[2024-01-24 14:30:30,686] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg69a04d67-56a5-404d-ab4a-6d1061d13d7c/dqc_reference
[2024-01-24 14:30:31,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,894] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f330fb6-d937-435f-9d93-c60d5a6c1732/GCF_003363155.1_ASM336315v1_genomic.fna.gz | prodigal -d GCF_003363155.1_ASM336315v1_genomic.fna/cds.fna -a GCF_003363155.1_ASM336315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:50,098] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:50,099] [INFO] Task started: HMMsearch
[2024-01-24 14:30:50,099] [INFO] Running command: hmmsearch --tblout GCF_003363155.1_ASM336315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69a04d67-56a5-404d-ab4a-6d1061d13d7c/dqc_reference/reference_markers.hmm GCF_003363155.1_ASM336315v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:50,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:50,412] [INFO] Found 6/6 markers.
[2024-01-24 14:30:50,458] [INFO] Query marker FASTA was written to GCF_003363155.1_ASM336315v1_genomic.fna/markers.fasta
[2024-01-24 14:30:50,458] [INFO] Task started: Blastn
[2024-01-24 14:30:50,458] [INFO] Running command: blastn -query GCF_003363155.1_ASM336315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69a04d67-56a5-404d-ab4a-6d1061d13d7c/dqc_reference/reference_markers.fasta -out GCF_003363155.1_ASM336315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:51,413] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:51,418] [INFO] Selected 13 target genomes.
[2024-01-24 14:30:51,418] [INFO] Target genome list was writen to GCF_003363155.1_ASM336315v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:51,431] [INFO] Task started: fastANI
[2024-01-24 14:30:51,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f330fb6-d937-435f-9d93-c60d5a6c1732/GCF_003363155.1_ASM336315v1_genomic.fna.gz --refList GCF_003363155.1_ASM336315v1_genomic.fna/target_genomes.txt --output GCF_003363155.1_ASM336315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:04,006] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:04,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69a04d67-56a5-404d-ab4a-6d1061d13d7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:04,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69a04d67-56a5-404d-ab4a-6d1061d13d7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:04,022] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:04,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:04,023] [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 monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	100.0	1622	1624	95	conclusive
Dyella nitratireducens	strain=CGMCC 1.15439	GCA_014642835.1	1849580	1849580	type	True	81.7334	945	1624	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	81.5499	842	1624	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.2584	899	1624	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	81.1407	809	1624	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	80.99	808	1624	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	80.6368	812	1624	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	80.5474	787	1624	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	80.5256	780	1624	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.5137	479	1624	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.3329	575	1624	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.1147	450	1624	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	77.2642	233	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:04,025] [INFO] DFAST Taxonomy check result was written to GCF_003363155.1_ASM336315v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:04,025] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:04,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:04,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69a04d67-56a5-404d-ab4a-6d1061d13d7c/dqc_reference/checkm_data
[2024-01-24 14:31:04,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:04,077] [INFO] Task started: CheckM
[2024-01-24 14:31:04,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003363155.1_ASM336315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003363155.1_ASM336315v1_genomic.fna/checkm_input GCF_003363155.1_ASM336315v1_genomic.fna/checkm_result
[2024-01-24 14:31:57,317] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:57,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:57,339] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:57,340] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:57,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003363155.1_ASM336315v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:57,341] [INFO] Task started: Blastn
[2024-01-24 14:31:57,341] [INFO] Running command: blastn -query GCF_003363155.1_ASM336315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69a04d67-56a5-404d-ab4a-6d1061d13d7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003363155.1_ASM336315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:59,139] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:59,144] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:59,144] [INFO] Target genome list was writen to GCF_003363155.1_ASM336315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:59,162] [INFO] Task started: fastANI
[2024-01-24 14:31:59,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f330fb6-d937-435f-9d93-c60d5a6c1732/GCF_003363155.1_ASM336315v1_genomic.fna.gz --refList GCF_003363155.1_ASM336315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003363155.1_ASM336315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:13,373] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:13,394] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:13,394] [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_003363155.1	s__Dyella_B monticola	100.0	1622	1624	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_014873315.1	s__Dyella_B sp014873315	81.7799	933	1624	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_014642835.1	s__Dyella_B nitratireducens	81.7397	945	1624	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_003977665.1	s__Dyella_B choica	81.5333	844	1624	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	81.269	898	1624	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_003363265.1	s__Dyella_B psychrodurans	81.1322	810	1624	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	80.9831	809	1624	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	80.629	813	1624	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_016865235.1	s__Dyella_B caseinilytica	80.5177	781	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903970555.1	s__Dyella_B sp903970555	80.1932	686	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655335.1	s__Dyella_B sp015655335	79.9776	599	1624	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	79.5093	620	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_014842975.1	s__Rhodanobacter sp014842975	79.3942	560	1624	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:13,396] [INFO] GTDB search result was written to GCF_003363155.1_ASM336315v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:13,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:13,401] [INFO] DFAST_QC result json was written to GCF_003363155.1_ASM336315v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:13,401] [INFO] DFAST_QC completed!
[2024-01-24 14:32:13,401] [INFO] Total running time: 0h1m43s