[2024-01-24 12:23:50,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,928] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3bb4324-5d9e-40af-a2e7-a42c6feb09c1/dqc_reference
[2024-01-24 12:23:52,237] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,238] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,238] [INFO] Running command: gunzip -c /var/lib/cwl/stg92e0a405-21be-47b7-8d03-412c1f9d2d2a/GCF_005887615.1_ASM588761v1_genomic.fna.gz | prodigal -d GCF_005887615.1_ASM588761v1_genomic.fna/cds.fna -a GCF_005887615.1_ASM588761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:05,072] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:05,073] [INFO] Task started: HMMsearch
[2024-01-24 12:24:05,073] [INFO] Running command: hmmsearch --tblout GCF_005887615.1_ASM588761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3bb4324-5d9e-40af-a2e7-a42c6feb09c1/dqc_reference/reference_markers.hmm GCF_005887615.1_ASM588761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:05,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:05,346] [INFO] Found 6/6 markers.
[2024-01-24 12:24:05,380] [INFO] Query marker FASTA was written to GCF_005887615.1_ASM588761v1_genomic.fna/markers.fasta
[2024-01-24 12:24:05,381] [INFO] Task started: Blastn
[2024-01-24 12:24:05,381] [INFO] Running command: blastn -query GCF_005887615.1_ASM588761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3bb4324-5d9e-40af-a2e7-a42c6feb09c1/dqc_reference/reference_markers.fasta -out GCF_005887615.1_ASM588761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:06,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:06,350] [INFO] Selected 27 target genomes.
[2024-01-24 12:24:06,351] [INFO] Target genome list was writen to GCF_005887615.1_ASM588761v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:06,358] [INFO] Task started: fastANI
[2024-01-24 12:24:06,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg92e0a405-21be-47b7-8d03-412c1f9d2d2a/GCF_005887615.1_ASM588761v1_genomic.fna.gz --refList GCF_005887615.1_ASM588761v1_genomic.fna/target_genomes.txt --output GCF_005887615.1_ASM588761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:26,800] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:26,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3bb4324-5d9e-40af-a2e7-a42c6feb09c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:26,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3bb4324-5d9e-40af-a2e7-a42c6feb09c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:26,825] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:26,825] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:26,825] [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
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	100.0	1306	1308	95	conclusive
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	79.077	604	1308	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	79.0084	607	1308	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.8309	554	1308	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.8057	560	1308	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.7212	561	1308	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.7136	582	1308	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.4987	488	1308	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.487	510	1308	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.4293	513	1308	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.3899	493	1308	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.3739	438	1308	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.3166	439	1308	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.2457	477	1308	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.2313	481	1308	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	78.1966	390	1308	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	78.1701	434	1308	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	78.1266	395	1308	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	78.0748	394	1308	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0643	379	1308	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	78.0259	468	1308	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.9683	380	1308	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9195	351	1308	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7586	338	1308	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.6171	303	1308	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.6118	317	1308	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	77.6006	352	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:26,827] [INFO] DFAST Taxonomy check result was written to GCF_005887615.1_ASM588761v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:26,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:26,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:26,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3bb4324-5d9e-40af-a2e7-a42c6feb09c1/dqc_reference/checkm_data
[2024-01-24 12:24:26,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:26,872] [INFO] Task started: CheckM
[2024-01-24 12:24:26,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005887615.1_ASM588761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005887615.1_ASM588761v1_genomic.fna/checkm_input GCF_005887615.1_ASM588761v1_genomic.fna/checkm_result
[2024-01-24 12:25:11,340] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:11,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:11,366] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:11,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:11,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005887615.1_ASM588761v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:11,367] [INFO] Task started: Blastn
[2024-01-24 12:25:11,367] [INFO] Running command: blastn -query GCF_005887615.1_ASM588761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3bb4324-5d9e-40af-a2e7-a42c6feb09c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_005887615.1_ASM588761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:13,115] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:13,120] [INFO] Selected 24 target genomes.
[2024-01-24 12:25:13,121] [INFO] Target genome list was writen to GCF_005887615.1_ASM588761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:13,134] [INFO] Task started: fastANI
[2024-01-24 12:25:13,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg92e0a405-21be-47b7-8d03-412c1f9d2d2a/GCF_005887615.1_ASM588761v1_genomic.fna.gz --refList GCF_005887615.1_ASM588761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005887615.1_ASM588761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:33,178] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:33,203] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:33,203] [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_005887615.1	s__Sulfitobacter_E sabulilitoris	100.0	1306	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003335585.1	s__Sulfitobacter sp003335585	79.4569	639	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	79.4289	630	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	79.2963	618	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	79.1821	606	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	79.1266	605	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	79.0436	607	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	79.0191	605	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_015644665.1	s__Roseobacter sp015644665	78.7026	546	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.6955	585	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.68	520	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	78.5173	453	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938225.1	s__Arenibacterium halophilum	78.5027	540	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_900156805.1	s__Roseivivax lentus	78.4902	489	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.4451	511	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.398	492	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	78.3042	522	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000014045.1	s__Roseobacter denitrificans	78.1268	395	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_007995245.1	s__Tateyamaria sp007995245	78.0858	453	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	78.0357	466	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	77.9683	380	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363255.1	s__Roseivivax sp009363255	77.9601	409	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
GCA_013002405.1	s__Sulfitobacter sp013002405	77.9492	411	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	77.9184	463	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:33,205] [INFO] GTDB search result was written to GCF_005887615.1_ASM588761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:33,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:33,292] [INFO] DFAST_QC result json was written to GCF_005887615.1_ASM588761v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:33,293] [INFO] DFAST_QC completed!
[2024-01-24 12:25:33,293] [INFO] Total running time: 0h1m42s