[2023-06-04 21:50:06,418] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:50:06,422] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:50:06,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg859ed5c8-e186-4da5-ac75-44e18669a870/dqc_reference
[2023-06-04 21:50:08,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:50:08,332] [INFO] Task started: Prodigal
[2023-06-04 21:50:08,332] [INFO] Running command: gunzip -c /var/lib/cwl/stgde09b046-2d18-4e1a-a151-f6f48f5315a4/GCA_902529005.1_AG-343-A05_genomic.fna.gz | prodigal -d GCA_902529005.1_AG-343-A05_genomic.fna/cds.fna -a GCA_902529005.1_AG-343-A05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:50:10,423] [INFO] Task succeeded: Prodigal
[2023-06-04 21:50:10,423] [INFO] Task started: HMMsearch
[2023-06-04 21:50:10,423] [INFO] Running command: hmmsearch --tblout GCA_902529005.1_AG-343-A05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg859ed5c8-e186-4da5-ac75-44e18669a870/dqc_reference/reference_markers.hmm GCA_902529005.1_AG-343-A05_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:50:10,604] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:50:10,606] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgde09b046-2d18-4e1a-a151-f6f48f5315a4/GCA_902529005.1_AG-343-A05_genomic.fna.gz]
[2023-06-04 21:50:10,623] [INFO] Query marker FASTA was written to GCA_902529005.1_AG-343-A05_genomic.fna/markers.fasta
[2023-06-04 21:50:10,624] [INFO] Task started: Blastn
[2023-06-04 21:50:10,624] [INFO] Running command: blastn -query GCA_902529005.1_AG-343-A05_genomic.fna/markers.fasta -db /var/lib/cwl/stg859ed5c8-e186-4da5-ac75-44e18669a870/dqc_reference/reference_markers.fasta -out GCA_902529005.1_AG-343-A05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:50:12,166] [INFO] Task succeeded: Blastn
[2023-06-04 21:50:12,171] [INFO] Selected 3 target genomes.
[2023-06-04 21:50:12,171] [INFO] Target genome list was writen to GCA_902529005.1_AG-343-A05_genomic.fna/target_genomes.txt
[2023-06-04 21:50:12,187] [INFO] Task started: fastANI
[2023-06-04 21:50:12,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgde09b046-2d18-4e1a-a151-f6f48f5315a4/GCA_902529005.1_AG-343-A05_genomic.fna.gz --refList GCA_902529005.1_AG-343-A05_genomic.fna/target_genomes.txt --output GCA_902529005.1_AG-343-A05_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:50:13,311] [INFO] Task succeeded: fastANI
[2023-06-04 21:50:13,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg859ed5c8-e186-4da5-ac75-44e18669a870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:50:13,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg859ed5c8-e186-4da5-ac75-44e18669a870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:50:13,318] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:50:13,318] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:50:13,318] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	78.4444	96	242	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:50:13,320] [INFO] DFAST Taxonomy check result was written to GCA_902529005.1_AG-343-A05_genomic.fna/tc_result.tsv
[2023-06-04 21:50:13,321] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:50:13,321] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:50:13,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg859ed5c8-e186-4da5-ac75-44e18669a870/dqc_reference/checkm_data
[2023-06-04 21:50:13,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:50:13,336] [INFO] Task started: CheckM
[2023-06-04 21:50:13,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902529005.1_AG-343-A05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902529005.1_AG-343-A05_genomic.fna/checkm_input GCA_902529005.1_AG-343-A05_genomic.fna/checkm_result
[2023-06-04 21:50:27,331] [INFO] Task succeeded: CheckM
[2023-06-04 21:50:27,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:50:27,353] [INFO] ===== Completeness check finished =====
[2023-06-04 21:50:27,354] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:50:27,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902529005.1_AG-343-A05_genomic.fna/markers.fasta)
[2023-06-04 21:50:27,355] [INFO] Task started: Blastn
[2023-06-04 21:50:27,355] [INFO] Running command: blastn -query GCA_902529005.1_AG-343-A05_genomic.fna/markers.fasta -db /var/lib/cwl/stg859ed5c8-e186-4da5-ac75-44e18669a870/dqc_reference/reference_markers_gtdb.fasta -out GCA_902529005.1_AG-343-A05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:50:27,949] [INFO] Task succeeded: Blastn
[2023-06-04 21:50:27,954] [INFO] Selected 10 target genomes.
[2023-06-04 21:50:27,954] [INFO] Target genome list was writen to GCA_902529005.1_AG-343-A05_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:50:27,984] [INFO] Task started: fastANI
[2023-06-04 21:50:27,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgde09b046-2d18-4e1a-a151-f6f48f5315a4/GCA_902529005.1_AG-343-A05_genomic.fna.gz --refList GCA_902529005.1_AG-343-A05_genomic.fna/target_genomes_gtdb.txt --output GCA_902529005.1_AG-343-A05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:50:29,927] [INFO] Task succeeded: fastANI
[2023-06-04 21:50:29,936] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:50:29,937] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902588255.1	s__Pelagibacter sp902588255	97.2701	150	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902582105.1	s__Pelagibacter sp902582105	90.9629	159	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557385.1	s__Pelagibacter sp902557385	90.2044	148	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.96	96.64	0.74	0.67	3	-
GCA_902608975.1	s__Pelagibacter sp902608975	87.3371	157	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588635.1	s__Pelagibacter sp902588635	85.0305	115	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569405.1	s__Pelagibacter sp902569405	84.919	185	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902564565.1	s__Pelagibacter sp902564565	84.4401	168	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902564265.1	s__Pelagibacter sp902564265	77.8699	63	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902553695.1	s__Pelagibacter sp902553695	77.6	54	242	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:50:29,939] [INFO] GTDB search result was written to GCA_902529005.1_AG-343-A05_genomic.fna/result_gtdb.tsv
[2023-06-04 21:50:29,940] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:50:29,943] [INFO] DFAST_QC result json was written to GCA_902529005.1_AG-343-A05_genomic.fna/dqc_result.json
[2023-06-04 21:50:29,943] [INFO] DFAST_QC completed!
[2023-06-04 21:50:29,943] [INFO] Total running time: 0h0m24s