[2024-01-24 13:31:57,438] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg562c9818-0ba6-4012-9796-35e8e5cdf3f6/dqc_reference
[2024-01-24 13:31:58,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,768] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg6973eb55-bc73-4c45-aebc-07d2414cbcd2/GCF_007991015.1_ASM799101v1_genomic.fna.gz | prodigal -d GCF_007991015.1_ASM799101v1_genomic.fna/cds.fna -a GCF_007991015.1_ASM799101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:04,891] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:04,891] [INFO] Task started: HMMsearch
[2024-01-24 13:32:04,891] [INFO] Running command: hmmsearch --tblout GCF_007991015.1_ASM799101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg562c9818-0ba6-4012-9796-35e8e5cdf3f6/dqc_reference/reference_markers.hmm GCF_007991015.1_ASM799101v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:05,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:05,080] [INFO] Found 6/6 markers.
[2024-01-24 13:32:05,103] [INFO] Query marker FASTA was written to GCF_007991015.1_ASM799101v1_genomic.fna/markers.fasta
[2024-01-24 13:32:05,103] [INFO] Task started: Blastn
[2024-01-24 13:32:05,103] [INFO] Running command: blastn -query GCF_007991015.1_ASM799101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg562c9818-0ba6-4012-9796-35e8e5cdf3f6/dqc_reference/reference_markers.fasta -out GCF_007991015.1_ASM799101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:05,812] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:05,815] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:05,815] [INFO] Target genome list was writen to GCF_007991015.1_ASM799101v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:05,820] [INFO] Task started: fastANI
[2024-01-24 13:32:05,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg6973eb55-bc73-4c45-aebc-07d2414cbcd2/GCF_007991015.1_ASM799101v1_genomic.fna.gz --refList GCF_007991015.1_ASM799101v1_genomic.fna/target_genomes.txt --output GCF_007991015.1_ASM799101v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:13,101] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:13,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg562c9818-0ba6-4012-9796-35e8e5cdf3f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:13,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg562c9818-0ba6-4012-9796-35e8e5cdf3f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:13,112] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:13,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:13,112] [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
Oceanithermus desulfurans	strain=NBRC 100063	GCA_007991015.1	227924	227924	type	True	100.0	789	791	95	conclusive
Oceanithermus desulfurans	strain=DSM 15757	GCA_014201675.1	227924	227924	type	True	99.9975	787	791	95	conclusive
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	92.6721	698	791	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	77.6149	291	791	95	below_threshold
Marinithermus hydrothermalis	strain=DSM 14884	GCA_000195335.1	186192	186192	type	True	77.5859	217	791	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	75.9152	117	791	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	75.8826	114	791	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	75.867	114	791	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	75.7041	111	791	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	74.8563	143	791	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	74.807	121	791	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:13,113] [INFO] DFAST Taxonomy check result was written to GCF_007991015.1_ASM799101v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:13,114] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:13,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:13,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg562c9818-0ba6-4012-9796-35e8e5cdf3f6/dqc_reference/checkm_data
[2024-01-24 13:32:13,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:13,162] [INFO] Task started: CheckM
[2024-01-24 13:32:13,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991015.1_ASM799101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991015.1_ASM799101v1_genomic.fna/checkm_input GCF_007991015.1_ASM799101v1_genomic.fna/checkm_result
[2024-01-24 13:32:35,201] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:35,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:35,219] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:35,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:35,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991015.1_ASM799101v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:35,220] [INFO] Task started: Blastn
[2024-01-24 13:32:35,220] [INFO] Running command: blastn -query GCF_007991015.1_ASM799101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg562c9818-0ba6-4012-9796-35e8e5cdf3f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991015.1_ASM799101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:36,386] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:36,390] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:36,390] [INFO] Target genome list was writen to GCF_007991015.1_ASM799101v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:36,397] [INFO] Task started: fastANI
[2024-01-24 13:32:36,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg6973eb55-bc73-4c45-aebc-07d2414cbcd2/GCF_007991015.1_ASM799101v1_genomic.fna.gz --refList GCF_007991015.1_ASM799101v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991015.1_ASM799101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:41,649] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:41,658] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:41,659] [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_014201675.1	s__Oceanithermus desulfurans	99.9975	787	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	97.68	96.67	0.93	0.89	5	conclusive
GCF_000183745.1	s__Oceanithermus profundus	92.6721	698	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330655.1	s__Oceanithermus profundus_A	88.9554	484	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494055.1	s__Oceanithermus sp015494055	87.137	505	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	99.03	99.03	0.84	0.84	2	-
GCA_015493285.1	s__Oceanithermus sp015493285	81.7689	286	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490435.1	s__WFXV01 sp015490435	78.8458	264	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195335.1	s__Marinithermus hydrothermalis	77.6045	215	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Marinithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	75.8797	113	791	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	74.8533	145	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,660] [INFO] GTDB search result was written to GCF_007991015.1_ASM799101v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:41,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:41,664] [INFO] DFAST_QC result json was written to GCF_007991015.1_ASM799101v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:41,665] [INFO] DFAST_QC completed!
[2024-01-24 13:32:41,665] [INFO] Total running time: 0h0m44s