[2024-01-24 15:10:54,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:54,145] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:54,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c0c04cd-e25f-4e53-b939-c6d3e519da93/dqc_reference
[2024-01-24 15:10:56,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,637] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg31730093-a3a0-40ef-8482-0b0d44168e8f/GCF_003634925.1_ASM363492v1_genomic.fna.gz | prodigal -d GCF_003634925.1_ASM363492v1_genomic.fna/cds.fna -a GCF_003634925.1_ASM363492v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:08,860] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:08,860] [INFO] Task started: HMMsearch
[2024-01-24 15:11:08,860] [INFO] Running command: hmmsearch --tblout GCF_003634925.1_ASM363492v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c0c04cd-e25f-4e53-b939-c6d3e519da93/dqc_reference/reference_markers.hmm GCF_003634925.1_ASM363492v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:09,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:09,138] [INFO] Found 6/6 markers.
[2024-01-24 15:11:09,171] [INFO] Query marker FASTA was written to GCF_003634925.1_ASM363492v1_genomic.fna/markers.fasta
[2024-01-24 15:11:09,172] [INFO] Task started: Blastn
[2024-01-24 15:11:09,172] [INFO] Running command: blastn -query GCF_003634925.1_ASM363492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c0c04cd-e25f-4e53-b939-c6d3e519da93/dqc_reference/reference_markers.fasta -out GCF_003634925.1_ASM363492v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:10,101] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:10,106] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:10,106] [INFO] Target genome list was writen to GCF_003634925.1_ASM363492v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:10,130] [INFO] Task started: fastANI
[2024-01-24 15:11:10,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg31730093-a3a0-40ef-8482-0b0d44168e8f/GCF_003634925.1_ASM363492v1_genomic.fna.gz --refList GCF_003634925.1_ASM363492v1_genomic.fna/target_genomes.txt --output GCF_003634925.1_ASM363492v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:23,850] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:23,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c0c04cd-e25f-4e53-b939-c6d3e519da93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:23,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c0c04cd-e25f-4e53-b939-c6d3e519da93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:23,868] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:23,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:23,868] [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 halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	100.0	1232	1233	95	conclusive
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	99.9999	1231	1233	95	conclusive
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	82.5614	753	1233	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	82.3498	765	1233	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	82.3191	769	1233	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	80.0471	619	1233	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	79.9136	590	1233	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	79.6335	570	1233	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.3402	569	1233	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.9637	432	1233	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.5149	450	1233	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.4878	460	1233	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.4477	398	1233	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.3801	375	1233	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	78.3271	324	1233	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7921	297	1233	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.743	391	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:23,870] [INFO] DFAST Taxonomy check result was written to GCF_003634925.1_ASM363492v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:23,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:23,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:23,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c0c04cd-e25f-4e53-b939-c6d3e519da93/dqc_reference/checkm_data
[2024-01-24 15:11:23,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:23,910] [INFO] Task started: CheckM
[2024-01-24 15:11:23,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634925.1_ASM363492v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634925.1_ASM363492v1_genomic.fna/checkm_input GCF_003634925.1_ASM363492v1_genomic.fna/checkm_result
[2024-01-24 15:12:04,895] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:04,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:04,922] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:04,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:04,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634925.1_ASM363492v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:04,923] [INFO] Task started: Blastn
[2024-01-24 15:12:04,924] [INFO] Running command: blastn -query GCF_003634925.1_ASM363492v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c0c04cd-e25f-4e53-b939-c6d3e519da93/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634925.1_ASM363492v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:06,567] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:06,572] [INFO] Selected 15 target genomes.
[2024-01-24 15:12:06,572] [INFO] Target genome list was writen to GCF_003634925.1_ASM363492v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:06,585] [INFO] Task started: fastANI
[2024-01-24 15:12:06,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg31730093-a3a0-40ef-8482-0b0d44168e8f/GCF_003634925.1_ASM363492v1_genomic.fna.gz --refList GCF_003634925.1_ASM363492v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634925.1_ASM363492v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:19,829] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:19,846] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:19,846] [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_900172255.1	s__Roseovarius halotolerans	99.9999	1231	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900142765.1	s__Roseovarius litoreus	82.5539	754	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_900142665.1	s__Roseovarius pacificus	82.3396	766	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_008728195.1	s__Roseovarius indicus	80.7499	693	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.5846	648	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002917925.1	s__Roseovarius confluentis	80.0561	618	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_009669325.1	s__Roseovarius bejariae	79.9152	589	1233	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	79.6874	582	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011601345.1	s__Roseovarius gahaiensis	79.6333	570	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	79.3501	583	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.2813	524	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002834145.1	s__Roseovarius salinarum	79.056	540	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	77.9415	425	1233	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	77.8608	361	1233	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	77.6811	286	1233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:19,848] [INFO] GTDB search result was written to GCF_003634925.1_ASM363492v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:19,849] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:19,852] [INFO] DFAST_QC result json was written to GCF_003634925.1_ASM363492v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:19,853] [INFO] DFAST_QC completed!
[2024-01-24 15:12:19,853] [INFO] Total running time: 0h1m26s