[2023-04-01 05:44:57,139 - INFO] Nephele, developed by BCBB/OCICB/NIAID/NIH version: 2.23.4, tag: Nephele_2023_March_28, commit: d9e1ff4
[2023-04-01 05:44:57,140 - INFO] Python version: 3.8.13
[2023-04-01 05:44:57,140 - INFO] Current time: 2023-04-01 05:44
[2023-04-01 05:44:57,140 - INFO] Pipeline name: QIIME2 16S
[2023-04-01 05:44:57,453 - INFO] Job Description: GIW23-testRun1-defaultQiime2
[2023-04-01 05:44:57,454 - INFO] Job parameters
job_id: 730cbe0e4737
inputs_dir: None
data_type: QIIME2_16S_SE
map_file: <_io.TextIOWrapper name='/nephele_data/inputs/testPool1_QIIME2_16S_pipeline_template_single_end_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
[2023-04-01 05:44:57,454 - INFO] Checking Mapfile for Gzipped inputs.
[2023-04-01 05:44:57,454 - INFO] Gzipped files listed in map file, attempting to rm .gz extension.
[2023-04-01 05:44:57,454 - INFO] Done. Attempting file decompression.
[2023-04-01 05:45:00,134 - INFO] Finished decompression.
[2023-04-01 05:45:00,134 - INFO] Skipping FASTQ file validation
[2023-04-01 05:45:00,134 - INFO] Starting QIIME2 16S pipeline...
[2023-04-01 05:45:00,135 - INFO] Generating manifest input file...
[2023-04-01 05:45:00,136 - INFO] Importing data. Type: QIIME2_16S_SE
[2023-04-01 05:58:21,748 - INFO] Prepare OTU reference sets for clustering...
[2023-04-01 05:58:24,220 - INFO] Running closed OTU strategy
[2023-04-01 07:26:27,262 - INFO] Exporting biom file...
[2023-04-01 07:26:28,293 - INFO] Create a phylogenetic tree: mafft with 12 threads
[2023-04-01 07:26:52,583 - INFO] Saving phylogenetic tree...
[2023-04-01 07:26:52,600 - INFO] Running Alpha rarefaction...
[2023-04-01 07:26:52,614 - INFO] Alpha rarefaction max_depth: 9468
[2023-04-01 07:27:19,256 - INFO] Taxonomy classification: sklearn...
[2023-04-01 07:31:40,129 - INFO] Exporting Taxonomy...
[2023-04-01 07:31:40,159 - INFO] Adding taxonomy and metadata into biom file...
[2023-04-01 07:31:40,228 - INFO] Generating feature-table.tsv from BIOM file...
[2023-04-01 07:31:40,987 - INFO] Making plots...
[2023-04-01 07:31:43,462 - INFO] The pipeline completed.
[2023-04-01 07:31:43,462 - INFO] 0