[2023-06-29 08:44:35,621] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:44:35,623] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:44:35,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc1976d-6093-41ef-863f-2e9471f41033/dqc_reference
[2023-06-29 08:44:36,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:44:36,890] [INFO] Task started: Prodigal
[2023-06-29 08:44:36,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgdaa1b3e5-4ffe-4fc3-8b15-be83bf11746a/GCA_027405315.1_ASM2740531v1_genomic.fna.gz | prodigal -d GCA_027405315.1_ASM2740531v1_genomic.fna/cds.fna -a GCA_027405315.1_ASM2740531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:44:42,541] [INFO] Task succeeded: Prodigal
[2023-06-29 08:44:42,542] [INFO] Task started: HMMsearch
[2023-06-29 08:44:42,542] [INFO] Running command: hmmsearch --tblout GCA_027405315.1_ASM2740531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc1976d-6093-41ef-863f-2e9471f41033/dqc_reference/reference_markers.hmm GCA_027405315.1_ASM2740531v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:44:42,769] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:44:42,770] [INFO] Found 6/6 markers.
[2023-06-29 08:44:42,801] [INFO] Query marker FASTA was written to GCA_027405315.1_ASM2740531v1_genomic.fna/markers.fasta
[2023-06-29 08:44:42,802] [INFO] Task started: Blastn
[2023-06-29 08:44:42,805] [INFO] Running command: blastn -query GCA_027405315.1_ASM2740531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc1976d-6093-41ef-863f-2e9471f41033/dqc_reference/reference_markers.fasta -out GCA_027405315.1_ASM2740531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:44:43,511] [INFO] Task succeeded: Blastn
[2023-06-29 08:44:43,534] [INFO] Selected 25 target genomes.
[2023-06-29 08:44:43,535] [INFO] Target genome list was writen to GCA_027405315.1_ASM2740531v1_genomic.fna/target_genomes.txt
[2023-06-29 08:44:43,544] [INFO] Task started: fastANI
[2023-06-29 08:44:43,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaa1b3e5-4ffe-4fc3-8b15-be83bf11746a/GCA_027405315.1_ASM2740531v1_genomic.fna.gz --refList GCA_027405315.1_ASM2740531v1_genomic.fna/target_genomes.txt --output GCA_027405315.1_ASM2740531v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:44:58,237] [INFO] Task succeeded: fastANI
[2023-06-29 08:44:58,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc1976d-6093-41ef-863f-2e9471f41033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:44:58,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc1976d-6093-41ef-863f-2e9471f41033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:44:58,254] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:44:58,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:44:58,255] [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
Deinobacterium chartae	strain=DSM 21458	GCA_014202645.1	521158	521158	type	True	76.777	102	743	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	76.3851	97	743	95	below_threshold
Deinococcus pimensis	strain=DSM 21231	GCA_000519345.1	309888	309888	type	True	76.2343	74	743	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	76.2133	73	743	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	76.1619	70	743	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	76.1072	58	743	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	76.0095	68	743	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	75.9977	78	743	95	below_threshold
Deinococcus reticulitermitis	strain=CGMCC 1.10218	GCA_900109185.1	856736	856736	type	True	75.9749	52	743	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	75.8485	59	743	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	75.8363	72	743	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	75.7949	90	743	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	75.7244	58	743	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	75.7126	70	743	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	75.7066	57	743	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	75.6824	62	743	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	75.6382	60	743	95	below_threshold
Deinococcus alpinitundrae	strain=LMG 24283	GCA_009982895.1	468913	468913	type	True	75.5095	76	743	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	75.4859	63	743	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	75.463	58	743	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:44:58,257] [INFO] DFAST Taxonomy check result was written to GCA_027405315.1_ASM2740531v1_genomic.fna/tc_result.tsv
[2023-06-29 08:44:58,257] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:44:58,258] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:44:58,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc1976d-6093-41ef-863f-2e9471f41033/dqc_reference/checkm_data
[2023-06-29 08:44:58,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:44:58,294] [INFO] Task started: CheckM
[2023-06-29 08:44:58,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027405315.1_ASM2740531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027405315.1_ASM2740531v1_genomic.fna/checkm_input GCA_027405315.1_ASM2740531v1_genomic.fna/checkm_result
[2023-06-29 08:45:21,189] [INFO] Task succeeded: CheckM
[2023-06-29 08:45:21,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:45:21,211] [INFO] ===== Completeness check finished =====
[2023-06-29 08:45:21,212] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:45:21,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027405315.1_ASM2740531v1_genomic.fna/markers.fasta)
[2023-06-29 08:45:21,213] [INFO] Task started: Blastn
[2023-06-29 08:45:21,213] [INFO] Running command: blastn -query GCA_027405315.1_ASM2740531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc1976d-6093-41ef-863f-2e9471f41033/dqc_reference/reference_markers_gtdb.fasta -out GCA_027405315.1_ASM2740531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:22,246] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:22,251] [INFO] Selected 25 target genomes.
[2023-06-29 08:45:22,252] [INFO] Target genome list was writen to GCA_027405315.1_ASM2740531v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:45:22,276] [INFO] Task started: fastANI
[2023-06-29 08:45:22,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaa1b3e5-4ffe-4fc3-8b15-be83bf11746a/GCA_027405315.1_ASM2740531v1_genomic.fna.gz --refList GCA_027405315.1_ASM2740531v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027405315.1_ASM2740531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:45:36,466] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:36,485] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:45:36,486] [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_014202645.1	s__Deinobacterium chartae	76.777	102	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	76.3851	97	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519345.1	s__Deinococcus_A pimensis	76.2343	74	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	76.2132	73	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001507665.1	s__Deinococcus actinosclerus	76.1619	70	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_018863415.1	s__Deinococcus sp018863415	76.1603	71	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485435.1	s__Deinococcus grandis	76.1072	58	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_014201885.1	s__Deinococcus budaensis	76.0173	77	743	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	76.0095	68	743	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	75.9004	57	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_014647075.1	s__Deinococcus aerophilus	75.8168	73	743	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	75.7949	90	743	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	75.7244	58	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_001424185.1	s__Deinococcus sp001424185	75.7131	61	743	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	75.6824	62	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_000183745.1	s__Oceanithermus profundus	75.6382	60	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009982895.1	s__Deinococcus alpinitundrae	75.5095	76	743	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:45:36,489] [INFO] GTDB search result was written to GCA_027405315.1_ASM2740531v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:45:36,489] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:45:36,494] [INFO] DFAST_QC result json was written to GCA_027405315.1_ASM2740531v1_genomic.fna/dqc_result.json
[2023-06-29 08:45:36,494] [INFO] DFAST_QC completed!
[2023-06-29 08:45:36,494] [INFO] Total running time: 0h1m1s