[2024-01-25 19:24:45,019] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,020] [INFO] DQC Reference Directory: /var/lib/cwl/stge5c12b87-8027-42a3-81c6-cebd70749ff5/dqc_reference
[2024-01-25 19:24:48,251] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,253] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgc001bd91-e992-4cb1-a0d9-cd15d51da7de/GCF_016888515.1_ASM1688851v1_genomic.fna.gz | prodigal -d GCF_016888515.1_ASM1688851v1_genomic.fna/cds.fna -a GCF_016888515.1_ASM1688851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:59,535] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:59,535] [INFO] Task started: HMMsearch
[2024-01-25 19:24:59,535] [INFO] Running command: hmmsearch --tblout GCF_016888515.1_ASM1688851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5c12b87-8027-42a3-81c6-cebd70749ff5/dqc_reference/reference_markers.hmm GCF_016888515.1_ASM1688851v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:59,762] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:59,763] [INFO] Found 6/6 markers.
[2024-01-25 19:24:59,798] [INFO] Query marker FASTA was written to GCF_016888515.1_ASM1688851v1_genomic.fna/markers.fasta
[2024-01-25 19:24:59,798] [INFO] Task started: Blastn
[2024-01-25 19:24:59,798] [INFO] Running command: blastn -query GCF_016888515.1_ASM1688851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5c12b87-8027-42a3-81c6-cebd70749ff5/dqc_reference/reference_markers.fasta -out GCF_016888515.1_ASM1688851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:00,725] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:00,728] [INFO] Selected 30 target genomes.
[2024-01-25 19:25:00,728] [INFO] Target genome list was writen to GCF_016888515.1_ASM1688851v1_genomic.fna/target_genomes.txt
[2024-01-25 19:25:00,768] [INFO] Task started: fastANI
[2024-01-25 19:25:00,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgc001bd91-e992-4cb1-a0d9-cd15d51da7de/GCF_016888515.1_ASM1688851v1_genomic.fna.gz --refList GCF_016888515.1_ASM1688851v1_genomic.fna/target_genomes.txt --output GCF_016888515.1_ASM1688851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:23,238] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:23,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5c12b87-8027-42a3-81c6-cebd70749ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:23,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5c12b87-8027-42a3-81c6-cebd70749ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:23,256] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:25:23,256] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:25:23,256] [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
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.328	506	1307	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.3244	535	1307	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	79.2322	489	1307	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	79.1782	404	1307	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.1379	528	1307	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.0852	556	1307	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.9998	496	1307	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.9961	487	1307	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.9942	501	1307	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.868	496	1307	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.7123	454	1307	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.6727	388	1307	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.6015	477	1307	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.455	484	1307	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.4262	494	1307	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.3654	449	1307	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	78.201	379	1307	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.1919	422	1307	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	78.1765	422	1307	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	78.0189	301	1307	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	78.0014	307	1307	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9759	354	1307	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.9716	396	1307	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.9705	412	1307	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.8858	330	1307	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.8602	372	1307	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.5788	330	1307	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.4637	335	1307	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.0092	205	1307	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.9806	216	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:23,258] [INFO] DFAST Taxonomy check result was written to GCF_016888515.1_ASM1688851v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:23,258] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:23,258] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:23,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5c12b87-8027-42a3-81c6-cebd70749ff5/dqc_reference/checkm_data
[2024-01-25 19:25:23,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:23,300] [INFO] Task started: CheckM
[2024-01-25 19:25:23,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016888515.1_ASM1688851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016888515.1_ASM1688851v1_genomic.fna/checkm_input GCF_016888515.1_ASM1688851v1_genomic.fna/checkm_result
[2024-01-25 19:26:03,810] [INFO] Task succeeded: CheckM
[2024-01-25 19:26:03,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:26:03,833] [INFO] ===== Completeness check finished =====
[2024-01-25 19:26:03,833] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:26:03,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016888515.1_ASM1688851v1_genomic.fna/markers.fasta)
[2024-01-25 19:26:03,834] [INFO] Task started: Blastn
[2024-01-25 19:26:03,834] [INFO] Running command: blastn -query GCF_016888515.1_ASM1688851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5c12b87-8027-42a3-81c6-cebd70749ff5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016888515.1_ASM1688851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:26:05,678] [INFO] Task succeeded: Blastn
[2024-01-25 19:26:05,681] [INFO] Selected 25 target genomes.
[2024-01-25 19:26:05,681] [INFO] Target genome list was writen to GCF_016888515.1_ASM1688851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:26:05,698] [INFO] Task started: fastANI
[2024-01-25 19:26:05,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgc001bd91-e992-4cb1-a0d9-cd15d51da7de/GCF_016888515.1_ASM1688851v1_genomic.fna.gz --refList GCF_016888515.1_ASM1688851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016888515.1_ASM1688851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:26:26,592] [INFO] Task succeeded: fastANI
[2024-01-25 19:26:26,607] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:26:26,607] [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_016888515.1	s__Shimia_A biformata	100.0	1307	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.3293	503	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.2871	590	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799325.1	s__Thalassobius vesicularis	79.9806	522	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	79.3839	599	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	79.3429	533	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	79.2275	489	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.1912	492	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	79.0973	555	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_008728195.1	s__Roseovarius indicus	79.0097	499	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900101475.1	s__Ruegeria_B marina	78.8681	495	1307	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_900109145.1	s__Marinovum algicola	78.8494	491	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_900109035.1	s__Cribrihabitans marinus	78.7767	524	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013031405.1	s__Ruegeria sp013031405	78.6119	540	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.5841	479	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.549	521	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_001975705.1	s__Salipiger abyssi	78.5013	448	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363715.1	s__Roseovarius sp009363715	78.2071	419	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129565.1	s__Salibaculum griseiflavum	78.201	379	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	78.1856	421	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013031245.1	s__Ruegeria lacuscaerulensis_C	78.1382	363	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	78.1115	353	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	78.0166	300	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002094885.1	s__Salibaculum halophilum	77.8656	332	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032095.1	s__Ruegeria atlantica_E	77.8478	360	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:26:26,608] [INFO] GTDB search result was written to GCF_016888515.1_ASM1688851v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:26:26,609] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:26:26,614] [INFO] DFAST_QC result json was written to GCF_016888515.1_ASM1688851v1_genomic.fna/dqc_result.json
[2024-01-25 19:26:26,614] [INFO] DFAST_QC completed!
[2024-01-25 19:26:26,614] [INFO] Total running time: 0h1m42s