[2024-01-24 13:28:43,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:43,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:43,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg083f3fe2-f077-46ec-9271-f11ab4fe9f5f/dqc_reference
[2024-01-24 13:28:44,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:44,696] [INFO] Task started: Prodigal
[2024-01-24 13:28:44,697] [INFO] Running command: gunzip -c /var/lib/cwl/stg19504417-55ed-4a98-8fda-939a72ba2d60/GCF_007855645.1_ASM785564v1_genomic.fna.gz | prodigal -d GCF_007855645.1_ASM785564v1_genomic.fna/cds.fna -a GCF_007855645.1_ASM785564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:57,791] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:57,791] [INFO] Task started: HMMsearch
[2024-01-24 13:28:57,791] [INFO] Running command: hmmsearch --tblout GCF_007855645.1_ASM785564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg083f3fe2-f077-46ec-9271-f11ab4fe9f5f/dqc_reference/reference_markers.hmm GCF_007855645.1_ASM785564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:58,081] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:58,084] [INFO] Found 6/6 markers.
[2024-01-24 13:28:58,123] [INFO] Query marker FASTA was written to GCF_007855645.1_ASM785564v1_genomic.fna/markers.fasta
[2024-01-24 13:28:58,124] [INFO] Task started: Blastn
[2024-01-24 13:28:58,124] [INFO] Running command: blastn -query GCF_007855645.1_ASM785564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg083f3fe2-f077-46ec-9271-f11ab4fe9f5f/dqc_reference/reference_markers.fasta -out GCF_007855645.1_ASM785564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:59,073] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:59,081] [INFO] Selected 30 target genomes.
[2024-01-24 13:28:59,082] [INFO] Target genome list was writen to GCF_007855645.1_ASM785564v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:59,098] [INFO] Task started: fastANI
[2024-01-24 13:28:59,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg19504417-55ed-4a98-8fda-939a72ba2d60/GCF_007855645.1_ASM785564v1_genomic.fna.gz --refList GCF_007855645.1_ASM785564v1_genomic.fna/target_genomes.txt --output GCF_007855645.1_ASM785564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:24,071] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:24,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg083f3fe2-f077-46ec-9271-f11ab4fe9f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:24,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg083f3fe2-f077-46ec-9271-f11ab4fe9f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:24,100] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:24,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:24,101] [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
Qingshengfaniella alkalisoli	strain=LN3S51	GCA_007855645.1	2599296	2599296	type	True	100.0	1306	1307	95	conclusive
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.8639	174	1307	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.7276	196	1307	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.7271	193	1307	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.6768	139	1307	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.6053	178	1307	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	77.567	201	1307	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.4779	216	1307	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.4017	201	1307	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.3928	197	1307	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	77.3804	208	1307	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	77.3619	204	1307	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.3528	171	1307	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	77.3241	147	1307	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.3069	210	1307	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.3032	210	1307	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.2364	152	1307	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.2217	225	1307	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	77.2103	201	1307	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.1741	196	1307	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.1278	204	1307	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.1102	212	1307	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.0552	213	1307	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	77.0351	229	1307	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.9823	148	1307	95	below_threshold
Aliiruegeria lutimaris	strain=DSM 25294	GCA_900099935.1	571298	571298	type	True	76.928	204	1307	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.8896	163	1307	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	76.807	172	1307	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.7729	187	1307	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.6075	181	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:24,103] [INFO] DFAST Taxonomy check result was written to GCF_007855645.1_ASM785564v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:24,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:24,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:24,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg083f3fe2-f077-46ec-9271-f11ab4fe9f5f/dqc_reference/checkm_data
[2024-01-24 13:29:24,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:24,155] [INFO] Task started: CheckM
[2024-01-24 13:29:24,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007855645.1_ASM785564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007855645.1_ASM785564v1_genomic.fna/checkm_input GCF_007855645.1_ASM785564v1_genomic.fna/checkm_result
[2024-01-24 13:30:06,039] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:06,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:06,069] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:06,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:06,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007855645.1_ASM785564v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:06,070] [INFO] Task started: Blastn
[2024-01-24 13:30:06,070] [INFO] Running command: blastn -query GCF_007855645.1_ASM785564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg083f3fe2-f077-46ec-9271-f11ab4fe9f5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007855645.1_ASM785564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:07,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:07,586] [INFO] Selected 29 target genomes.
[2024-01-24 13:30:07,586] [INFO] Target genome list was writen to GCF_007855645.1_ASM785564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:07,617] [INFO] Task started: fastANI
[2024-01-24 13:30:07,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg19504417-55ed-4a98-8fda-939a72ba2d60/GCF_007855645.1_ASM785564v1_genomic.fna.gz --refList GCF_007855645.1_ASM785564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007855645.1_ASM785564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:27,830] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:27,856] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:27,856] [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_007855645.1	s__Qingshengfaniella alkalisoli	100.0	1306	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Qingshengfaniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018139985.1	s__JAGSOU01 sp018139985	77.8786	213	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003172915.1	s__Fluviibacterium sp003172915	77.748	243	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.7442	195	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_002797755.1	s__Brevirhabdus pacifica	77.7319	193	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.6942	176	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	77.6756	241	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360145.1	s__Aliiroseovarius marinus	77.6725	140	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014901205.1	s__Fluviibacterium sp014901205	77.6132	252	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	77.6001	232	1307	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_004000255.1	s__Nioella ostreopsis	77.567	201	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938225.1	s__Arenibacterium halophilum	77.5366	228	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_015220045.1	s__Marivivens aquimaris	77.5203	173	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.4779	216	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_002210105.1	s__Pseudooceanicola sp002210105	77.4273	216	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	77.3608	203	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	77.3339	206	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.3022	210	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	77.2975	237	1307	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_004358185.1	s__Antarcticimicrobium luteum	77.1603	197	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156805.1	s__Roseivivax lentus	77.1268	205	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	77.1099	151	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	77.0913	201	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054285.1	s__Litoreibacter ponti	77.0875	182	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	77.0675	212	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003122205.1	s__QEYE01 sp003122205	77.0553	187	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	77.0351	229	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	77.0091	232	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	76.7617	188	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:27,858] [INFO] GTDB search result was written to GCF_007855645.1_ASM785564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:27,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:27,864] [INFO] DFAST_QC result json was written to GCF_007855645.1_ASM785564v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:27,864] [INFO] DFAST_QC completed!
[2024-01-24 13:30:27,864] [INFO] Total running time: 0h1m44s