[2024-01-24 11:58:57,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg98d48d2a-dd8b-4941-ba46-6517d357b3d9/dqc_reference
[2024-01-24 11:58:58,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,769] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,769] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6d19f09-12dd-468f-b136-9669cc089f95/GCF_008757455.1_ASM875745v1_genomic.fna.gz | prodigal -d GCF_008757455.1_ASM875745v1_genomic.fna/cds.fna -a GCF_008757455.1_ASM875745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:14,713] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:14,713] [INFO] Task started: HMMsearch
[2024-01-24 11:59:14,713] [INFO] Running command: hmmsearch --tblout GCF_008757455.1_ASM875745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98d48d2a-dd8b-4941-ba46-6517d357b3d9/dqc_reference/reference_markers.hmm GCF_008757455.1_ASM875745v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:15,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:15,056] [INFO] Found 6/6 markers.
[2024-01-24 11:59:15,097] [INFO] Query marker FASTA was written to GCF_008757455.1_ASM875745v1_genomic.fna/markers.fasta
[2024-01-24 11:59:15,098] [INFO] Task started: Blastn
[2024-01-24 11:59:15,098] [INFO] Running command: blastn -query GCF_008757455.1_ASM875745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98d48d2a-dd8b-4941-ba46-6517d357b3d9/dqc_reference/reference_markers.fasta -out GCF_008757455.1_ASM875745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:16,065] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:16,070] [INFO] Selected 17 target genomes.
[2024-01-24 11:59:16,070] [INFO] Target genome list was writen to GCF_008757455.1_ASM875745v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:16,077] [INFO] Task started: fastANI
[2024-01-24 11:59:16,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d19f09-12dd-468f-b136-9669cc089f95/GCF_008757455.1_ASM875745v1_genomic.fna.gz --refList GCF_008757455.1_ASM875745v1_genomic.fna/target_genomes.txt --output GCF_008757455.1_ASM875745v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:35,305] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:35,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98d48d2a-dd8b-4941-ba46-6517d357b3d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:35,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98d48d2a-dd8b-4941-ba46-6517d357b3d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:35,326] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:35,327] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:35,327] [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 brassicacearum	strain=CDVBN77	GCA_008757455.1	2580413	2580413	type	True	100.0	1695	1698	95	conclusive
Microvirga antarctica	strain=3D7	GCA_017921815.1	2819233	2819233	type	True	81.4064	718	1698	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	79.9674	694	1698	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	79.9148	617	1698	95	below_threshold
Microvirga aerophila	strain=DSM 21344	GCA_003332305.1	670291	670291	type	True	79.8848	586	1698	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	79.8155	673	1698	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	79.7698	599	1698	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	79.7358	720	1698	95	below_threshold
Microvirga aerophila	strain=NBRC 106136	GCA_007991675.1	670291	670291	type	True	79.7278	605	1698	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	79.6963	602	1698	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	79.6658	630	1698	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	79.6291	656	1698	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	79.5868	590	1698	95	below_threshold
Microvirga flavescens	strain=c27j1	GCA_003290125.1	2249811	2249811	type	True	79.5619	485	1698	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	79.4852	575	1698	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.9026	371	1698	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	77.7343	394	1698	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:35,329] [INFO] DFAST Taxonomy check result was written to GCF_008757455.1_ASM875745v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:35,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:35,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:35,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98d48d2a-dd8b-4941-ba46-6517d357b3d9/dqc_reference/checkm_data
[2024-01-24 11:59:35,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:35,392] [INFO] Task started: CheckM
[2024-01-24 11:59:35,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008757455.1_ASM875745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008757455.1_ASM875745v1_genomic.fna/checkm_input GCF_008757455.1_ASM875745v1_genomic.fna/checkm_result
[2024-01-24 12:00:20,902] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:20,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:20,923] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:20,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:20,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008757455.1_ASM875745v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:20,924] [INFO] Task started: Blastn
[2024-01-24 12:00:20,925] [INFO] Running command: blastn -query GCF_008757455.1_ASM875745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98d48d2a-dd8b-4941-ba46-6517d357b3d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_008757455.1_ASM875745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:22,768] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:22,772] [INFO] Selected 15 target genomes.
[2024-01-24 12:00:22,772] [INFO] Target genome list was writen to GCF_008757455.1_ASM875745v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:22,795] [INFO] Task started: fastANI
[2024-01-24 12:00:22,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d19f09-12dd-468f-b136-9669cc089f95/GCF_008757455.1_ASM875745v1_genomic.fna.gz --refList GCF_008757455.1_ASM875745v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008757455.1_ASM875745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:38,091] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:38,103] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:38,104] [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_008757455.1	s__Microvirga brassicacearum	100.0	1695	1698	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_017921815.1	s__Microvirga sp017921815	81.4094	718	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350535.1	s__Microvirga subterranea	79.9634	693	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332305.1	s__Microvirga aerophila	79.917	582	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	99.85	99.85	0.93	0.93	2	-
GCF_003151255.1	s__Microvirga sp003151255	79.8245	623	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735695.1	s__Microvirga zambiensis	79.8152	673	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694465.1	s__Microvirga sp015694465	79.7836	597	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777495.1	s__Microvirga sp011777495	79.7056	565	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427565.1	s__Microvirga sp016427565	79.6878	603	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	79.6288	656	1698	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	79.626	633	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363855.1	s__Microvirga thermotolerans	79.5868	590	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003290125.1	s__Microvirga flavescens	79.5827	483	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069605.1	s__Microvirga sp018069605	79.5042	591	1698	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016892705.1	s__Microvirga sp016892705	79.2783	543	1698	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 12:00:38,106] [INFO] GTDB search result was written to GCF_008757455.1_ASM875745v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:38,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:38,110] [INFO] DFAST_QC result json was written to GCF_008757455.1_ASM875745v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:38,110] [INFO] DFAST_QC completed!
[2024-01-24 12:00:38,110] [INFO] Total running time: 0h1m41s