[2024-01-25 17:38:50,498] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:50,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:50,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg1527b960-3356-41e3-ba4a-20a79f395ed9/dqc_reference
[2024-01-25 17:38:51,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:51,744] [INFO] Task started: Prodigal
[2024-01-25 17:38:51,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d3d4dbe-0772-4890-be25-9ab1c1622a80/GCF_000378445.1_ASM37844v1_genomic.fna.gz | prodigal -d GCF_000378445.1_ASM37844v1_genomic.fna/cds.fna -a GCF_000378445.1_ASM37844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:04,723] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:04,724] [INFO] Task started: HMMsearch
[2024-01-25 17:39:04,724] [INFO] Running command: hmmsearch --tblout GCF_000378445.1_ASM37844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1527b960-3356-41e3-ba4a-20a79f395ed9/dqc_reference/reference_markers.hmm GCF_000378445.1_ASM37844v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:04,987] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:04,988] [INFO] Found 6/6 markers.
[2024-01-25 17:39:05,033] [INFO] Query marker FASTA was written to GCF_000378445.1_ASM37844v1_genomic.fna/markers.fasta
[2024-01-25 17:39:05,033] [INFO] Task started: Blastn
[2024-01-25 17:39:05,034] [INFO] Running command: blastn -query GCF_000378445.1_ASM37844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1527b960-3356-41e3-ba4a-20a79f395ed9/dqc_reference/reference_markers.fasta -out GCF_000378445.1_ASM37844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:05,664] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:05,667] [INFO] Selected 18 target genomes.
[2024-01-25 17:39:05,667] [INFO] Target genome list was writen to GCF_000378445.1_ASM37844v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:05,697] [INFO] Task started: fastANI
[2024-01-25 17:39:05,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3d4dbe-0772-4890-be25-9ab1c1622a80/GCF_000378445.1_ASM37844v1_genomic.fna.gz --refList GCF_000378445.1_ASM37844v1_genomic.fna/target_genomes.txt --output GCF_000378445.1_ASM37844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:20,655] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:20,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1527b960-3356-41e3-ba4a-20a79f395ed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:20,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1527b960-3356-41e3-ba4a-20a79f395ed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:20,667] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:20,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:20,667] [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 aquatilis	strain=DSM 23025	GCA_000378445.1	519440	519440	type	True	100.0	1605	1610	95	conclusive
Deinococcus puniceus	strain=DY1	GCA_001644565.1	1182568	1182568	type	True	86.3766	866	1610	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	78.7065	534	1610	95	below_threshold
Deinococcus marmoris	strain=DSM 12784	GCA_000701405.1	249408	249408	type	True	78.58	560	1610	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	78.5023	533	1610	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	78.3404	484	1610	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	78.2848	510	1610	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	78.1913	517	1610	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	78.1757	479	1610	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	78.1597	469	1610	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	78.1123	500	1610	95	below_threshold
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	78.0885	494	1610	95	below_threshold
Deinococcus humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	78.0834	498	1610	95	below_threshold
Deinococcus radiodurans	strain=ATCC 13939	GCA_020546685.1	1299	1299	type	True	77.8675	396	1610	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	77.8661	394	1610	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	77.8638	389	1610	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	77.7657	415	1610	95	below_threshold
Deinococcus deserti	strain=VCD115	GCA_000020685.1	310783	310783	type	True	77.7655	349	1610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:20,668] [INFO] DFAST Taxonomy check result was written to GCF_000378445.1_ASM37844v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:20,669] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:20,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:20,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1527b960-3356-41e3-ba4a-20a79f395ed9/dqc_reference/checkm_data
[2024-01-25 17:39:20,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:20,720] [INFO] Task started: CheckM
[2024-01-25 17:39:20,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378445.1_ASM37844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378445.1_ASM37844v1_genomic.fna/checkm_input GCF_000378445.1_ASM37844v1_genomic.fna/checkm_result
[2024-01-25 17:40:01,320] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:01,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:01,343] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:01,343] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:01,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378445.1_ASM37844v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:01,344] [INFO] Task started: Blastn
[2024-01-25 17:40:01,344] [INFO] Running command: blastn -query GCF_000378445.1_ASM37844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1527b960-3356-41e3-ba4a-20a79f395ed9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378445.1_ASM37844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:02,289] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:02,292] [INFO] Selected 16 target genomes.
[2024-01-25 17:40:02,292] [INFO] Target genome list was writen to GCF_000378445.1_ASM37844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:02,315] [INFO] Task started: fastANI
[2024-01-25 17:40:02,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3d4dbe-0772-4890-be25-9ab1c1622a80/GCF_000378445.1_ASM37844v1_genomic.fna.gz --refList GCF_000378445.1_ASM37844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378445.1_ASM37844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:17,202] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:17,212] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:17,213] [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_000378445.1	s__Deinococcus aquatilis	100.0	1605	1610	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_001644565.1	s__Deinococcus puniceus	86.3656	867	1610	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	85.3873	981	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335125.1	s__Deinococcus radiopugnans	78.6632	542	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_000701405.1	s__Deinococcus marmoris	78.6121	555	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949125.1	s__Deinococcus marmoris_A	78.5246	595	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599865.1	s__Deinococcus phoenicis	78.4993	534	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	78.3498	484	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	78.2721	513	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648115.1	s__Deinococcus seoulensis	78.1369	472	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_002017875.1	s__Deinococcus sp002017875	78.1143	480	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_002198095.1	s__Deinococcus indicus	77.8938	482	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_000008565.1	s__Deinococcus radiodurans	77.8603	389	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_014647435.1	s__Deinococcus radiotolerans	77.8057	421	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020685.1	s__Deinococcus deserti	77.7681	348	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745175.1	s__Deinococcus sp000745175	77.2057	340	1610	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:17,214] [INFO] GTDB search result was written to GCF_000378445.1_ASM37844v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:17,215] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:17,218] [INFO] DFAST_QC result json was written to GCF_000378445.1_ASM37844v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:17,219] [INFO] DFAST_QC completed!
[2024-01-25 17:40:17,219] [INFO] Total running time: 0h1m27s