[2024-01-25 17:53:05,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:05,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:05,668] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa97f688-e2b6-46e6-b593-e4a5e1bcab59/dqc_reference
[2024-01-25 17:53:06,869] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:06,869] [INFO] Task started: Prodigal
[2024-01-25 17:53:06,870] [INFO] Running command: gunzip -c /var/lib/cwl/stg46de60e1-e8de-4b59-93d3-84277fe9fe11/GCF_017498545.1_ASM1749854v1_genomic.fna.gz | prodigal -d GCF_017498545.1_ASM1749854v1_genomic.fna/cds.fna -a GCF_017498545.1_ASM1749854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:55:44,200] [INFO] Task succeeded: Prodigal
[2024-01-25 17:55:44,201] [INFO] Task started: HMMsearch
[2024-01-25 17:55:44,201] [INFO] Running command: hmmsearch --tblout GCF_017498545.1_ASM1749854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa97f688-e2b6-46e6-b593-e4a5e1bcab59/dqc_reference/reference_markers.hmm GCF_017498545.1_ASM1749854v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:55:44,613] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:55:44,615] [INFO] Found 6/6 markers.
[2024-01-25 17:55:44,690] [INFO] Query marker FASTA was written to GCF_017498545.1_ASM1749854v1_genomic.fna/markers.fasta
[2024-01-25 17:55:44,690] [INFO] Task started: Blastn
[2024-01-25 17:55:44,690] [INFO] Running command: blastn -query GCF_017498545.1_ASM1749854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa97f688-e2b6-46e6-b593-e4a5e1bcab59/dqc_reference/reference_markers.fasta -out GCF_017498545.1_ASM1749854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:45,299] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:45,302] [INFO] Selected 23 target genomes.
[2024-01-25 17:55:45,302] [INFO] Target genome list was writen to GCF_017498545.1_ASM1749854v1_genomic.fna/target_genomes.txt
[2024-01-25 17:55:45,318] [INFO] Task started: fastANI
[2024-01-25 17:55:45,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg46de60e1-e8de-4b59-93d3-84277fe9fe11/GCF_017498545.1_ASM1749854v1_genomic.fna.gz --refList GCF_017498545.1_ASM1749854v1_genomic.fna/target_genomes.txt --output GCF_017498545.1_ASM1749854v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:56:09,703] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:09,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa97f688-e2b6-46e6-b593-e4a5e1bcab59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:56:09,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa97f688-e2b6-46e6-b593-e4a5e1bcab59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:56:09,713] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:56:09,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:56:09,714] [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
Sulfidibacter corallicola	strain=M133	GCA_017498545.1	2818388	2818388	type	True	100.0	3927	3928	95	conclusive
Acanthopleuribacter pedis	strain=KCTC 12899	GCA_017377855.1	442870	442870	type	True	76.6288	440	3928	95	below_threshold
Tepidimonas aquatica	strain=CLN-1	GCA_007556585.1	247482	247482	type	True	75.5182	51	3928	95	below_threshold
Tepidimonas ignava	strain=SPS-1037	GCA_007556615.1	114249	114249	type	True	75.5112	53	3928	95	below_threshold
Tepidimonas ignava	strain=DSM 12034	GCA_004342625.1	114249	114249	type	True	75.448	52	3928	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	75.2921	73	3928	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.2635	64	3928	95	below_threshold
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	75.0229	77	3928	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	74.9984	60	3928	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	74.9688	132	3928	95	below_threshold
Paraburkholderia caballeronis	strain=TNe-841	GCA_900104845.1	416943	416943	type	True	74.9306	92	3928	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	74.8527	80	3928	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	74.8237	112	3928	95	below_threshold
Paraburkholderia caballeronis	strain=LMG 26416	GCA_900109675.1	416943	416943	type	True	74.7262	88	3928	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	74.712	57	3928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:56:09,715] [INFO] DFAST Taxonomy check result was written to GCF_017498545.1_ASM1749854v1_genomic.fna/tc_result.tsv
[2024-01-25 17:56:09,716] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:56:09,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:56:09,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa97f688-e2b6-46e6-b593-e4a5e1bcab59/dqc_reference/checkm_data
[2024-01-25 17:56:09,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:56:09,821] [INFO] Task started: CheckM
[2024-01-25 17:56:09,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017498545.1_ASM1749854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017498545.1_ASM1749854v1_genomic.fna/checkm_input GCF_017498545.1_ASM1749854v1_genomic.fna/checkm_result
[2024-01-25 18:03:54,641] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:54,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:54,663] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:54,664] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:54,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017498545.1_ASM1749854v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:54,665] [INFO] Task started: Blastn
[2024-01-25 18:03:54,665] [INFO] Running command: blastn -query GCF_017498545.1_ASM1749854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa97f688-e2b6-46e6-b593-e4a5e1bcab59/dqc_reference/reference_markers_gtdb.fasta -out GCF_017498545.1_ASM1749854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:55,667] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:55,669] [INFO] Selected 23 target genomes.
[2024-01-25 18:03:55,670] [INFO] Target genome list was writen to GCF_017498545.1_ASM1749854v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:55,699] [INFO] Task started: fastANI
[2024-01-25 18:03:55,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg46de60e1-e8de-4b59-93d3-84277fe9fe11/GCF_017498545.1_ASM1749854v1_genomic.fna.gz --refList GCF_017498545.1_ASM1749854v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017498545.1_ASM1749854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:18,481] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:18,488] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:18,489] [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
GCA_017498545.1	s__Acanthopleuribacter sp017498545	100.0	3926	3928	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Acanthopleuribacterales;f__Acanthopleuribacteraceae;g__Acanthopleuribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017377855.1	s__Acanthopleuribacter pedis	76.6187	442	3928	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Acanthopleuribacterales;f__Acanthopleuribacteraceae;g__Acanthopleuribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	75.2754	63	3928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422565.1	s__Aminidesulfovibrio aminophilus	75.2621	50	3928	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Aminidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898825.1	s__Magnetospirillum sp001898825	75.0317	55	3928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCA_015494165.1	s__S144-34 sp015494165	75.0298	53	3928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136035.1	s__JAGVUW01 sp019136035	74.8526	50	3928	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__JAGVUW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001619955.1	s__Sphingomonas hankookensis	74.8419	51	3928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.49	99.35	0.90	0.87	3	-
GCF_002885955.2	s__Achromobacter pulmonis_A	74.831	102	3928	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_014648675.1	s__Spirillospora livida	74.6552	109	3928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:18,490] [INFO] GTDB search result was written to GCF_017498545.1_ASM1749854v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:18,491] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:18,494] [INFO] DFAST_QC result json was written to GCF_017498545.1_ASM1749854v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:18,495] [INFO] DFAST_QC completed!
[2024-01-25 18:04:18,495] [INFO] Total running time: 0h11m13s