[2024-01-25 18:07:20,358] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:20,362] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:20,362] [INFO] DQC Reference Directory: /var/lib/cwl/stg57d26a22-cc35-4bd4-893a-ca19be65dbd7/dqc_reference
[2024-01-25 18:07:21,471] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:21,471] [INFO] Task started: Prodigal
[2024-01-25 18:07:21,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e8f997e-e920-45bc-b5da-120a5c0f7d2b/GCF_002901445.1_ASM290144v1_genomic.fna.gz | prodigal -d GCF_002901445.1_ASM290144v1_genomic.fna/cds.fna -a GCF_002901445.1_ASM290144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:32,547] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:32,547] [INFO] Task started: HMMsearch
[2024-01-25 18:07:32,547] [INFO] Running command: hmmsearch --tblout GCF_002901445.1_ASM290144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57d26a22-cc35-4bd4-893a-ca19be65dbd7/dqc_reference/reference_markers.hmm GCF_002901445.1_ASM290144v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:32,777] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:32,778] [INFO] Found 6/6 markers.
[2024-01-25 18:07:32,814] [INFO] Query marker FASTA was written to GCF_002901445.1_ASM290144v1_genomic.fna/markers.fasta
[2024-01-25 18:07:32,815] [INFO] Task started: Blastn
[2024-01-25 18:07:32,815] [INFO] Running command: blastn -query GCF_002901445.1_ASM290144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57d26a22-cc35-4bd4-893a-ca19be65dbd7/dqc_reference/reference_markers.fasta -out GCF_002901445.1_ASM290144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:33,473] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:33,475] [INFO] Selected 19 target genomes.
[2024-01-25 18:07:33,475] [INFO] Target genome list was writen to GCF_002901445.1_ASM290144v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:33,493] [INFO] Task started: fastANI
[2024-01-25 18:07:33,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e8f997e-e920-45bc-b5da-120a5c0f7d2b/GCF_002901445.1_ASM290144v1_genomic.fna.gz --refList GCF_002901445.1_ASM290144v1_genomic.fna/target_genomes.txt --output GCF_002901445.1_ASM290144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:51,490] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:51,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57d26a22-cc35-4bd4-893a-ca19be65dbd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:51,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57d26a22-cc35-4bd4-893a-ca19be65dbd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:51,502] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:51,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:51,502] [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 koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	100.0	1497	1497	95	conclusive
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	82.5474	963	1497	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	81.0028	745	1497	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	80.6633	789	1497	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	80.6366	775	1497	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	80.5628	778	1497	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	80.5621	763	1497	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	80.4865	725	1497	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	80.485	776	1497	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	80.3857	716	1497	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	80.2819	740	1497	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	80.2453	723	1497	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	80.0361	720	1497	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	79.9521	677	1497	95	below_threshold
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	79.9436	653	1497	95	below_threshold
Deinococcus ficus	strain=DSM 19119	GCA_000430865.1	317577	317577	type	True	79.769	656	1497	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	79.7549	695	1497	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	79.7157	667	1497	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	79.674	686	1497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:51,503] [INFO] DFAST Taxonomy check result was written to GCF_002901445.1_ASM290144v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:51,504] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:51,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:51,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57d26a22-cc35-4bd4-893a-ca19be65dbd7/dqc_reference/checkm_data
[2024-01-25 18:07:51,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:51,549] [INFO] Task started: CheckM
[2024-01-25 18:07:51,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002901445.1_ASM290144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002901445.1_ASM290144v1_genomic.fna/checkm_input GCF_002901445.1_ASM290144v1_genomic.fna/checkm_result
[2024-01-25 18:08:27,129] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:27,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:27,148] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:27,148] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:27,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002901445.1_ASM290144v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:27,149] [INFO] Task started: Blastn
[2024-01-25 18:08:27,150] [INFO] Running command: blastn -query GCF_002901445.1_ASM290144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57d26a22-cc35-4bd4-893a-ca19be65dbd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002901445.1_ASM290144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:28,157] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:28,159] [INFO] Selected 17 target genomes.
[2024-01-25 18:08:28,159] [INFO] Target genome list was writen to GCF_002901445.1_ASM290144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:28,169] [INFO] Task started: fastANI
[2024-01-25 18:08:28,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e8f997e-e920-45bc-b5da-120a5c0f7d2b/GCF_002901445.1_ASM290144v1_genomic.fna.gz --refList GCF_002901445.1_ASM290144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002901445.1_ASM290144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:44,544] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:44,554] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:44,554] [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_002901445.1	s__Deinococcus koreensis	100.0	1497	1497	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_014201805.1	s__Deinococcus metalli	82.5517	963	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004801415.1	s__Deinococcus sp004801415	81.7186	875	1497	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	80.9892	747	1497	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	80.9111	773	1497	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	80.8224	779	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_006335125.1	s__Deinococcus radiopugnans	80.7497	768	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_001485435.1	s__Deinococcus grandis	80.5952	758	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_014648115.1	s__Deinococcus seoulensis	80.4935	775	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_014647075.1	s__Deinococcus aerophilus	80.4836	725	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	80.3908	714	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337115.1	s__Deinococcus sp013337115	80.23	752	1497	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	80.0165	723	1497	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	79.9429	678	1497	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	79.9316	659	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_004758605.1	s__Deinococcus metallilatus	79.8272	684	1497	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_018863415.1	s__Deinococcus sp018863415	79.3959	725	1497	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 18:08:44,556] [INFO] GTDB search result was written to GCF_002901445.1_ASM290144v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:44,556] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:44,560] [INFO] DFAST_QC result json was written to GCF_002901445.1_ASM290144v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:44,560] [INFO] DFAST_QC completed!
[2024-01-25 18:08:44,560] [INFO] Total running time: 0h1m24s