[2024-01-24 10:57:11,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:11,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:11,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f805e8b-b58a-401f-ab15-54e1ea32db69/dqc_reference
[2024-01-24 10:57:12,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:12,940] [INFO] Task started: Prodigal
[2024-01-24 10:57:12,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg53c01bb5-770c-4ce1-8675-196fcfcf5daa/GCF_002834145.1_ASM283414v1_genomic.fna.gz | prodigal -d GCF_002834145.1_ASM283414v1_genomic.fna/cds.fna -a GCF_002834145.1_ASM283414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:23,419] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:23,420] [INFO] Task started: HMMsearch
[2024-01-24 10:57:23,420] [INFO] Running command: hmmsearch --tblout GCF_002834145.1_ASM283414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f805e8b-b58a-401f-ab15-54e1ea32db69/dqc_reference/reference_markers.hmm GCF_002834145.1_ASM283414v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:23,708] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:23,709] [INFO] Found 6/6 markers.
[2024-01-24 10:57:23,758] [INFO] Query marker FASTA was written to GCF_002834145.1_ASM283414v1_genomic.fna/markers.fasta
[2024-01-24 10:57:23,759] [INFO] Task started: Blastn
[2024-01-24 10:57:23,759] [INFO] Running command: blastn -query GCF_002834145.1_ASM283414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f805e8b-b58a-401f-ab15-54e1ea32db69/dqc_reference/reference_markers.fasta -out GCF_002834145.1_ASM283414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:24,817] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:24,821] [INFO] Selected 25 target genomes.
[2024-01-24 10:57:24,822] [INFO] Target genome list was writen to GCF_002834145.1_ASM283414v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:24,873] [INFO] Task started: fastANI
[2024-01-24 10:57:24,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg53c01bb5-770c-4ce1-8675-196fcfcf5daa/GCF_002834145.1_ASM283414v1_genomic.fna.gz --refList GCF_002834145.1_ASM283414v1_genomic.fna/target_genomes.txt --output GCF_002834145.1_ASM283414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:47,156] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:47,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f805e8b-b58a-401f-ab15-54e1ea32db69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:47,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f805e8b-b58a-401f-ab15-54e1ea32db69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:47,176] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:47,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:47,177] [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 nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	79.3209	563	1108	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.3109	602	1108	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.3039	597	1108	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	79.2418	602	1108	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	79.2244	454	1108	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.1693	524	1108	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.1365	526	1108	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.1285	531	1108	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.1034	535	1108	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.9902	515	1108	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.9582	514	1108	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.8734	518	1108	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.405	436	1108	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	78.3528	404	1108	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.3444	432	1108	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.3104	420	1108	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.3	436	1108	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.2963	443	1108	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.2689	443	1108	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.0369	451	1108	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.0111	376	1108	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.971	396	1108	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9469	376	1108	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.8097	379	1108	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.7344	334	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:47,179] [INFO] DFAST Taxonomy check result was written to GCF_002834145.1_ASM283414v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:47,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:47,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:47,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f805e8b-b58a-401f-ab15-54e1ea32db69/dqc_reference/checkm_data
[2024-01-24 10:57:47,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:47,216] [INFO] Task started: CheckM
[2024-01-24 10:57:47,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002834145.1_ASM283414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002834145.1_ASM283414v1_genomic.fna/checkm_input GCF_002834145.1_ASM283414v1_genomic.fna/checkm_result
[2024-01-24 10:58:38,492] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:38,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:38,513] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:38,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:38,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002834145.1_ASM283414v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:38,514] [INFO] Task started: Blastn
[2024-01-24 10:58:38,514] [INFO] Running command: blastn -query GCF_002834145.1_ASM283414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f805e8b-b58a-401f-ab15-54e1ea32db69/dqc_reference/reference_markers_gtdb.fasta -out GCF_002834145.1_ASM283414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:40,486] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:40,490] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:40,490] [INFO] Target genome list was writen to GCF_002834145.1_ASM283414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:40,504] [INFO] Task started: fastANI
[2024-01-24 10:58:40,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg53c01bb5-770c-4ce1-8675-196fcfcf5daa/GCF_002834145.1_ASM283414v1_genomic.fna.gz --refList GCF_002834145.1_ASM283414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002834145.1_ASM283414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:53,741] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:53,759] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:53,759] [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_002834145.1	s__Roseovarius salinarum	100.0	1103	1108	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_002166865.1	s__Roseovarius sp002166865	81.5978	683	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	79.5174	538	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	79.4802	566	1108	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	79.3307	562	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_008728195.1	s__Roseovarius indicus	79.3196	596	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_002094885.1	s__Salibaculum halophilum	79.2143	456	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.1602	525	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900172255.1	s__Roseovarius halotolerans	79.1113	533	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107235.1	s__Citreimonas salinaria	79.0455	507	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	79.0243	381	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	78.9992	514	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_003260265.1	s__Roseovarius sp003260265	78.9268	533	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.8898	517	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	78.622	357	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	78.4747	328	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.3367	433	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	77.8755	388	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:53,764] [INFO] GTDB search result was written to GCF_002834145.1_ASM283414v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:53,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:53,769] [INFO] DFAST_QC result json was written to GCF_002834145.1_ASM283414v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:53,769] [INFO] DFAST_QC completed!
[2024-01-24 10:58:53,769] [INFO] Total running time: 0h1m42s