[2024-01-24 11:26:02,986] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:02,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:02,988] [INFO] DQC Reference Directory: /var/lib/cwl/stgac68fa12-c8bc-446c-a5ae-39e571ec86d0/dqc_reference
[2024-01-24 11:26:04,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,158] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg2767020f-0606-4b94-b8fa-ff2ae2a6f39d/GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/cds.fna -a GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:17,759] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:17,760] [INFO] Task started: HMMsearch
[2024-01-24 11:26:17,760] [INFO] Running command: hmmsearch --tblout GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac68fa12-c8bc-446c-a5ae-39e571ec86d0/dqc_reference/reference_markers.hmm GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:17,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:17,976] [INFO] Found 6/6 markers.
[2024-01-24 11:26:18,005] [INFO] Query marker FASTA was written to GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:26:18,006] [INFO] Task started: Blastn
[2024-01-24 11:26:18,006] [INFO] Running command: blastn -query GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgac68fa12-c8bc-446c-a5ae-39e571ec86d0/dqc_reference/reference_markers.fasta -out GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:18,719] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:18,722] [INFO] Selected 32 target genomes.
[2024-01-24 11:26:18,723] [INFO] Target genome list was writen to GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:26:18,767] [INFO] Task started: fastANI
[2024-01-24 11:26:18,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg2767020f-0606-4b94-b8fa-ff2ae2a6f39d/GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna.gz --refList GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:38,028] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:38,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac68fa12-c8bc-446c-a5ae-39e571ec86d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:38,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac68fa12-c8bc-446c-a5ae-39e571ec86d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:38,049] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:38,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:38,050] [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
Pontivivens insulae	strain=DSM 103361	GCA_003385715.1	1639689	1639689	type	True	77.8096	271	1231	95	below_threshold
Pontivivens insulae	strain=CeCT 8812	GCA_900302495.1	1639689	1639689	type	True	77.7875	273	1231	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.2712	286	1231	95	below_threshold
Rubricella aquisinus	strain=DSM 103377	GCA_014199445.1	2028108	2028108	type	True	76.6797	214	1231	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.5853	132	1231	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.4739	109	1231	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.4657	119	1231	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.4643	123	1231	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.4605	142	1231	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	76.4529	129	1231	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.4476	145	1231	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.4435	140	1231	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.4306	93	1231	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	76.4192	156	1231	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	76.389	148	1231	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	76.3844	128	1231	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.3491	146	1231	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.3366	113	1231	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.3355	144	1231	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.3349	138	1231	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.3241	125	1231	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	76.2671	134	1231	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	76.2492	115	1231	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.2267	124	1231	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	76.1799	143	1231	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	76.1458	104	1231	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	76.0887	116	1231	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.0443	106	1231	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	75.9828	92	1231	95	below_threshold
Haematobacter massiliensis	strain=CCUG 47968	GCA_000740795.1	195105	195105	type	True	75.8034	93	1231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:38,052] [INFO] DFAST Taxonomy check result was written to GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:26:38,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:38,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:38,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac68fa12-c8bc-446c-a5ae-39e571ec86d0/dqc_reference/checkm_data
[2024-01-24 11:26:38,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:38,089] [INFO] Task started: CheckM
[2024-01-24 11:26:38,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/checkm_input GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:27:18,306] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:18,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:18,323] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:18,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:18,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:27:18,324] [INFO] Task started: Blastn
[2024-01-24 11:27:18,324] [INFO] Running command: blastn -query GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgac68fa12-c8bc-446c-a5ae-39e571ec86d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:19,468] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:19,471] [INFO] Selected 22 target genomes.
[2024-01-24 11:27:19,471] [INFO] Target genome list was writen to GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:19,496] [INFO] Task started: fastANI
[2024-01-24 11:27:19,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg2767020f-0606-4b94-b8fa-ff2ae2a6f39d/GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna.gz --refList GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:33,616] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,633] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:33,634] [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_900231835.1	s__Monaibacterium marinum	100.0	1230	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011290545.1	s__Monaibacterium sp011290545	80.2583	608	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	96.75	96.75	0.88	0.88	2	-
GCF_900302495.1	s__Pontivivens insulae	77.7993	272	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontivivens	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015679265.1	s__MT2928 sp015679265	77.2615	287	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199445.1	s__Rubricella aquisinus	76.6797	214	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubricella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	76.5853	132	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123675.1	s__Leisingera sp004123675	76.5763	123	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCF_003116585.1	s__Albibacillus kandeliae	76.4912	134	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	76.4548	142	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	76.4306	93	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830335.1	s__Paracoccus sulfuroxidans	76.3907	116	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	76.3844	128	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155465.1	s__Alterinioella nitratireducens	76.3159	171	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_008086115.1	s__Muriiphilus fusiformis	76.2947	114	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	98.34	98.34	0.92	0.92	2	-
GCF_002210165.1	s__CAU-1492 sp002210165	76.283	135	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	76.2803	133	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	76.2627	106	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	76.1799	143	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008085915.1	s__Oceaniglobus sp008085915	76.177	120	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	76.102	122	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	76.0887	116	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_008124525.1	s__Oceanicella actignis	76.0596	105	1231	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,635] [INFO] GTDB search result was written to GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:33,636] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:33,640] [INFO] DFAST_QC result json was written to GCF_900231835.1_IMG-taxon_2710264757_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:27:33,641] [INFO] DFAST_QC completed!
[2024-01-24 11:27:33,641] [INFO] Total running time: 0h1m31s