2024-01-11 13:42:54 pipits_process started
2024-01-11 13:42:54 Downloading UNITE trained database, version: 27.10.2022
2024-01-11 13:48:38 ... Unpacking
2024-01-11 13:48:51 ... done
2024-01-11 13:48:51 Downloading database for SINTAX
2024-01-11 13:49:24 ... Unpacking
2024-01-11 13:49:25 ... done
2024-01-11 13:49:25 Downloading WARCUP trained database: 
2024-01-11 13:49:46 ... Unpacking
2024-01-11 13:49:47 ... done
2024-01-11 13:49:47 Downloading UCHIME database for chimera filtering: 
2024-01-11 13:49:55 ... Unpacking
2024-01-11 13:49:55 ... done
2024-01-11 13:49:55 Dereplicating and removing unique sequences prior to picking OTUs
vsearch v2.26.1_linux_x86_64, 15.5GB RAM, 12 cores
https://github.com/torognes/vsearch

Dereplicating file funits_out/ITS.fasta 100%
882802030 nt in 3525785 seqs, min 100, max 482, avg 250
Sorting 100%
307813 unique sequences, avg cluster 11.5, median 1, max 146595
Writing FASTA output file 100%
2024-01-11 13:49:59 Picking OTUs [VSEARCH]
vsearch v2.26.1_linux_x86_64, 15.5GB RAM, 12 cores
https://github.com/torognes/vsearch

Reading file process_out/intermediate/input_nr.fasta 100%
84061458 nt in 307813 seqs, min 100, max 482, avg 273
Masking 100%
Sorting by length 100%
Counting k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 18750 Size min 1, max 11914, avg 16.4
Singletons: 13416, 4.4% of seqs, 71.6% of clusters
2024-01-11 13:50:33 Removing chimeras [VSEARCH]
vsearch v2.26.1_linux_x86_64, 15.5GB RAM, 12 cores
https://github.com/torognes/vsearch

Reading file pipits_db/uchime_reference_dataset_28.06.2017/uchime_reference_dataset_28.06.2017.fasta 100%
16786547 nt in 30555 seqs, min 146, max 2570, avg 549
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Detecting chimeras 100%
Found 96 (0.5%) chimeras, 18638 (99.4%) non-chimeras,
and 16 (0.1%) borderline sequences in 18750 unique sequences.
Taking abundance information into account, this corresponds to
7322 (1.8%) chimeras, 402368 (98.2%) non-chimeras,
and 156 (0.0%) borderline sequences in 409846 total sequences.
2024-01-11 13:50:39 Renaming OTUs
2024-01-11 13:50:39 Mapping reads onto centroids [VSEARCH]
vsearch v2.26.1_linux_x86_64, 15.5GB RAM, 12 cores
https://github.com/torognes/vsearch

Reading file process_out/intermediate/input_nr_otus_nonchimeras_relabelled.fasta 100%
4421074 nt in 18638 seqs, min 100, max 482, avg 237
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching 100%
Matching unique query sequences: 3514479 of 3525785 (99.68%)
2024-01-11 13:54:55 Making OTU table
2024-01-11 13:55:04 Converting classic tabular OTU into a BIOM format [BIOM]
2024-01-11 13:55:10 Assigning taxonomy with VSEARCH-SINTAX [VSEARCH]
vsearch v2.26.1_linux_x86_64, 15.5GB RAM, 12 cores
https://github.com/torognes/vsearch

Reading file pipits_db/UNITE_retrained_27.10.2022.sintax.fa/UNITE_retrained_27.10.2022.sintax.fa 100%
189392914 nt in 326300 seqs, min 140, max 1501, avg 580
Counting k-mers 100%
Creating k-mer index 100%
Classifying sequences 100%
Classified 14934 of 18638 sequences (80.13%)
2024-01-11 13:56:57 Adding SINTAX assignment to OTU table [BIOM]
2024-01-11 13:56:58 Converting OTU table with taxa assignment into a BIOM format [BIOM]
2024-01-11 13:57:00 Phylotyping OTU table
2024-01-11 13:57:04 Assigning taxonomy with UNITE [RDP Classifier]
2024-01-11 16:16:51 Error: None zero returncode: classifier -Xms4g -Xmx16g classify -t pipits_db/UNITE_retrained_27.10.2022/UNITE_retrained/rRNAClassifier.properties -o process_out/assigned_taxonomy_rdp_raw.txt process_out/intermed
iate/input_nr_otus_nonchimeras_relabelled.fasta