[2023-06-18 21:22:02,421] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:22:02,423] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:22:02,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg6536e58a-3d4a-48a8-8315-d35910af5e9e/dqc_reference
[2023-06-18 21:22:04,570] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:22:04,571] [INFO] Task started: Prodigal
[2023-06-18 21:22:04,572] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3948cfc-63ea-469a-889e-2e1ce64c1676/GCA_018402035.1_ASM1840203v1_genomic.fna.gz | prodigal -d GCA_018402035.1_ASM1840203v1_genomic.fna/cds.fna -a GCA_018402035.1_ASM1840203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:22:14,833] [INFO] Task succeeded: Prodigal
[2023-06-18 21:22:14,834] [INFO] Task started: HMMsearch
[2023-06-18 21:22:14,834] [INFO] Running command: hmmsearch --tblout GCA_018402035.1_ASM1840203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6536e58a-3d4a-48a8-8315-d35910af5e9e/dqc_reference/reference_markers.hmm GCA_018402035.1_ASM1840203v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:22:15,084] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:22:15,086] [INFO] Found 6/6 markers.
[2023-06-18 21:22:15,120] [INFO] Query marker FASTA was written to GCA_018402035.1_ASM1840203v1_genomic.fna/markers.fasta
[2023-06-18 21:22:15,121] [INFO] Task started: Blastn
[2023-06-18 21:22:15,121] [INFO] Running command: blastn -query GCA_018402035.1_ASM1840203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6536e58a-3d4a-48a8-8315-d35910af5e9e/dqc_reference/reference_markers.fasta -out GCA_018402035.1_ASM1840203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:22:15,973] [INFO] Task succeeded: Blastn
[2023-06-18 21:22:15,977] [INFO] Selected 26 target genomes.
[2023-06-18 21:22:15,977] [INFO] Target genome list was writen to GCA_018402035.1_ASM1840203v1_genomic.fna/target_genomes.txt
[2023-06-18 21:22:15,980] [INFO] Task started: fastANI
[2023-06-18 21:22:15,980] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3948cfc-63ea-469a-889e-2e1ce64c1676/GCA_018402035.1_ASM1840203v1_genomic.fna.gz --refList GCA_018402035.1_ASM1840203v1_genomic.fna/target_genomes.txt --output GCA_018402035.1_ASM1840203v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:22:32,830] [INFO] Task succeeded: fastANI
[2023-06-18 21:22:32,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6536e58a-3d4a-48a8-8315-d35910af5e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:22:32,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6536e58a-3d4a-48a8-8315-d35910af5e9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:22:32,855] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:22:32,855] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 21:22:32,855] [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
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.7318	452	962	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9901	272	962	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.8388	301	962	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	77.7417	311	962	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	77.6446	301	962	95	below_threshold
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	77.6431	209	962	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	77.5305	276	962	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.5121	268	962	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	77.4733	241	962	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	77.4693	316	962	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.38	318	962	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.3541	306	962	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.2411	232	962	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	77.2125	218	962	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.198	203	962	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.1408	247	962	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.1321	258	962	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.1246	206	962	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.1114	205	962	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.1071	203	962	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.088	226	962	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.0856	244	962	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.9969	200	962	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.8828	202	962	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.8402	201	962	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	76.6614	170	962	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 21:22:32,859] [INFO] DFAST Taxonomy check result was written to GCA_018402035.1_ASM1840203v1_genomic.fna/tc_result.tsv
[2023-06-18 21:22:32,860] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:22:32,860] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:22:32,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6536e58a-3d4a-48a8-8315-d35910af5e9e/dqc_reference/checkm_data
[2023-06-18 21:22:32,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:22:32,894] [INFO] Task started: CheckM
[2023-06-18 21:22:32,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018402035.1_ASM1840203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018402035.1_ASM1840203v1_genomic.fna/checkm_input GCA_018402035.1_ASM1840203v1_genomic.fna/checkm_result
[2023-06-18 21:23:06,949] [INFO] Task succeeded: CheckM
[2023-06-18 21:23:06,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:23:06,978] [INFO] ===== Completeness check finished =====
[2023-06-18 21:23:06,978] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:23:06,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018402035.1_ASM1840203v1_genomic.fna/markers.fasta)
[2023-06-18 21:23:06,979] [INFO] Task started: Blastn
[2023-06-18 21:23:06,979] [INFO] Running command: blastn -query GCA_018402035.1_ASM1840203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6536e58a-3d4a-48a8-8315-d35910af5e9e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018402035.1_ASM1840203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:23:08,501] [INFO] Task succeeded: Blastn
[2023-06-18 21:23:08,508] [INFO] Selected 9 target genomes.
[2023-06-18 21:23:08,508] [INFO] Target genome list was writen to GCA_018402035.1_ASM1840203v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:23:08,516] [INFO] Task started: fastANI
[2023-06-18 21:23:08,517] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3948cfc-63ea-469a-889e-2e1ce64c1676/GCA_018402035.1_ASM1840203v1_genomic.fna.gz --refList GCA_018402035.1_ASM1840203v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018402035.1_ASM1840203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:23:14,574] [INFO] Task succeeded: fastANI
[2023-06-18 21:23:14,586] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:23:14,586] [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_018402035.1	s__Roseicyclus sp018402035	100.0	961	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015689735.1	s__Roseicyclus sp015689735	85.307	768	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401965.1	s__Roseicyclus sp018401965	80.8323	520	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	80.3628	602	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401055.1	s__Roseicyclus sp018401055	80.0568	491	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.3183	553	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	79.3174	510	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359765.1	s__Roseovarius sp014359765	77.6479	248	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	76.9152	209	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 21:23:14,589] [INFO] GTDB search result was written to GCA_018402035.1_ASM1840203v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:23:14,589] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:23:14,594] [INFO] DFAST_QC result json was written to GCA_018402035.1_ASM1840203v1_genomic.fna/dqc_result.json
[2023-06-18 21:23:14,594] [INFO] DFAST_QC completed!
[2023-06-18 21:23:14,595] [INFO] Total running time: 0h1m12s