[2023-06-29 13:32:46,089] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:32:46,092] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:32:46,092] [INFO] DQC Reference Directory: /var/lib/cwl/stg30c40e93-7bae-420e-ae00-6ea12b854e2f/dqc_reference
[2023-06-29 13:32:47,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:32:47,309] [INFO] Task started: Prodigal
[2023-06-29 13:32:47,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg6523b67f-a925-4ff6-9c07-bbf7f5286e4f/GCA_021785475.1_ASM2178547v1_genomic.fna.gz | prodigal -d GCA_021785475.1_ASM2178547v1_genomic.fna/cds.fna -a GCA_021785475.1_ASM2178547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:32:57,176] [INFO] Task succeeded: Prodigal
[2023-06-29 13:32:57,177] [INFO] Task started: HMMsearch
[2023-06-29 13:32:57,177] [INFO] Running command: hmmsearch --tblout GCA_021785475.1_ASM2178547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30c40e93-7bae-420e-ae00-6ea12b854e2f/dqc_reference/reference_markers.hmm GCA_021785475.1_ASM2178547v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:32:57,402] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:32:57,403] [INFO] Found 6/6 markers.
[2023-06-29 13:32:57,439] [INFO] Query marker FASTA was written to GCA_021785475.1_ASM2178547v1_genomic.fna/markers.fasta
[2023-06-29 13:32:57,439] [INFO] Task started: Blastn
[2023-06-29 13:32:57,439] [INFO] Running command: blastn -query GCA_021785475.1_ASM2178547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30c40e93-7bae-420e-ae00-6ea12b854e2f/dqc_reference/reference_markers.fasta -out GCA_021785475.1_ASM2178547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:32:58,336] [INFO] Task succeeded: Blastn
[2023-06-29 13:32:58,340] [INFO] Selected 19 target genomes.
[2023-06-29 13:32:58,341] [INFO] Target genome list was writen to GCA_021785475.1_ASM2178547v1_genomic.fna/target_genomes.txt
[2023-06-29 13:32:58,343] [INFO] Task started: fastANI
[2023-06-29 13:32:58,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg6523b67f-a925-4ff6-9c07-bbf7f5286e4f/GCA_021785475.1_ASM2178547v1_genomic.fna.gz --refList GCA_021785475.1_ASM2178547v1_genomic.fna/target_genomes.txt --output GCA_021785475.1_ASM2178547v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:33:14,747] [INFO] Task succeeded: fastANI
[2023-06-29 13:33:14,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30c40e93-7bae-420e-ae00-6ea12b854e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:33:14,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30c40e93-7bae-420e-ae00-6ea12b854e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:33:14,772] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 13:33:14,772] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 13:33:14,773] [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
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	96.519	815	936	95	conclusive
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	96.4143	845	936	95	conclusive
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	79.0323	413	936	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	79.0256	440	936	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	78.4536	395	936	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	78.3115	329	936	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.2776	349	936	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	78.2067	336	936	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.8526	259	936	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	77.8343	289	936	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.6679	329	936	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	77.6057	251	936	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.5882	315	936	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.4636	321	936	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.4579	299	936	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	77.1496	245	936	95	below_threshold
Lysobacter pythonis	strain=4284/11	GCA_003697345.1	2483112	2483112	type	True	77.1105	203	936	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	75.5593	245	936	95	below_threshold
Cupriavidus basilensis	strain=DSM 11853	GCA_008801925.2	68895	68895	suspected-type	True	75.5007	174	936	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:33:14,775] [INFO] DFAST Taxonomy check result was written to GCA_021785475.1_ASM2178547v1_genomic.fna/tc_result.tsv
[2023-06-29 13:33:14,776] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:33:14,776] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:33:14,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30c40e93-7bae-420e-ae00-6ea12b854e2f/dqc_reference/checkm_data
[2023-06-29 13:33:14,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:33:14,809] [INFO] Task started: CheckM
[2023-06-29 13:33:14,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021785475.1_ASM2178547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021785475.1_ASM2178547v1_genomic.fna/checkm_input GCA_021785475.1_ASM2178547v1_genomic.fna/checkm_result
[2023-06-29 13:33:54,523] [INFO] Task succeeded: CheckM
[2023-06-29 13:33:54,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 13:33:54,545] [INFO] ===== Completeness check finished =====
[2023-06-29 13:33:54,546] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:33:54,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021785475.1_ASM2178547v1_genomic.fna/markers.fasta)
[2023-06-29 13:33:54,546] [INFO] Task started: Blastn
[2023-06-29 13:33:54,547] [INFO] Running command: blastn -query GCA_021785475.1_ASM2178547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30c40e93-7bae-420e-ae00-6ea12b854e2f/dqc_reference/reference_markers_gtdb.fasta -out GCA_021785475.1_ASM2178547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:33:56,266] [INFO] Task succeeded: Blastn
[2023-06-29 13:33:56,272] [INFO] Selected 23 target genomes.
[2023-06-29 13:33:56,273] [INFO] Target genome list was writen to GCA_021785475.1_ASM2178547v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:33:56,280] [INFO] Task started: fastANI
[2023-06-29 13:33:56,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg6523b67f-a925-4ff6-9c07-bbf7f5286e4f/GCA_021785475.1_ASM2178547v1_genomic.fna.gz --refList GCA_021785475.1_ASM2178547v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021785475.1_ASM2178547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:34:13,188] [INFO] Task succeeded: fastANI
[2023-06-29 13:34:13,210] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:34:13,210] [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_002077135.1	s__Metallibacterium scheffleri	96.4354	844	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Metallibacterium	95.0	98.26	96.51	0.97	0.94	3	conclusive
GCF_000953855.2	s__Mizugakiibacter sediminis	79.1227	434	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	79.0499	437	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	78.8648	405	936	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_001617365.1	s__Rhodanobacter sp001617365	78.6953	383	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	78.6838	404	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182895.1	s__Frateuria_B defendens	78.617	388	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	78.5776	392	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013620825.1	s__Rhodanobacter sp001899565	78.5765	406	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_000230695.2	s__Rhodanobacter denitrificans	78.4898	392	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.49	98.47	0.91	0.89	4	-
GCF_000334915.1	s__Dyella_A ginsengisoli	78.4743	351	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	78.3825	395	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_003967035.1	s__Aerosticca soli	78.3697	344	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Aerosticca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279065.1	s__Dyella_A sp002279065	78.2949	360	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900115705.1	s__Frateuria_A terrea	78.1952	337	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009996615.1	s__Dokdonella_A sp009996615	78.1671	377	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242445.1	s__SZAS-103 sp018242445	77.9337	280	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014338185.1	s__Dokdonella_A sp014338185	77.8822	311	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	96.24	96.24	0.88	0.88	2	-
GCF_004296575.1	s__Dyella sp004296575	77.8339	289	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242485.1	s__SZAS-103 sp018242485	77.8244	264	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483055.1	s__Dokdonella sp002483055	77.6726	277	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977665.1	s__Dyella_B choica	77.5934	252	936	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_011759365.1	s__Luteibacter anthropi	77.1717	243	936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:34:13,212] [INFO] GTDB search result was written to GCA_021785475.1_ASM2178547v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:34:13,213] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:34:13,217] [INFO] DFAST_QC result json was written to GCA_021785475.1_ASM2178547v1_genomic.fna/dqc_result.json
[2023-06-29 13:34:13,217] [INFO] DFAST_QC completed!
[2023-06-29 13:34:13,217] [INFO] Total running time: 0h1m27s