[2024-01-24 14:47:26,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:26,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:26,970] [INFO] DQC Reference Directory: /var/lib/cwl/stgafce8c97-5620-4a65-9005-6b6b7146555b/dqc_reference
[2024-01-24 14:47:28,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:28,316] [INFO] Task started: Prodigal
[2024-01-24 14:47:28,316] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e288334-9422-4cf8-bee6-b7d90551df30/GCF_014646895.1_ASM1464689v1_genomic.fna.gz | prodigal -d GCF_014646895.1_ASM1464689v1_genomic.fna/cds.fna -a GCF_014646895.1_ASM1464689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:48,736] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:48,737] [INFO] Task started: HMMsearch
[2024-01-24 14:47:48,737] [INFO] Running command: hmmsearch --tblout GCF_014646895.1_ASM1464689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafce8c97-5620-4a65-9005-6b6b7146555b/dqc_reference/reference_markers.hmm GCF_014646895.1_ASM1464689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:49,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:49,073] [INFO] Found 6/6 markers.
[2024-01-24 14:47:49,126] [INFO] Query marker FASTA was written to GCF_014646895.1_ASM1464689v1_genomic.fna/markers.fasta
[2024-01-24 14:47:49,127] [INFO] Task started: Blastn
[2024-01-24 14:47:49,127] [INFO] Running command: blastn -query GCF_014646895.1_ASM1464689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafce8c97-5620-4a65-9005-6b6b7146555b/dqc_reference/reference_markers.fasta -out GCF_014646895.1_ASM1464689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:49,778] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:49,782] [INFO] Selected 13 target genomes.
[2024-01-24 14:47:49,782] [INFO] Target genome list was writen to GCF_014646895.1_ASM1464689v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:49,798] [INFO] Task started: fastANI
[2024-01-24 14:47:49,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e288334-9422-4cf8-bee6-b7d90551df30/GCF_014646895.1_ASM1464689v1_genomic.fna.gz --refList GCF_014646895.1_ASM1464689v1_genomic.fna/target_genomes.txt --output GCF_014646895.1_ASM1464689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:00,485] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:00,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafce8c97-5620-4a65-9005-6b6b7146555b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:00,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafce8c97-5620-4a65-9005-6b6b7146555b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:00,499] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:00,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:00,500] [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 roseus	strain=JCM 14370	GCA_014646895.1	392414	392414	type	True	100.0	1842	1848	95	conclusive
Deinococcus cellulosilyticus	strain=NBRC 106333	GCA_007990775.1	401558	401558	type	True	82.8185	1221	1848	95	below_threshold
Deinococcus misasensis	strain=DSM 22328	GCA_000745915.1	392413	392413	type	True	81.4202	998	1848	95	below_threshold
Deinococcus proteolyticus	strain=MRP	GCA_000190555.1	55148	55148	type	True	76.4076	88	1848	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	76.3226	83	1848	95	below_threshold
Deinococcus deserti	strain=VCD115	GCA_000020685.1	310783	310783	type	True	76.1998	104	1848	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	76.1885	109	1848	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	76.1354	102	1848	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	76.1069	78	1848	95	below_threshold
Deinococcus murrayi	strain=DSM 11303	GCA_000482805.1	68910	68910	type	True	76.0653	65	1848	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	76.0651	77	1848	95	below_threshold
Deinococcus aquatilis	strain=DSM 23025	GCA_000378445.1	519440	519440	type	True	75.9943	106	1848	95	below_threshold
Deinococcus frigens	strain=DSM 12807	GCA_000701425.1	249403	249403	type	True	75.939	94	1848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:00,502] [INFO] DFAST Taxonomy check result was written to GCF_014646895.1_ASM1464689v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:00,502] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:00,502] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:00,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafce8c97-5620-4a65-9005-6b6b7146555b/dqc_reference/checkm_data
[2024-01-24 14:48:00,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:00,556] [INFO] Task started: CheckM
[2024-01-24 14:48:00,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646895.1_ASM1464689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646895.1_ASM1464689v1_genomic.fna/checkm_input GCF_014646895.1_ASM1464689v1_genomic.fna/checkm_result
[2024-01-24 14:49:25,509] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:25,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:25,541] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:25,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:25,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646895.1_ASM1464689v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:25,542] [INFO] Task started: Blastn
[2024-01-24 14:49:25,542] [INFO] Running command: blastn -query GCF_014646895.1_ASM1464689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafce8c97-5620-4a65-9005-6b6b7146555b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646895.1_ASM1464689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:26,360] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:26,364] [INFO] Selected 17 target genomes.
[2024-01-24 14:49:26,365] [INFO] Target genome list was writen to GCF_014646895.1_ASM1464689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:26,420] [INFO] Task started: fastANI
[2024-01-24 14:49:26,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e288334-9422-4cf8-bee6-b7d90551df30/GCF_014646895.1_ASM1464689v1_genomic.fna.gz --refList GCF_014646895.1_ASM1464689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646895.1_ASM1464689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:40,491] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:40,502] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:40,503] [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_014646895.1	s__Deinococcus_C roseus	100.0	1842	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007990775.1	s__Deinococcus_C cellulosilyticus	82.8251	1219	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745915.1	s__Deinococcus_C misasensis	81.4201	997	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190555.1	s__Deinococcus proteolyticus	76.4076	88	1848	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	76.3835	103	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_014653275.1	s__Deinococcus piscis	76.2373	78	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020685.1	s__Deinococcus deserti	76.2166	103	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	76.1885	109	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	76.1354	102	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008565.1	s__Deinococcus radiodurans	76.0651	77	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_000378445.1	s__Deinococcus aquatilis	75.9943	106	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701425.1	s__Deinococcus frigens	75.939	94	1848	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745175.1	s__Deinococcus sp000745175	75.594	64	1848	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 14:49:40,504] [INFO] GTDB search result was written to GCF_014646895.1_ASM1464689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:40,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:40,509] [INFO] DFAST_QC result json was written to GCF_014646895.1_ASM1464689v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:40,509] [INFO] DFAST_QC completed!
[2024-01-24 14:49:40,509] [INFO] Total running time: 0h2m14s