[2024-01-24 13:49:00,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2942926-c2fc-4139-9879-c57771e96483/dqc_reference
[2024-01-24 13:49:01,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,550] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e1a0e1f-88d7-4174-89a8-862eb0f0d856/GCF_001620265.1_ASM162026v1_genomic.fna.gz | prodigal -d GCF_001620265.1_ASM162026v1_genomic.fna/cds.fna -a GCF_001620265.1_ASM162026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:16,926] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:16,926] [INFO] Task started: HMMsearch
[2024-01-24 13:49:16,927] [INFO] Running command: hmmsearch --tblout GCF_001620265.1_ASM162026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2942926-c2fc-4139-9879-c57771e96483/dqc_reference/reference_markers.hmm GCF_001620265.1_ASM162026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:17,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:17,222] [INFO] Found 6/6 markers.
[2024-01-24 13:49:17,271] [INFO] Query marker FASTA was written to GCF_001620265.1_ASM162026v1_genomic.fna/markers.fasta
[2024-01-24 13:49:17,272] [INFO] Task started: Blastn
[2024-01-24 13:49:17,272] [INFO] Running command: blastn -query GCF_001620265.1_ASM162026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2942926-c2fc-4139-9879-c57771e96483/dqc_reference/reference_markers.fasta -out GCF_001620265.1_ASM162026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:18,210] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:18,213] [INFO] Selected 10 target genomes.
[2024-01-24 13:49:18,213] [INFO] Target genome list was writen to GCF_001620265.1_ASM162026v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:18,218] [INFO] Task started: fastANI
[2024-01-24 13:49:18,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e1a0e1f-88d7-4174-89a8-862eb0f0d856/GCF_001620265.1_ASM162026v1_genomic.fna.gz --refList GCF_001620265.1_ASM162026v1_genomic.fna/target_genomes.txt --output GCF_001620265.1_ASM162026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:28,721] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:28,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2942926-c2fc-4139-9879-c57771e96483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:28,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2942926-c2fc-4139-9879-c57771e96483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:28,731] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:28,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:28,731] [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
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	100.0	1661	1661	95	conclusive
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	89.9873	1088	1661	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	89.9444	1085	1661	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	89.9441	1085	1661	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	89.9413	1075	1661	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.466	607	1661	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.4487	585	1661	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.1672	631	1661	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.1466	551	1661	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.9424	512	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:28,733] [INFO] DFAST Taxonomy check result was written to GCF_001620265.1_ASM162026v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:28,734] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:28,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:28,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2942926-c2fc-4139-9879-c57771e96483/dqc_reference/checkm_data
[2024-01-24 13:49:28,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:28,786] [INFO] Task started: CheckM
[2024-01-24 13:49:28,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001620265.1_ASM162026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001620265.1_ASM162026v1_genomic.fna/checkm_input GCF_001620265.1_ASM162026v1_genomic.fna/checkm_result
[2024-01-24 13:50:23,233] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:23,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:23,263] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:23,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:23,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001620265.1_ASM162026v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:23,264] [INFO] Task started: Blastn
[2024-01-24 13:50:23,265] [INFO] Running command: blastn -query GCF_001620265.1_ASM162026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2942926-c2fc-4139-9879-c57771e96483/dqc_reference/reference_markers_gtdb.fasta -out GCF_001620265.1_ASM162026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:25,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:25,005] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:25,005] [INFO] Target genome list was writen to GCF_001620265.1_ASM162026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:25,041] [INFO] Task started: fastANI
[2024-01-24 13:50:25,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e1a0e1f-88d7-4174-89a8-862eb0f0d856/GCF_001620265.1_ASM162026v1_genomic.fna.gz --refList GCF_001620265.1_ASM162026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001620265.1_ASM162026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:37,367] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:37,383] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:37,384] [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
GCF_001620265.1	s__Frigidibacter mobilis	100.0	1661	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009908165.1	s__Frigidibacter albus	89.9736	1072	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCA_002423245.1	s__Frigidibacter sp002423245	86.5292	745	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCF_003993775.1	s__Frigidibacter sp003993775	82.1125	792	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	79.7816	586	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCA_016124615.1	s__Solirhodobacter sp016124615	79.6416	633	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	79.623	630	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCA_017599285.1	s__Cereibacter_A azotoformans	79.5867	525	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCF_003034995.1	s__Phaeovulum veldkampii	79.5217	563	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_000622145.1	s__Paracoccus yeei	79.1777	558	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCA_002356635.1	s__QY30 sp002356635	79.1371	539	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QY30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	78.9506	564	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	78.8149	546	1661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,386] [INFO] GTDB search result was written to GCF_001620265.1_ASM162026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:37,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:37,389] [INFO] DFAST_QC result json was written to GCF_001620265.1_ASM162026v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:37,390] [INFO] DFAST_QC completed!
[2024-01-24 13:50:37,390] [INFO] Total running time: 0h1m37s