[2024-01-24 14:14:20,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgf57876c1-6c25-4015-8288-018b2a654e9d/dqc_reference
[2024-01-24 14:14:21,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,918] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,918] [INFO] Running command: gunzip -c /var/lib/cwl/stga5dd3d8e-2d69-4fd2-8834-de4c909120d5/GCF_016427565.1_ASM1642756v1_genomic.fna.gz | prodigal -d GCF_016427565.1_ASM1642756v1_genomic.fna/cds.fna -a GCF_016427565.1_ASM1642756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:37,843] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:37,844] [INFO] Task started: HMMsearch
[2024-01-24 14:14:37,844] [INFO] Running command: hmmsearch --tblout GCF_016427565.1_ASM1642756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf57876c1-6c25-4015-8288-018b2a654e9d/dqc_reference/reference_markers.hmm GCF_016427565.1_ASM1642756v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:38,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:38,134] [INFO] Found 6/6 markers.
[2024-01-24 14:14:38,181] [INFO] Query marker FASTA was written to GCF_016427565.1_ASM1642756v1_genomic.fna/markers.fasta
[2024-01-24 14:14:38,182] [INFO] Task started: Blastn
[2024-01-24 14:14:38,182] [INFO] Running command: blastn -query GCF_016427565.1_ASM1642756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf57876c1-6c25-4015-8288-018b2a654e9d/dqc_reference/reference_markers.fasta -out GCF_016427565.1_ASM1642756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:39,216] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:39,220] [INFO] Selected 17 target genomes.
[2024-01-24 14:14:39,221] [INFO] Target genome list was writen to GCF_016427565.1_ASM1642756v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:39,261] [INFO] Task started: fastANI
[2024-01-24 14:14:39,261] [INFO] Running command: fastANI --query /var/lib/cwl/stga5dd3d8e-2d69-4fd2-8834-de4c909120d5/GCF_016427565.1_ASM1642756v1_genomic.fna.gz --refList GCF_016427565.1_ASM1642756v1_genomic.fna/target_genomes.txt --output GCF_016427565.1_ASM1642756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:02,820] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:02,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf57876c1-6c25-4015-8288-018b2a654e9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:02,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf57876c1-6c25-4015-8288-018b2a654e9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:02,834] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:02,834] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:02,835] [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
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	100.0	1698	1702	95	conclusive
Microvirga arabica	strain=SV2184P	GCA_016811235.1	1128671	1128671	type	True	88.8386	1216	1702	95	below_threshold
Microvirga soli	strain=R491	GCA_016734765.1	1854496	1854496	type	True	87.7828	1278	1702	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	85.205	939	1702	95	below_threshold
Microvirga mediterraneensis	strain=Marseille-Q2068	GCA_013520865.1	2754695	2754695	type	True	84.9525	1056	1702	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	84.934	1061	1702	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	84.7343	1115	1702	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	84.5389	1070	1702	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	84.5036	1089	1702	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	83.321	928	1702	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	83.012	902	1702	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	82.7905	913	1702	95	below_threshold
Microvirga makkahensis	strain=KCTC 23863	GCA_009830105.1	1128670	1128670	type	True	82.4054	885	1702	95	below_threshold
Microvirga vignae	strain=BR3299	GCA_001017175.1	1225564	1225564	type	True	82.3187	876	1702	95	below_threshold
Microvirga rosea	strain=CGMCC1.16488	GCA_020595095.1	2715425	2715425	type	True	80.0496	684	1702	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	79.198	625	1702	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	78.5981	577	1702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:02,836] [INFO] DFAST Taxonomy check result was written to GCF_016427565.1_ASM1642756v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:02,837] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:02,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:02,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf57876c1-6c25-4015-8288-018b2a654e9d/dqc_reference/checkm_data
[2024-01-24 14:15:02,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:02,887] [INFO] Task started: CheckM
[2024-01-24 14:15:02,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016427565.1_ASM1642756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016427565.1_ASM1642756v1_genomic.fna/checkm_input GCF_016427565.1_ASM1642756v1_genomic.fna/checkm_result
[2024-01-24 14:15:47,671] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:47,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:47,690] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:47,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:47,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016427565.1_ASM1642756v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:47,691] [INFO] Task started: Blastn
[2024-01-24 14:15:47,691] [INFO] Running command: blastn -query GCF_016427565.1_ASM1642756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf57876c1-6c25-4015-8288-018b2a654e9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016427565.1_ASM1642756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:49,472] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:49,475] [INFO] Selected 11 target genomes.
[2024-01-24 14:15:49,475] [INFO] Target genome list was writen to GCF_016427565.1_ASM1642756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:49,485] [INFO] Task started: fastANI
[2024-01-24 14:15:49,486] [INFO] Running command: fastANI --query /var/lib/cwl/stga5dd3d8e-2d69-4fd2-8834-de4c909120d5/GCF_016427565.1_ASM1642756v1_genomic.fna.gz --refList GCF_016427565.1_ASM1642756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016427565.1_ASM1642756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:04,979] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:04,989] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:04,989] [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_016427565.1	s__Microvirga sp016427565	100.0	1698	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000739015.1	s__Microvirga sp000739015	88.993	1240	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811235.1	s__Microvirga arabica	88.7997	1219	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699075.1	s__Microvirga sp014699075	88.1423	1282	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734765.1	s__Microvirga soli	87.8114	1275	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191055.1	s__Microvirga lupini_A	87.7178	1207	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694425.1	s__Microvirga sp015694425	87.5359	1133	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013520865.1	s__Microvirga mediterraneensis	84.9493	1056	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743775.1	s__Microvirga aerilata	84.9193	1062	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741015.1	s__Microvirga ossetica	84.7344	1114	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347665.1	s__Microvirga calopogonii	84.4201	1065	1702	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:04,990] [INFO] GTDB search result was written to GCF_016427565.1_ASM1642756v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:04,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:04,994] [INFO] DFAST_QC result json was written to GCF_016427565.1_ASM1642756v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:04,995] [INFO] DFAST_QC completed!
[2024-01-24 14:16:04,995] [INFO] Total running time: 0h1m44s