[2023-06-07 21:13:39,286] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:39,288] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:39,288] [INFO] DQC Reference Directory: /var/lib/cwl/stgadae5a0e-21c6-41d0-9f8b-54d77e4a2168/dqc_reference
[2023-06-07 21:13:42,874] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:42,876] [INFO] Task started: Prodigal
[2023-06-07 21:13:42,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg98b15379-c866-4648-8379-3c852b4c027b/GCA_902613335.1_AG-918-L17_genomic.fna.gz | prodigal -d GCA_902613335.1_AG-918-L17_genomic.fna/cds.fna -a GCA_902613335.1_AG-918-L17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:44,089] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:44,090] [INFO] Task started: HMMsearch
[2023-06-07 21:13:44,090] [INFO] Running command: hmmsearch --tblout GCA_902613335.1_AG-918-L17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadae5a0e-21c6-41d0-9f8b-54d77e4a2168/dqc_reference/reference_markers.hmm GCA_902613335.1_AG-918-L17_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:44,364] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:44,366] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg98b15379-c866-4648-8379-3c852b4c027b/GCA_902613335.1_AG-918-L17_genomic.fna.gz]
[2023-06-07 21:13:44,383] [INFO] Query marker FASTA was written to GCA_902613335.1_AG-918-L17_genomic.fna/markers.fasta
[2023-06-07 21:13:44,383] [INFO] Task started: Blastn
[2023-06-07 21:13:44,384] [INFO] Running command: blastn -query GCA_902613335.1_AG-918-L17_genomic.fna/markers.fasta -db /var/lib/cwl/stgadae5a0e-21c6-41d0-9f8b-54d77e4a2168/dqc_reference/reference_markers.fasta -out GCA_902613335.1_AG-918-L17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:47,404] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:47,410] [INFO] Selected 5 target genomes.
[2023-06-07 21:13:47,411] [INFO] Target genome list was writen to GCA_902613335.1_AG-918-L17_genomic.fna/target_genomes.txt
[2023-06-07 21:13:47,412] [INFO] Task started: fastANI
[2023-06-07 21:13:47,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg98b15379-c866-4648-8379-3c852b4c027b/GCA_902613335.1_AG-918-L17_genomic.fna.gz --refList GCA_902613335.1_AG-918-L17_genomic.fna/target_genomes.txt --output GCA_902613335.1_AG-918-L17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:13:50,018] [INFO] Task succeeded: fastANI
[2023-06-07 21:13:50,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadae5a0e-21c6-41d0-9f8b-54d77e4a2168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:13:50,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadae5a0e-21c6-41d0-9f8b-54d77e4a2168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:13:50,024] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:13:50,025] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:13:50,025] [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	78.714	128	232	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:13:50,027] [INFO] DFAST Taxonomy check result was written to GCA_902613335.1_AG-918-L17_genomic.fna/tc_result.tsv
[2023-06-07 21:13:50,028] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:13:50,028] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:13:50,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadae5a0e-21c6-41d0-9f8b-54d77e4a2168/dqc_reference/checkm_data
[2023-06-07 21:13:50,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:13:50,047] [INFO] Task started: CheckM
[2023-06-07 21:13:50,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902613335.1_AG-918-L17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902613335.1_AG-918-L17_genomic.fna/checkm_input GCA_902613335.1_AG-918-L17_genomic.fna/checkm_result
[2023-06-07 21:14:02,311] [INFO] Task succeeded: CheckM
[2023-06-07 21:14:02,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:14:02,336] [INFO] ===== Completeness check finished =====
[2023-06-07 21:14:02,337] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:14:02,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902613335.1_AG-918-L17_genomic.fna/markers.fasta)
[2023-06-07 21:14:02,338] [INFO] Task started: Blastn
[2023-06-07 21:14:02,338] [INFO] Running command: blastn -query GCA_902613335.1_AG-918-L17_genomic.fna/markers.fasta -db /var/lib/cwl/stgadae5a0e-21c6-41d0-9f8b-54d77e4a2168/dqc_reference/reference_markers_gtdb.fasta -out GCA_902613335.1_AG-918-L17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:14:03,082] [INFO] Task succeeded: Blastn
[2023-06-07 21:14:03,086] [INFO] Selected 7 target genomes.
[2023-06-07 21:14:03,087] [INFO] Target genome list was writen to GCA_902613335.1_AG-918-L17_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:14:03,087] [INFO] Task started: fastANI
[2023-06-07 21:14:03,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg98b15379-c866-4648-8379-3c852b4c027b/GCA_902613335.1_AG-918-L17_genomic.fna.gz --refList GCA_902613335.1_AG-918-L17_genomic.fna/target_genomes_gtdb.txt --output GCA_902613335.1_AG-918-L17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:14:04,716] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:04,725] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-07 21:14:04,725] [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_003209915.1	s__Pelagibacter sp003209915	97.9237	188	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.70	95.04	0.84	0.76	80	inconclusive
GCA_902540595.1	s__Pelagibacter sp902540595	95.0202	179	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.43	95.31	0.77	0.75	3	inconclusive
GCA_014654235.1	s__Pelagibacter sp014654235	93.2111	122	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014653985.1	s__Pelagibacter sp014653985	92.6783	202	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622795.1	s__Pelagibacter sp902622795	90.4457	178	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.61	99.61	0.85	0.85	2	-
GCA_902604525.1	s__Pelagibacter sp902604525	89.6824	168	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539165.1	s__Pelagibacter sp902539165	88.6585	166	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.84	98.84	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-07 21:14:04,727] [INFO] GTDB search result was written to GCA_902613335.1_AG-918-L17_genomic.fna/result_gtdb.tsv
[2023-06-07 21:14:04,727] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:14:04,730] [INFO] DFAST_QC result json was written to GCA_902613335.1_AG-918-L17_genomic.fna/dqc_result.json
[2023-06-07 21:14:04,730] [INFO] DFAST_QC completed!
[2023-06-07 21:14:04,730] [INFO] Total running time: 0h0m25s