[2024-01-24 11:43:25,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,083] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd6ab4cc-c808-403f-b9c9-821926751e6d/dqc_reference
[2024-01-24 11:43:30,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,057] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg507f05da-de78-4958-8dcf-640124a0c27c/GCF_010614805.1_ASM1061480v1_genomic.fna.gz | prodigal -d GCF_010614805.1_ASM1061480v1_genomic.fna/cds.fna -a GCF_010614805.1_ASM1061480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:43,162] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:43,163] [INFO] Task started: HMMsearch
[2024-01-24 11:43:43,163] [INFO] Running command: hmmsearch --tblout GCF_010614805.1_ASM1061480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd6ab4cc-c808-403f-b9c9-821926751e6d/dqc_reference/reference_markers.hmm GCF_010614805.1_ASM1061480v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:43,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:43,454] [INFO] Found 6/6 markers.
[2024-01-24 11:43:43,490] [INFO] Query marker FASTA was written to GCF_010614805.1_ASM1061480v1_genomic.fna/markers.fasta
[2024-01-24 11:43:43,490] [INFO] Task started: Blastn
[2024-01-24 11:43:43,490] [INFO] Running command: blastn -query GCF_010614805.1_ASM1061480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd6ab4cc-c808-403f-b9c9-821926751e6d/dqc_reference/reference_markers.fasta -out GCF_010614805.1_ASM1061480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:44,381] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:44,386] [INFO] Selected 21 target genomes.
[2024-01-24 11:43:44,386] [INFO] Target genome list was writen to GCF_010614805.1_ASM1061480v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:44,393] [INFO] Task started: fastANI
[2024-01-24 11:43:44,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg507f05da-de78-4958-8dcf-640124a0c27c/GCF_010614805.1_ASM1061480v1_genomic.fna.gz --refList GCF_010614805.1_ASM1061480v1_genomic.fna/target_genomes.txt --output GCF_010614805.1_ASM1061480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:01,124] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:01,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd6ab4cc-c808-403f-b9c9-821926751e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:01,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd6ab4cc-c808-403f-b9c9-821926751e6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:01,144] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:01,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:01,145] [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
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	100.0	1395	1397	95	conclusive
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.7787	603	1397	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	79.5866	422	1397	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	79.4981	428	1397	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.3481	603	1397	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.2527	595	1397	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.245	562	1397	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.191	561	1397	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.1704	533	1397	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	78.9998	521	1397	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.9322	393	1397	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.7637	551	1397	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	78.4703	441	1397	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.387	483	1397	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	77.9908	370	1397	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.8865	388	1397	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.8533	400	1397	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.8206	420	1397	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.8091	424	1397	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.6324	330	1397	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.5084	391	1397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:01,147] [INFO] DFAST Taxonomy check result was written to GCF_010614805.1_ASM1061480v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:01,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:01,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:01,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd6ab4cc-c808-403f-b9c9-821926751e6d/dqc_reference/checkm_data
[2024-01-24 11:44:01,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:01,190] [INFO] Task started: CheckM
[2024-01-24 11:44:01,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010614805.1_ASM1061480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010614805.1_ASM1061480v1_genomic.fna/checkm_input GCF_010614805.1_ASM1061480v1_genomic.fna/checkm_result
[2024-01-24 11:44:49,221] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:49,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:49,247] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:49,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:49,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010614805.1_ASM1061480v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:49,248] [INFO] Task started: Blastn
[2024-01-24 11:44:49,249] [INFO] Running command: blastn -query GCF_010614805.1_ASM1061480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd6ab4cc-c808-403f-b9c9-821926751e6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_010614805.1_ASM1061480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:50,858] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:50,863] [INFO] Selected 23 target genomes.
[2024-01-24 11:44:50,863] [INFO] Target genome list was writen to GCF_010614805.1_ASM1061480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:50,887] [INFO] Task started: fastANI
[2024-01-24 11:44:50,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg507f05da-de78-4958-8dcf-640124a0c27c/GCF_010614805.1_ASM1061480v1_genomic.fna.gz --refList GCF_010614805.1_ASM1061480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010614805.1_ASM1061480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:12,762] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:12,795] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:12,796] [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_010614805.1	s__Pseudooceanicola sp010614805	100.0	1396	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000768315.1	s__Pseudooceanicola atlanticus	80.1775	638	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.8576	573	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.7525	606	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000152725.1	s__Pseudooceanicola batsensis	79.6301	568	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	79.626	441	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	79.6197	420	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	79.329	602	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003344785.1	s__Puniceibacterium profundi	79.2243	513	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	79.2166	557	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109145.1	s__Marinovum algicola	79.1867	515	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_003590145.2	s__Pseudooceanicola algae	79.0352	521	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	78.8695	500	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.862	603	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.8612	566	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.775	549	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	78.6994	424	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.6602	494	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003575965.1	s__Pseudooceanicola sediminis	78.555	507	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.4217	484	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCA_006226775.1	s__Marinovum sp006226775	78.41	493	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	78.3914	456	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	77.943	436	1397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:12,798] [INFO] GTDB search result was written to GCF_010614805.1_ASM1061480v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:12,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:12,805] [INFO] DFAST_QC result json was written to GCF_010614805.1_ASM1061480v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:12,805] [INFO] DFAST_QC completed!
[2024-01-24 11:45:12,805] [INFO] Total running time: 0h1m48s