[2024-01-24 11:06:05,028] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:05,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:05,030] [INFO] DQC Reference Directory: /var/lib/cwl/stge675cd1a-4e0d-461a-a4d8-43ca64c43e42/dqc_reference
[2024-01-24 11:06:07,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,011] [INFO] Running command: gunzip -c /var/lib/cwl/stgc186e5db-d091-41ac-85e9-d4763c3e3354/GCF_003977665.1_ASM397766v1_genomic.fna.gz | prodigal -d GCF_003977665.1_ASM397766v1_genomic.fna/cds.fna -a GCF_003977665.1_ASM397766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:28,203] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:28,204] [INFO] Task started: HMMsearch
[2024-01-24 11:06:28,204] [INFO] Running command: hmmsearch --tblout GCF_003977665.1_ASM397766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge675cd1a-4e0d-461a-a4d8-43ca64c43e42/dqc_reference/reference_markers.hmm GCF_003977665.1_ASM397766v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:28,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:28,510] [INFO] Found 6/6 markers.
[2024-01-24 11:06:28,558] [INFO] Query marker FASTA was written to GCF_003977665.1_ASM397766v1_genomic.fna/markers.fasta
[2024-01-24 11:06:28,559] [INFO] Task started: Blastn
[2024-01-24 11:06:28,559] [INFO] Running command: blastn -query GCF_003977665.1_ASM397766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge675cd1a-4e0d-461a-a4d8-43ca64c43e42/dqc_reference/reference_markers.fasta -out GCF_003977665.1_ASM397766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:29,544] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:29,556] [INFO] Selected 14 target genomes.
[2024-01-24 11:06:29,556] [INFO] Target genome list was writen to GCF_003977665.1_ASM397766v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:29,563] [INFO] Task started: fastANI
[2024-01-24 11:06:29,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgc186e5db-d091-41ac-85e9-d4763c3e3354/GCF_003977665.1_ASM397766v1_genomic.fna.gz --refList GCF_003977665.1_ASM397766v1_genomic.fna/target_genomes.txt --output GCF_003977665.1_ASM397766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:43,566] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:43,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge675cd1a-4e0d-461a-a4d8-43ca64c43e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:43,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge675cd1a-4e0d-461a-a4d8-43ca64c43e42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:43,584] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:43,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:43,584] [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
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	100.0	1786	1793	95	conclusive
Dyella nitratireducens	strain=CGMCC 1.15439	GCA_014642835.1	1849580	1849580	type	True	83.0353	1112	1793	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.7694	931	1793	95	below_threshold
Dyella monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	81.4806	853	1793	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	81.2642	866	1793	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	81.1641	835	1793	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	81.0132	823	1793	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	80.5379	804	1793	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	80.5157	795	1793	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.1326	618	1793	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	80.1241	649	1793	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.9812	545	1793	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.8546	533	1793	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.7272	280	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:43,585] [INFO] DFAST Taxonomy check result was written to GCF_003977665.1_ASM397766v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:43,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:43,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:43,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge675cd1a-4e0d-461a-a4d8-43ca64c43e42/dqc_reference/checkm_data
[2024-01-24 11:06:43,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:43,636] [INFO] Task started: CheckM
[2024-01-24 11:06:43,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003977665.1_ASM397766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003977665.1_ASM397766v1_genomic.fna/checkm_input GCF_003977665.1_ASM397766v1_genomic.fna/checkm_result
[2024-01-24 11:07:44,449] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:44,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:44,474] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:44,474] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:44,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003977665.1_ASM397766v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:44,475] [INFO] Task started: Blastn
[2024-01-24 11:07:44,475] [INFO] Running command: blastn -query GCF_003977665.1_ASM397766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge675cd1a-4e0d-461a-a4d8-43ca64c43e42/dqc_reference/reference_markers_gtdb.fasta -out GCF_003977665.1_ASM397766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:46,339] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:46,343] [INFO] Selected 12 target genomes.
[2024-01-24 11:07:46,343] [INFO] Target genome list was writen to GCF_003977665.1_ASM397766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:46,358] [INFO] Task started: fastANI
[2024-01-24 11:07:46,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgc186e5db-d091-41ac-85e9-d4763c3e3354/GCF_003977665.1_ASM397766v1_genomic.fna.gz --refList GCF_003977665.1_ASM397766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003977665.1_ASM397766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:59,400] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:59,414] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:59,415] [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_003977665.1	s__Dyella_B choica	100.0	1786	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014642835.1	s__Dyella_B nitratireducens	83.0472	1110	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873315.1	s__Dyella_B sp014873315	82.8016	982	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863405.1	s__Dyella_B sp014863405	81.7536	933	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363155.1	s__Dyella_B monticola	81.4889	852	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904945.1	s__Dyella_B mobilis	81.254	867	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904955.1	s__Dyella_B flava	81.0181	822	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	80.6828	713	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_001428405.1	s__Frateuria_A sp001428405	80.5475	638	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865235.1	s__Dyella_B caseinilytica	80.5264	806	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014842975.1	s__Rhodanobacter sp014842975	80.5028	616	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	80.1386	597	1793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:59,416] [INFO] GTDB search result was written to GCF_003977665.1_ASM397766v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:59,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:59,420] [INFO] DFAST_QC result json was written to GCF_003977665.1_ASM397766v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:59,420] [INFO] DFAST_QC completed!
[2024-01-24 11:07:59,420] [INFO] Total running time: 0h1m54s