[2022-11-30 22:56:07,047 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.21.5, tag: Nephele_2022_October_06, commit: c1eb66c
[2022-11-30 22:56:07,047 - INFO] Python version: 3.8.13
[2022-11-30 22:56:07,047 - INFO] Current time: 2022-11-30 22:56
[2022-11-30 22:56:07,047 - INFO] Pipeline name: QIIME2 16S
[2022-11-30 22:56:07,562 - INFO] Job Description: EM-v4_Qiime2_221130
[2022-11-30 22:56:07,563 - INFO] Job parameters
job_id: b3f3625567ec
inputs_dir: None
data_type: QIIME2_16S_SE
map_file: <_io.TextIOWrapper name='/nephele_data/inputs/EMv4-Y-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: sklearn
sklearn_options: silva_v4
perc_identity: 0.97
trim_length: None
min_quality: 20
min_frequency: 2000
wurlitzer_stdout: file
wurlitzer_stderr: file
[2022-11-30 22:56:07,563 - INFO] Checking Mapfile for Gzipped inputs.
[2022-11-30 22:56:07,563 - INFO] Gzipped files listed in map file, attempting to rm .gz extension.
[2022-11-30 22:56:07,563 - INFO] Done. Attempting file decompression.
[2022-11-30 22:56:23,734 - INFO] Finished decompression.
[2022-11-30 22:56:23,734 - INFO] Starting QIIME2 16S pipeline...
[2022-11-30 22:56:23,735 - INFO] Generating manifest input file...
[2022-11-30 22:56:23,736 - INFO] Importing data. Type: QIIME2_16S_SE
[2022-12-01 00:33:13,396 - INFO] Prepare OTU reference sets for clustering...
[2022-12-01 00:33:15,977 - INFO] Running closed OTU strategy
[2022-12-01 01:50:25,077 - INFO] Exporting biom file...
[2022-12-01 01:50:29,532 - INFO] Create a phylogenetic tree: mafft with 12 threads
[2022-12-01 01:52:52,355 - INFO] Saving phylogenetic tree...
[2022-12-01 01:52:52,398 - INFO] Running Alpha rarefaction...
[2022-12-01 01:52:52,427 - INFO] Alpha rarefaction max_depth: 180535
[2022-12-01 01:53:43,238 - INFO] Taxonomy classification: sklearn...
[2022-12-01 02:03:09,760 - INFO] Exporting Taxonomy...
[2022-12-01 02:03:09,825 - INFO] Adding taxonomy and metadata into biom file...
[2022-12-01 02:03:10,090 - INFO] Making plots...
[2022-12-01 02:03:21,458 - INFO] The pipeline completed.
[2022-12-01 02:03:21,458 - INFO] 0