[2022-12-04 21:34:58,922 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.21.5, tag: Nephele_2022_October_06, commit: c1eb66c
[2022-12-04 21:34:58,922 - INFO] Python version: 3.8.13
[2022-12-04 21:34:58,922 - INFO] Current time: 2022-12-04 21:34
[2022-12-04 21:34:58,923 - INFO] Pipeline name: QIIME2 16S
[2022-12-04 21:34:59,300 - INFO] Job Description: Ill-v34-R_Qiime2vsearch_221204
[2022-12-04 21:34:59,300 - INFO] Job parameters
job_id: 33ef0b0ae4e0
inputs_dir: None
data_type: QIIME2_16S_SE
map_file: <_io.TextIOWrapper name='/nephele_data/inputs/Illv34-R-Qiime2metadata_corrected.txt' mode='r' encoding='UTF-8'>
algorithms: clustering
otu_strategy: closed
otu_reference: 97
chimeras: None
phylogenetic: mafft
sepp_reference: None
taxonomy_methods: vsearch
sklearn_options: None
perc_identity: 0.97
trim_length: None
min_quality: 20
min_frequency: 2000
wurlitzer_stdout: file
wurlitzer_stderr: file
[2022-12-04 21:34:59,300 - INFO] Checking Mapfile for Gzipped inputs.
[2022-12-04 21:34:59,301 - INFO] Gzipped files listed in map file, attempting to rm .gz extension.
[2022-12-04 21:34:59,301 - INFO] Done. Attempting file decompression.
[2022-12-04 21:35:24,857 - INFO] Finished decompression.
[2022-12-04 21:35:24,858 - INFO] Starting QIIME2 16S pipeline...
[2022-12-04 21:35:24,858 - INFO] Generating manifest input file...
[2022-12-04 21:35:24,859 - INFO] Importing data. Type: QIIME2_16S_SE
[2022-12-04 23:05:57,225 - INFO] Prepare OTU reference sets for clustering...
[2022-12-04 23:05:59,948 - INFO] Running closed OTU strategy
[2022-12-05 01:20:38,915 - INFO] Exporting biom file...
[2022-12-05 01:20:43,647 - INFO] Create a phylogenetic tree: mafft with 12 threads
[2022-12-05 01:24:19,110 - INFO] Saving phylogenetic tree...
[2022-12-05 01:24:19,151 - INFO] Running Alpha rarefaction...
[2022-12-05 01:24:19,179 - INFO] Alpha rarefaction max_depth: 93196
[2022-12-05 01:25:12,443 - INFO] Taxonomy classification: vsearch...
[2022-12-05 01:25:16,236 - INFO] Running vsearch classification with 12 threads
[2022-12-05 04:50:03,541 - INFO] Exporting Taxonomy...
[2022-12-05 04:50:03,585 - INFO] Adding taxonomy and metadata into biom file...
[2022-12-05 04:50:03,838 - INFO] Making plots...
[2022-12-05 04:50:13,413 - INFO] The pipeline completed.
[2022-12-05 04:50:13,413 - INFO] 0