[2024-01-25 17:49:50,663] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:50,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:50,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f330716-7368-4d96-9557-3e90ddd766e8/dqc_reference
[2024-01-25 17:49:51,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:51,815] [INFO] Task started: Prodigal
[2024-01-25 17:49:51,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg40391e55-bc7a-4990-945c-ee8f68d5a991/GCF_002094875.1_ASM209487v1_genomic.fna.gz | prodigal -d GCF_002094875.1_ASM209487v1_genomic.fna/cds.fna -a GCF_002094875.1_ASM209487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:59,283] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:59,284] [INFO] Task started: HMMsearch
[2024-01-25 17:49:59,284] [INFO] Running command: hmmsearch --tblout GCF_002094875.1_ASM209487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f330716-7368-4d96-9557-3e90ddd766e8/dqc_reference/reference_markers.hmm GCF_002094875.1_ASM209487v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:59,514] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:59,515] [INFO] Found 6/6 markers.
[2024-01-25 17:49:59,547] [INFO] Query marker FASTA was written to GCF_002094875.1_ASM209487v1_genomic.fna/markers.fasta
[2024-01-25 17:49:59,547] [INFO] Task started: Blastn
[2024-01-25 17:49:59,547] [INFO] Running command: blastn -query GCF_002094875.1_ASM209487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f330716-7368-4d96-9557-3e90ddd766e8/dqc_reference/reference_markers.fasta -out GCF_002094875.1_ASM209487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:00,588] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:00,590] [INFO] Selected 25 target genomes.
[2024-01-25 17:50:00,591] [INFO] Target genome list was writen to GCF_002094875.1_ASM209487v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:00,607] [INFO] Task started: fastANI
[2024-01-25 17:50:00,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg40391e55-bc7a-4990-945c-ee8f68d5a991/GCF_002094875.1_ASM209487v1_genomic.fna.gz --refList GCF_002094875.1_ASM209487v1_genomic.fna/target_genomes.txt --output GCF_002094875.1_ASM209487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:18,605] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:18,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f330716-7368-4d96-9557-3e90ddd766e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:18,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f330716-7368-4d96-9557-3e90ddd766e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:18,620] [INFO] Found 25 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:50:18,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:18,621] [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
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	100.0	914	926	95	conclusive
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	99.9673	909	926	95	conclusive
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	79.3835	323	926	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.196	333	926	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.1748	398	926	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.1659	397	926	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.9626	350	926	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.8487	332	926	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.8276	364	926	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.7201	369	926	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.7004	378	926	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.6704	363	926	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.6476	324	926	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.5885	319	926	95	below_threshold
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	78.5143	337	926	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.4203	298	926	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.3576	287	926	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	78.2628	335	926	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	78.051	255	926	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.961	206	926	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	77.8788	205	926	95	below_threshold
Aliiruegeria sabulilitoris	strain=GJMS-35	GCA_001558155.1	1510458	1510458	type	True	77.822	265	926	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.792	222	926	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	77.7239	256	926	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.673	202	926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:18,632] [INFO] DFAST Taxonomy check result was written to GCF_002094875.1_ASM209487v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:18,632] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:18,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:18,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f330716-7368-4d96-9557-3e90ddd766e8/dqc_reference/checkm_data
[2024-01-25 17:50:18,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:18,670] [INFO] Task started: CheckM
[2024-01-25 17:50:18,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002094875.1_ASM209487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002094875.1_ASM209487v1_genomic.fna/checkm_input GCF_002094875.1_ASM209487v1_genomic.fna/checkm_result
[2024-01-25 17:50:45,158] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:45,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:45,179] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:45,179] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:45,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002094875.1_ASM209487v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:45,180] [INFO] Task started: Blastn
[2024-01-25 17:50:45,180] [INFO] Running command: blastn -query GCF_002094875.1_ASM209487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f330716-7368-4d96-9557-3e90ddd766e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002094875.1_ASM209487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:47,147] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:47,152] [INFO] Selected 27 target genomes.
[2024-01-25 17:50:47,153] [INFO] Target genome list was writen to GCF_002094875.1_ASM209487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:47,169] [INFO] Task started: fastANI
[2024-01-25 17:50:47,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg40391e55-bc7a-4990-945c-ee8f68d5a991/GCF_002094875.1_ASM209487v1_genomic.fna.gz --refList GCF_002094875.1_ASM209487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002094875.1_ASM209487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:06,657] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:06,674] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:06,674] [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_002797755.1	s__Brevirhabdus pacifica	99.9673	909	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	conclusive
GCF_018139985.1	s__JAGSOU01 sp018139985	79.7819	443	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014901205.1	s__Fluviibacterium sp014901205	79.5375	368	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	79.3861	368	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	79.3674	324	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	79.3023	365	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.2317	382	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.2202	392	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.1145	417	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	79.0313	362	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	78.998	363	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156535.1	s__Roseovarius nanhaiticus	78.9682	286	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004799325.1	s__Thalassobius vesicularis	78.9269	341	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	78.9235	277	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	78.7525	241	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	78.6532	364	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	78.5528	324	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.5317	379	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	78.5209	334	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.4245	329	926	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_003217255.1	s__Pseudoroseicyclus aestuarii	78.4071	299	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	78.3576	287	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048225.1	s__Paracoccus gahaiensis	78.2848	333	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	78.2198	329	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	78.184	317	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	77.9669	205	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013042605.1	s__IMCC34051 sp013042605	77.8626	243	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:06,676] [INFO] GTDB search result was written to GCF_002094875.1_ASM209487v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:06,676] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:06,681] [INFO] DFAST_QC result json was written to GCF_002094875.1_ASM209487v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:06,682] [INFO] DFAST_QC completed!
[2024-01-25 17:51:06,682] [INFO] Total running time: 0h1m16s