[2024-01-24 13:12:55,268] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,273] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,273] [INFO] DQC Reference Directory: /var/lib/cwl/stg09ed61f2-220f-4e25-b034-a156d880274b/dqc_reference
[2024-01-24 13:12:56,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:56,737] [INFO] Task started: Prodigal
[2024-01-24 13:12:56,737] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc0afdbb-bdc3-49b9-b7d9-5739b6f25a1f/GCF_014647655.1_ASM1464765v1_genomic.fna.gz | prodigal -d GCF_014647655.1_ASM1464765v1_genomic.fna/cds.fna -a GCF_014647655.1_ASM1464765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:09,761] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:09,761] [INFO] Task started: HMMsearch
[2024-01-24 13:13:09,762] [INFO] Running command: hmmsearch --tblout GCF_014647655.1_ASM1464765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09ed61f2-220f-4e25-b034-a156d880274b/dqc_reference/reference_markers.hmm GCF_014647655.1_ASM1464765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:10,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:10,057] [INFO] Found 6/6 markers.
[2024-01-24 13:13:10,094] [INFO] Query marker FASTA was written to GCF_014647655.1_ASM1464765v1_genomic.fna/markers.fasta
[2024-01-24 13:13:10,094] [INFO] Task started: Blastn
[2024-01-24 13:13:10,094] [INFO] Running command: blastn -query GCF_014647655.1_ASM1464765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ed61f2-220f-4e25-b034-a156d880274b/dqc_reference/reference_markers.fasta -out GCF_014647655.1_ASM1464765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:10,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:10,743] [INFO] Selected 24 target genomes.
[2024-01-24 13:13:10,743] [INFO] Target genome list was writen to GCF_014647655.1_ASM1464765v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:10,757] [INFO] Task started: fastANI
[2024-01-24 13:13:10,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc0afdbb-bdc3-49b9-b7d9-5739b6f25a1f/GCF_014647655.1_ASM1464765v1_genomic.fna.gz --refList GCF_014647655.1_ASM1464765v1_genomic.fna/target_genomes.txt --output GCF_014647655.1_ASM1464765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:33,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:33,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09ed61f2-220f-4e25-b034-a156d880274b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:33,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09ed61f2-220f-4e25-b034-a156d880274b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:33,302] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:33,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:33,303] [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
Deinococcus malanensis	strain=JCM 30331	GCA_014647655.1	1706855	1706855	type	True	100.0	1442	1448	95	conclusive
Deinococcus deserti	strain=VCD115	GCA_000020685.1	310783	310783	type	True	84.9228	935	1448	95	below_threshold
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	79.3866	531	1448	95	below_threshold
Deinococcus aquaedulcis	strain=SYSU M42101	GCA_019693445.1	2840455	2840455	type	True	79.3192	555	1448	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	79.3113	539	1448	95	below_threshold
Deinococcus ficus	strain=DSM 19119	GCA_000430865.1	317577	317577	type	True	79.2788	544	1448	95	below_threshold
Deinococcus multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	79.2152	562	1448	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	79.1728	550	1448	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	79.0889	503	1448	95	below_threshold
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	79.0656	524	1448	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	78.9984	483	1448	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	78.997	528	1448	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	78.987	538	1448	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	78.9676	525	1448	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	78.9293	522	1448	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	78.9135	539	1448	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	78.8932	502	1448	95	below_threshold
Deinococcus humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	78.4277	478	1448	95	below_threshold
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	78.3819	483	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:33,304] [INFO] DFAST Taxonomy check result was written to GCF_014647655.1_ASM1464765v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:33,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:33,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:33,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09ed61f2-220f-4e25-b034-a156d880274b/dqc_reference/checkm_data
[2024-01-24 13:13:33,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:33,353] [INFO] Task started: CheckM
[2024-01-24 13:13:33,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647655.1_ASM1464765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647655.1_ASM1464765v1_genomic.fna/checkm_input GCF_014647655.1_ASM1464765v1_genomic.fna/checkm_result
[2024-01-24 13:14:14,178] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:14,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:14,202] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:14,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:14,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647655.1_ASM1464765v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:14,204] [INFO] Task started: Blastn
[2024-01-24 13:14:14,204] [INFO] Running command: blastn -query GCF_014647655.1_ASM1464765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ed61f2-220f-4e25-b034-a156d880274b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647655.1_ASM1464765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:15,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:15,113] [INFO] Selected 20 target genomes.
[2024-01-24 13:14:15,113] [INFO] Target genome list was writen to GCF_014647655.1_ASM1464765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:15,133] [INFO] Task started: fastANI
[2024-01-24 13:14:15,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc0afdbb-bdc3-49b9-b7d9-5739b6f25a1f/GCF_014647655.1_ASM1464765v1_genomic.fna.gz --refList GCF_014647655.1_ASM1464765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647655.1_ASM1464765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:31,204] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:31,224] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:31,225] [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_014647655.1	s__Deinococcus malanensis	100.0	1442	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000020685.1	s__Deinococcus deserti	84.9243	936	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003444775.1	s__Deinococcus ficus	79.3634	534	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_014647075.1	s__Deinococcus aerophilus	79.3337	537	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507665.1	s__Deinococcus actinosclerus	79.2555	501	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_002901445.1	s__Deinococcus koreensis	79.1984	547	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002017875.1	s__Deinococcus sp002017875	79.0982	537	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_000252445.1	s__Deinococcus gobiensis	79.0736	504	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647055.1	s__Deinococcus aerolatus	79.0653	522	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001007995.1	s__Deinococcus soli	79.0372	486	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_006335125.1	s__Deinococcus radiopugnans	78.9859	525	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_014648115.1	s__Deinococcus seoulensis	78.9846	523	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_014201805.1	s__Deinococcus metalli	78.9259	522	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009755355.1	s__Deinococcus sp009755355	78.89	493	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647435.1	s__Deinococcus radiotolerans	78.8687	503	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377345.1	s__Deinococcus sp009377345	78.5682	422	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201875.1	s__Deinococcus humi	78.4277	478	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000381345.1	s__Deinococcus apachensis	78.2074	450	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801315.1	s__Deinococcus sp004801315	77.0882	240	1448	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216565.1	s__Leptothrix mobilis	75.217	64	1448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:31,226] [INFO] GTDB search result was written to GCF_014647655.1_ASM1464765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:31,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:31,232] [INFO] DFAST_QC result json was written to GCF_014647655.1_ASM1464765v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:31,232] [INFO] DFAST_QC completed!
[2024-01-24 13:14:31,232] [INFO] Total running time: 0h1m36s