[2024-01-24 13:39:59,615] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:39:59,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:39:59,617] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8c9976b-9129-4876-b924-cd75f1c37780/dqc_reference
[2024-01-24 13:40:00,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:00,961] [INFO] Task started: Prodigal
[2024-01-24 13:40:00,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a5d7aee-8a66-4bb8-b9ac-c3bb4c4d526a/GCF_000430865.1_ASM43086v1_genomic.fna.gz | prodigal -d GCF_000430865.1_ASM43086v1_genomic.fna/cds.fna -a GCF_000430865.1_ASM43086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:12,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:12,857] [INFO] Task started: HMMsearch
[2024-01-24 13:40:12,857] [INFO] Running command: hmmsearch --tblout GCF_000430865.1_ASM43086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8c9976b-9129-4876-b924-cd75f1c37780/dqc_reference/reference_markers.hmm GCF_000430865.1_ASM43086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:13,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:13,138] [INFO] Found 6/6 markers.
[2024-01-24 13:40:13,175] [INFO] Query marker FASTA was written to GCF_000430865.1_ASM43086v1_genomic.fna/markers.fasta
[2024-01-24 13:40:13,175] [INFO] Task started: Blastn
[2024-01-24 13:40:13,176] [INFO] Running command: blastn -query GCF_000430865.1_ASM43086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8c9976b-9129-4876-b924-cd75f1c37780/dqc_reference/reference_markers.fasta -out GCF_000430865.1_ASM43086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:13,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:13,847] [INFO] Selected 14 target genomes.
[2024-01-24 13:40:13,847] [INFO] Target genome list was writen to GCF_000430865.1_ASM43086v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:13,852] [INFO] Task started: fastANI
[2024-01-24 13:40:13,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5d7aee-8a66-4bb8-b9ac-c3bb4c4d526a/GCF_000430865.1_ASM43086v1_genomic.fna.gz --refList GCF_000430865.1_ASM43086v1_genomic.fna/target_genomes.txt --output GCF_000430865.1_ASM43086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:27,021] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:27,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8c9976b-9129-4876-b924-cd75f1c37780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:27,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8c9976b-9129-4876-b924-cd75f1c37780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:27,039] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:27,039] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:27,039] [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	100.0	1359	1359	95	conclusive
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	99.9992	1355	1359	95	conclusive
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	81.6446	700	1359	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	81.6342	705	1359	95	below_threshold
Deinococcus grandis	strain=ATCC 43672	GCA_001485435.1	57498	57498	type	True	81.5776	738	1359	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	81.5283	684	1359	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	81.522	704	1359	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	81.484	736	1359	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	81.428	740	1359	95	below_threshold
Deinococcus sedimenti	strain=JCM 31405	GCA_014648135.1	1867090	1867090	type	True	81.3661	734	1359	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	81.3183	751	1359	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	81.2605	744	1359	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	81.245	750	1359	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	80.5863	712	1359	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:27,041] [INFO] DFAST Taxonomy check result was written to GCF_000430865.1_ASM43086v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:27,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:27,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:27,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8c9976b-9129-4876-b924-cd75f1c37780/dqc_reference/checkm_data
[2024-01-24 13:40:27,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:27,084] [INFO] Task started: CheckM
[2024-01-24 13:40:27,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430865.1_ASM43086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430865.1_ASM43086v1_genomic.fna/checkm_input GCF_000430865.1_ASM43086v1_genomic.fna/checkm_result
[2024-01-24 13:41:10,379] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:10,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:10,403] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:10,404] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:10,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430865.1_ASM43086v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:10,404] [INFO] Task started: Blastn
[2024-01-24 13:41:10,404] [INFO] Running command: blastn -query GCF_000430865.1_ASM43086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8c9976b-9129-4876-b924-cd75f1c37780/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430865.1_ASM43086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:11,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:11,620] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:11,620] [INFO] Target genome list was writen to GCF_000430865.1_ASM43086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:11,623] [INFO] Task started: fastANI
[2024-01-24 13:41:11,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5d7aee-8a66-4bb8-b9ac-c3bb4c4d526a/GCF_000430865.1_ASM43086v1_genomic.fna.gz --refList GCF_000430865.1_ASM43086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430865.1_ASM43086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:22,593] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,604] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:22,604] [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	99.9992	1355	1359	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_001507665.1	s__Deinococcus actinosclerus	81.6557	700	1359	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_014648115.1	s__Deinococcus seoulensis	81.6108	707	1359	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_002198095.1	s__Deinococcus indicus	81.5921	732	1359	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_001485435.1	s__Deinococcus grandis	81.5607	740	1359	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_001007995.1	s__Deinococcus soli	81.5422	685	1359	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	81.4204	728	1359	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648135.1	s__Deinococcus sedimenti	81.3354	739	1359	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	81.2734	746	1359	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	80.5783	714	1359	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	79.2999	537	1359	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,619] [INFO] GTDB search result was written to GCF_000430865.1_ASM43086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:22,621] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:22,624] [INFO] DFAST_QC result json was written to GCF_000430865.1_ASM43086v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:22,625] [INFO] DFAST_QC completed!
[2024-01-24 13:41:22,625] [INFO] Total running time: 0h1m23s