[2024-01-24 15:10:40,870] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg751c7d1e-fc2e-4fb2-a77b-035f4a874b44/dqc_reference
[2024-01-24 15:10:42,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,243] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg400f881d-b7b7-4634-b99f-e0534a107f25/GCF_030804085.1_ASM3080408v1_genomic.fna.gz | prodigal -d GCF_030804085.1_ASM3080408v1_genomic.fna/cds.fna -a GCF_030804085.1_ASM3080408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:54,137] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:54,137] [INFO] Task started: HMMsearch
[2024-01-24 15:10:54,138] [INFO] Running command: hmmsearch --tblout GCF_030804085.1_ASM3080408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg751c7d1e-fc2e-4fb2-a77b-035f4a874b44/dqc_reference/reference_markers.hmm GCF_030804085.1_ASM3080408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:54,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:54,421] [INFO] Found 6/6 markers.
[2024-01-24 15:10:54,460] [INFO] Query marker FASTA was written to GCF_030804085.1_ASM3080408v1_genomic.fna/markers.fasta
[2024-01-24 15:10:54,461] [INFO] Task started: Blastn
[2024-01-24 15:10:54,461] [INFO] Running command: blastn -query GCF_030804085.1_ASM3080408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg751c7d1e-fc2e-4fb2-a77b-035f4a874b44/dqc_reference/reference_markers.fasta -out GCF_030804085.1_ASM3080408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:55,172] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:55,174] [INFO] Selected 21 target genomes.
[2024-01-24 15:10:55,175] [INFO] Target genome list was writen to GCF_030804085.1_ASM3080408v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:55,183] [INFO] Task started: fastANI
[2024-01-24 15:10:55,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg400f881d-b7b7-4634-b99f-e0534a107f25/GCF_030804085.1_ASM3080408v1_genomic.fna.gz --refList GCF_030804085.1_ASM3080408v1_genomic.fna/target_genomes.txt --output GCF_030804085.1_ASM3080408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:13,712] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:13,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg751c7d1e-fc2e-4fb2-a77b-035f4a874b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:13,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg751c7d1e-fc2e-4fb2-a77b-035f4a874b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:13,728] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:13,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:13,729] [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 ficus	strain=DSM 19119	GCA_000430865.1	317577	317577	type	True	97.28	1167	1344	95	conclusive
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	97.233	1172	1344	95	conclusive
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	81.7469	719	1344	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	81.7319	679	1344	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	81.6941	692	1344	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	81.6712	717	1344	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	81.6215	706	1344	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	81.5995	677	1344	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	81.5704	721	1344	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	81.5094	740	1344	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	81.4876	741	1344	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	81.1792	721	1344	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	80.6688	698	1344	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	79.217	606	1344	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	79.2154	598	1344	95	below_threshold
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	78.9531	565	1344	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875835.1	980427	980427	type	True	78.8997	469	1344	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875875.1	980427	980427	type	True	78.8995	459	1344	95	below_threshold
Deinococcus wulumuqiensis	strain=R12	GCA_014875975.1	980427	980427	type	True	78.8674	488	1344	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	78.6763	449	1344	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	78.6116	457	1344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:13,730] [INFO] DFAST Taxonomy check result was written to GCF_030804085.1_ASM3080408v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:13,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:13,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:13,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg751c7d1e-fc2e-4fb2-a77b-035f4a874b44/dqc_reference/checkm_data
[2024-01-24 15:11:13,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:13,773] [INFO] Task started: CheckM
[2024-01-24 15:11:13,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030804085.1_ASM3080408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030804085.1_ASM3080408v1_genomic.fna/checkm_input GCF_030804085.1_ASM3080408v1_genomic.fna/checkm_result
[2024-01-24 15:11:55,699] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:55,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:55,724] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:55,724] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:55,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030804085.1_ASM3080408v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:55,725] [INFO] Task started: Blastn
[2024-01-24 15:11:55,725] [INFO] Running command: blastn -query GCF_030804085.1_ASM3080408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg751c7d1e-fc2e-4fb2-a77b-035f4a874b44/dqc_reference/reference_markers_gtdb.fasta -out GCF_030804085.1_ASM3080408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:56,657] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:56,669] [INFO] Selected 16 target genomes.
[2024-01-24 15:11:56,669] [INFO] Target genome list was writen to GCF_030804085.1_ASM3080408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:56,682] [INFO] Task started: fastANI
[2024-01-24 15:11:56,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg400f881d-b7b7-4634-b99f-e0534a107f25/GCF_030804085.1_ASM3080408v1_genomic.fna.gz --refList GCF_030804085.1_ASM3080408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030804085.1_ASM3080408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:12,227] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:12,243] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:12,243] [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_003444775.1	s__Deinococcus ficus	97.2525	1171	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	conclusive
GCF_002198095.1	s__Deinococcus indicus	81.738	715	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_001507665.1	s__Deinococcus actinosclerus	81.6934	693	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_002017875.1	s__Deinococcus sp002017875	81.6687	720	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_014648115.1	s__Deinococcus seoulensis	81.6463	704	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_001007995.1	s__Deinococcus soli	81.6254	674	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_013337115.1	s__Deinococcus sp013337115	81.5969	701	1344	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	81.508	741	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_014648135.1	s__Deinococcus sedimenti	81.3711	727	1344	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	81.1967	719	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201805.1	s__Deinococcus metalli	80.7207	691	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647655.1	s__Deinococcus malanensis	79.1393	546	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646915.1	s__Deinococcus aquiradiocola	79.0597	508	1344	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	78.9351	568	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755355.1	s__Deinococcus sp009755355	78.6043	524	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389865.1	s__JAABTL01 sp011389865	75.5003	129	1344	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAABTL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:12,245] [INFO] GTDB search result was written to GCF_030804085.1_ASM3080408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:12,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:12,249] [INFO] DFAST_QC result json was written to GCF_030804085.1_ASM3080408v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:12,250] [INFO] DFAST_QC completed!
[2024-01-24 15:12:12,250] [INFO] Total running time: 0h1m31s