[2024-01-24 12:39:35,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg45c2edf8-81c6-462e-b59c-e9d7601e1cad/dqc_reference
[2024-01-24 12:39:36,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,856] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,856] [INFO] Running command: gunzip -c /var/lib/cwl/stgd66febf0-6ba4-4da7-97da-599042141655/GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna.gz | prodigal -d GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/cds.fna -a GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:44,782] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:44,782] [INFO] Task started: HMMsearch
[2024-01-24 12:39:44,782] [INFO] Running command: hmmsearch --tblout GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45c2edf8-81c6-462e-b59c-e9d7601e1cad/dqc_reference/reference_markers.hmm GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:45,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:45,059] [INFO] Found 6/6 markers.
[2024-01-24 12:39:45,090] [INFO] Query marker FASTA was written to GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/markers.fasta
[2024-01-24 12:39:45,091] [INFO] Task started: Blastn
[2024-01-24 12:39:45,091] [INFO] Running command: blastn -query GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/markers.fasta -db /var/lib/cwl/stg45c2edf8-81c6-462e-b59c-e9d7601e1cad/dqc_reference/reference_markers.fasta -out GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:45,694] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:45,698] [INFO] Selected 17 target genomes.
[2024-01-24 12:39:45,699] [INFO] Target genome list was writen to GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/target_genomes.txt
[2024-01-24 12:39:45,705] [INFO] Task started: fastANI
[2024-01-24 12:39:45,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgd66febf0-6ba4-4da7-97da-599042141655/GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna.gz --refList GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/target_genomes.txt --output GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:57,756] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:57,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45c2edf8-81c6-462e-b59c-e9d7601e1cad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:57,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45c2edf8-81c6-462e-b59c-e9d7601e1cad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:57,774] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:39:57,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:57,775] [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
Kurthia huakuii	strain=LAM0618	GCA_000505545.1	1421019	1421019	type	True	100.0	1154	1160	95	conclusive
Kurthia massiliensis	strain=JC30	GCA_000285555.1	1033739	1033739	type	True	82.051	610	1160	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	80.7628	453	1160	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	79.2252	78	1160	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	78.7426	247	1160	95	below_threshold
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	78.6953	241	1160	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	78.6647	238	1160	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	78.0361	170	1160	95	below_threshold
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	78.0138	162	1160	95	below_threshold
Caryophanon tenue	strain=DSM 14152	GCA_001700315.1	33978	33978	type	True	77.9087	177	1160	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.7902	190	1160	95	below_threshold
Lysinibacillus mangiferihumi	strain=CCTCC AB 2010389	GCA_005217845.1	1130819	1130819	type	True	77.715	155	1160	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	77.4253	121	1160	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	77.4233	146	1160	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	77.404	114	1160	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.5675	64	1160	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:57,776] [INFO] DFAST Taxonomy check result was written to GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/tc_result.tsv
[2024-01-24 12:39:57,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:57,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:57,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45c2edf8-81c6-462e-b59c-e9d7601e1cad/dqc_reference/checkm_data
[2024-01-24 12:39:57,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:57,819] [INFO] Task started: CheckM
[2024-01-24 12:39:57,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/checkm_input GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/checkm_result
[2024-01-24 12:40:27,591] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:27,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:27,618] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:27,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:27,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/markers.fasta)
[2024-01-24 12:40:27,620] [INFO] Task started: Blastn
[2024-01-24 12:40:27,620] [INFO] Running command: blastn -query GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/markers.fasta -db /var/lib/cwl/stg45c2edf8-81c6-462e-b59c-e9d7601e1cad/dqc_reference/reference_markers_gtdb.fasta -out GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:28,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:28,453] [INFO] Selected 8 target genomes.
[2024-01-24 12:40:28,453] [INFO] Target genome list was writen to GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:28,459] [INFO] Task started: fastANI
[2024-01-24 12:40:28,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgd66febf0-6ba4-4da7-97da-599042141655/GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna.gz --refList GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/target_genomes_gtdb.txt --output GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:34,866] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:34,874] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:34,875] [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_000505545.1	s__Kurthia huakuii	100.0	1155	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_003991225.1	s__Kurthia intestinigallinarum	85.1572	860	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
GCF_000285555.1	s__Kurthia massiliensis	81.999	615	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000285595.1	s__Kurthia senegalensis	80.7628	453	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006539985.1	s__Kurthia gibsonii	78.7256	248	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	97.46	97.18	0.93	0.90	4	-
GCF_003143955.1	s__Kurthia zopfii	78.6474	239	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.54	98.21	0.97	0.90	5	-
GCF_007896435.1	s__Rummeliibacillus suwonensis	78.0138	162	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
GCF_001274945.1	s__Viridibacillus arvi	77.9941	172	1160	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	95.96	95.96	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,876] [INFO] GTDB search result was written to GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:34,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:34,880] [INFO] DFAST_QC result json was written to GCF_000505545.1_draft_genome_sequence_of_Kurthia_huakuii_LAM0618_genomic.fna/dqc_result.json
[2024-01-24 12:40:34,880] [INFO] DFAST_QC completed!
[2024-01-24 12:40:34,880] [INFO] Total running time: 0h0m59s