: # Create fasta file of step3 failures command filter_fasta.py -f open_reference_otus2//step1_otus/failures.fasta -s open_reference_otus2//step3_otus//failures_failures.txt -o open_reference_otus2//step3_otus//failures_failures.fasta Stdout: Stderr: # Pick de novo OTUs on step3 failures command pick_otus.py -i open_reference_otus2//step3_otus//failures_failures.fasta -o open_reference_otus2//step4_otus/ -m uclust --denovo_otu_id_prefix New.CleanUp.ReferenceOTU Stdout: Stderr: # Merge OTU maps command cat open_reference_otus2//step1_otus/filtered_R1_otus.txt open_reference_otus2//step3_otus//failures_otus.txt open_reference_otus2//step4_otus//failures_failures_otus.txt > open_reference_otus2//final_otu_map.txt Stdout: Stderr: # Pick representative set for subsampled failures command pick_rep_set.py -i open_reference_otus2//step4_otus//failures_failures_otus.txt -o open_reference_otus2//step4_otus//step4_rep_set.fna -f open_reference_otus2//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('/workspace/scratch/obrett/processing/open_reference_otus2/final_otu_map.txt', '/workspace/scratch/obrett/processing/open_reference_otus2/final_otu_map_mc2.txt', '2')" # Write non-singleton otus representative sequences from step1 to the final rep set file: open_reference_otus2//rep_set.fna # Copy the full input refseqs file to the new refseq file cp /home/obrett/my_env/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta open_reference_otus2//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 (open_reference_otus2//rep_set.fna and open_reference_otus2//new_refseqs.fna respectively) Executing commands. # Make the otu table command make_otu_table.py -i open_reference_otus2//final_otu_map_mc2.txt -o open_reference_otus2//otu_table_mc2.biom Stdout: Stderr: Executing commands. # Assign taxonomy command assign_taxonomy.py -o open_reference_otus2//uclust_assigned_taxonomy -i open_reference_otus2//rep_set.fna --reference_seqs_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta --id_to_taxonomy_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_taxonomy_qiime_ver7_97_s_31.01.2016.txt *** ERROR RAISED DURING STEP: Assign taxonomy Command run was: assign_taxonomy.py -o open_reference_otus2//uclust_assigned_taxonomy -i open_reference_otus2//rep_set.fna --reference_seqs_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta --id_to_taxonomy_fp /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_taxonomy_qiime_ver7_97_s_31.01.2016.txt Command returned exit status: 1 Stdout: Stderr Traceback (most recent call last): File "/home/obrett/my_env/bin/assign_taxonomy.py", line 417, in main() File "/home/obrett/my_env/bin/assign_taxonomy.py", line 394, in main log_path=log_path) File "/home/obrett/my_env/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 1304, in __call__ '--uc': uc_path}) File "/home/obrett/my_env/lib/python2.7/site-packages/burrito/util.py", line 285, in __call__ 'StdErr:\n%s\n' % open(errfile).read()) burrito.util.ApplicationError: Unacceptable application exit status: 1 Command: cd "/workspace/scratch/obrett/processing/"; uclust --input "open_reference_otus2//rep_set.fna" --id 0.9 --rev --maxaccepts 3 --allhits --libonly --lib "/home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta" --uc "/tmp/UclustConsensusTaxonAssigner_BFM7JJ.uc" > "/tmp/tmp8VgeHyyxrozlU0powGor.txt" 2> "/tmp/tmp1HGoZDMOPEKfhLBlQr5A.txt" StdOut: StdErr: uclust v1.2.22q (C) Copyright 2009-10 Robert C. Edgar Licensed ONLY for use in PyNAST and QIIME. 00:00 37Mb 0.0% Reading lib, 0 seeds ---Fatal error--- Input is not FASTA file uclust --input open_reference_otus2//rep_set.fna --id 0.9 --rev --maxaccepts 3 --allhits --libonly --lib /home/obrett/UNITE/sh_qiime_release_s_31.01.2016/sh_refs_qiime_ver7_97_s_31.01.2016.fasta --uc /tmp/UclustConsensusTaxonAssigner_BFM7JJ.uc Elapsed time: 0 Logging stopped at 15:13:06 on 24 May 2016