[2024-01-24 14:39:15,641] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,643] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg2297d35a-0237-4b63-8637-44b77a71f176/dqc_reference
[2024-01-24 14:39:18,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:18,583] [INFO] Task started: Prodigal
[2024-01-24 14:39:18,583] [INFO] Running command: gunzip -c /var/lib/cwl/stgda87ba63-5293-4ea2-bf6a-f8fd80303882/GCF_900445995.1_48290_B02_genomic.fna.gz | prodigal -d GCF_900445995.1_48290_B02_genomic.fna/cds.fna -a GCF_900445995.1_48290_B02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:28,563] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:28,564] [INFO] Task started: HMMsearch
[2024-01-24 14:39:28,564] [INFO] Running command: hmmsearch --tblout GCF_900445995.1_48290_B02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2297d35a-0237-4b63-8637-44b77a71f176/dqc_reference/reference_markers.hmm GCF_900445995.1_48290_B02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:28,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:28,830] [INFO] Found 6/6 markers.
[2024-01-24 14:39:28,867] [INFO] Query marker FASTA was written to GCF_900445995.1_48290_B02_genomic.fna/markers.fasta
[2024-01-24 14:39:28,867] [INFO] Task started: Blastn
[2024-01-24 14:39:28,867] [INFO] Running command: blastn -query GCF_900445995.1_48290_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stg2297d35a-0237-4b63-8637-44b77a71f176/dqc_reference/reference_markers.fasta -out GCF_900445995.1_48290_B02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:29,747] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:29,751] [INFO] Selected 15 target genomes.
[2024-01-24 14:39:29,751] [INFO] Target genome list was writen to GCF_900445995.1_48290_B02_genomic.fna/target_genomes.txt
[2024-01-24 14:39:29,764] [INFO] Task started: fastANI
[2024-01-24 14:39:29,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgda87ba63-5293-4ea2-bf6a-f8fd80303882/GCF_900445995.1_48290_B02_genomic.fna.gz --refList GCF_900445995.1_48290_B02_genomic.fna/target_genomes.txt --output GCF_900445995.1_48290_B02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:41,107] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:41,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2297d35a-0237-4b63-8637-44b77a71f176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:41,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2297d35a-0237-4b63-8637-44b77a71f176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:41,123] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:41,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:41,124] [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
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	100.0	1144	1145	95	conclusive
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	99.7115	1115	1145	95	conclusive
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	90.209	827	1145	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	89.8912	786	1145	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	87.088	818	1145	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	83.0845	667	1145	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	82.7938	673	1145	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	80.4012	503	1145	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.3123	522	1145	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.0853	402	1145	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	76.6419	102	1145	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.6185	105	1145	95	below_threshold
Aurantiacibacter arachoides	strain=CGMCC 1.15507	GCA_014643415.1	1850444	1850444	type	True	76.5248	91	1145	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	76.3773	125	1145	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	76.3402	138	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:41,126] [INFO] DFAST Taxonomy check result was written to GCF_900445995.1_48290_B02_genomic.fna/tc_result.tsv
[2024-01-24 14:39:41,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:41,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:41,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2297d35a-0237-4b63-8637-44b77a71f176/dqc_reference/checkm_data
[2024-01-24 14:39:41,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:41,174] [INFO] Task started: CheckM
[2024-01-24 14:39:41,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445995.1_48290_B02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445995.1_48290_B02_genomic.fna/checkm_input GCF_900445995.1_48290_B02_genomic.fna/checkm_result
[2024-01-24 14:40:13,041] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:13,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,071] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:13,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:13,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445995.1_48290_B02_genomic.fna/markers.fasta)
[2024-01-24 14:40:13,073] [INFO] Task started: Blastn
[2024-01-24 14:40:13,073] [INFO] Running command: blastn -query GCF_900445995.1_48290_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stg2297d35a-0237-4b63-8637-44b77a71f176/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445995.1_48290_B02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:14,657] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:14,661] [INFO] Selected 14 target genomes.
[2024-01-24 14:40:14,661] [INFO] Target genome list was writen to GCF_900445995.1_48290_B02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:14,685] [INFO] Task started: fastANI
[2024-01-24 14:40:14,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgda87ba63-5293-4ea2-bf6a-f8fd80303882/GCF_900445995.1_48290_B02_genomic.fna.gz --refList GCF_900445995.1_48290_B02_genomic.fna/target_genomes_gtdb.txt --output GCF_900445995.1_48290_B02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:26,618] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:26,632] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:26,633] [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_000204035.1	s__Brevundimonas diminuta	99.7115	1115	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.62	95.74	0.88	0.81	19	conclusive
GCA_002430835.1	s__Brevundimonas sp002430835	94.1466	761	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.55	99.55	0.86	0.86	2	-
GCF_003938605.1	s__Brevundimonas sp003938605	93.4711	870	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.78	96.68	0.85	0.83	3	-
GCF_900163625.1	s__Brevundimonas diminuta_A	92.8708	877	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002386585.1	s__Brevundimonas sp002386585	92.0176	705	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.28	96.28	0.79	0.79	2	-
GCA_017308115.1	s__Brevundimonas sp017308115	91.262	738	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000318405.1	s__Brevundimonas diminuta_B	90.764	828	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.76	96.50	0.85	0.82	10	-
GCF_000635915.2	s__Brevundimonas naejangsanensis_A	90.3566	795	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.68	97.40	0.91	0.88	5	-
GCF_000421705.1	s__Brevundimonas naejangsanensis	90.219	827	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.43	97.43	0.89	0.89	2	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	89.7733	791	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	81.7609	605	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116065.1	s__Brevundimonas viscosa	81.392	597	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419815.1	s__Brevundimonas sp002419815	80.5821	556	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724985.1	s__Phenylobacterium sp001724985	79.1647	304	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:26,635] [INFO] GTDB search result was written to GCF_900445995.1_48290_B02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:26,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:26,639] [INFO] DFAST_QC result json was written to GCF_900445995.1_48290_B02_genomic.fna/dqc_result.json
[2024-01-24 14:40:26,639] [INFO] DFAST_QC completed!
[2024-01-24 14:40:26,639] [INFO] Total running time: 0h1m11s