[2024-01-24 14:28:18,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg8929ed9d-5cb6-40e3-95e0-4b12d60f93e1/dqc_reference
[2024-01-24 14:28:20,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,481] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg262eb6c5-4587-4cf1-a92e-5e51daeebd3d/GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/cds.fna -a GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:33,332] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:33,332] [INFO] Task started: HMMsearch
[2024-01-24 14:28:33,332] [INFO] Running command: hmmsearch --tblout GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8929ed9d-5cb6-40e3-95e0-4b12d60f93e1/dqc_reference/reference_markers.hmm GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:33,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:33,642] [INFO] Found 6/6 markers.
[2024-01-24 14:28:33,680] [INFO] Query marker FASTA was written to GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:28:33,681] [INFO] Task started: Blastn
[2024-01-24 14:28:33,681] [INFO] Running command: blastn -query GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8929ed9d-5cb6-40e3-95e0-4b12d60f93e1/dqc_reference/reference_markers.fasta -out GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:34,656] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:34,659] [INFO] Selected 19 target genomes.
[2024-01-24 14:28:34,660] [INFO] Target genome list was writen to GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:28:34,667] [INFO] Task started: fastANI
[2024-01-24 14:28:34,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg262eb6c5-4587-4cf1-a92e-5e51daeebd3d/GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna.gz --refList GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:51,671] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:51,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8929ed9d-5cb6-40e3-95e0-4b12d60f93e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:51,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8929ed9d-5cb6-40e3-95e0-4b12d60f93e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:51,689] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:51,689] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:51,689] [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
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	100.0	1262	1262	95	conclusive
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	81.801	769	1262	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	81.698	741	1262	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	80.6363	685	1262	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	80.2169	660	1262	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	79.9398	672	1262	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	79.9208	669	1262	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.7766	580	1262	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.7392	583	1262	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.4511	592	1262	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.3238	579	1262	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	79.3042	486	1262	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.1161	524	1262	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.5675	415	1262	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4511	417	1262	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.2589	496	1262	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.1262	317	1262	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.7193	131	1262	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6974	252	1262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:51,691] [INFO] DFAST Taxonomy check result was written to GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:28:51,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:51,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:51,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8929ed9d-5cb6-40e3-95e0-4b12d60f93e1/dqc_reference/checkm_data
[2024-01-24 14:28:51,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:51,740] [INFO] Task started: CheckM
[2024-01-24 14:28:51,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/checkm_input GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:29:31,767] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:31,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:31,787] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:31,787] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:31,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:29:31,788] [INFO] Task started: Blastn
[2024-01-24 14:29:31,788] [INFO] Running command: blastn -query GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8929ed9d-5cb6-40e3-95e0-4b12d60f93e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:33,578] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:33,582] [INFO] Selected 15 target genomes.
[2024-01-24 14:29:33,582] [INFO] Target genome list was writen to GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:33,593] [INFO] Task started: fastANI
[2024-01-24 14:29:33,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg262eb6c5-4587-4cf1-a92e-5e51daeebd3d/GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna.gz --refList GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:46,891] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:46,904] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:46,904] [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_900109455.1	s__Roseovarius azorensis	100.0	1262	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002783205.1	s__Roseovarius sp002783205	82.8349	750	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.90	99.90	0.93	0.93	2	-
GCF_000744325.1	s__Roseovarius sp000744325	81.9227	757	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768555.3	s__Roseovarius mucosus	81.8189	767	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.95	96.93	0.91	0.89	3	-
GCA_018066915.1	s__Roseovarius sp018066915	81.7491	674	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_900109855.1	s__Roseovarius tolerans	81.7076	740	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_000152845.1	s__Roseovarius sp000152845	81.5322	772	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.99	97.99	0.83	0.83	2	-
GCF_002072155.1	s__Roseovarius sp002072155	81.5227	733	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080415.1	s__Roseovarius mucosus_A	81.2121	752	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCA_002720475.1	s__Roseovarius sp002720475	80.8751	482	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_014359765.1	s__Roseovarius sp014359765	80.7997	548	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	80.7382	542	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002925845.1	s__Roseovarius nitratireducens	80.6469	683	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_900142665.1	s__Roseovarius pacificus	79.7422	584	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_003072125.1	s__Roseovarius sediminicola	79.2966	488	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:46,906] [INFO] GTDB search result was written to GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:46,907] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:46,912] [INFO] DFAST_QC result json was written to GCF_900109455.1_IMG-taxon_2693429884_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:29:46,912] [INFO] DFAST_QC completed!
[2024-01-24 14:29:46,912] [INFO] Total running time: 0h1m29s