[2024-01-24 12:30:19,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:19,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:19,252] [INFO] DQC Reference Directory: /var/lib/cwl/stg8aa257c3-163f-4ff0-992a-5f635aaa365b/dqc_reference
[2024-01-24 12:30:20,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:20,529] [INFO] Task started: Prodigal
[2024-01-24 12:30:20,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f76493f-88a1-48e4-8a87-cfa46ef5ae0a/GCF_003143955.1_ASM314395v1_genomic.fna.gz | prodigal -d GCF_003143955.1_ASM314395v1_genomic.fna/cds.fna -a GCF_003143955.1_ASM314395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:26,116] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:26,116] [INFO] Task started: HMMsearch
[2024-01-24 12:30:26,116] [INFO] Running command: hmmsearch --tblout GCF_003143955.1_ASM314395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8aa257c3-163f-4ff0-992a-5f635aaa365b/dqc_reference/reference_markers.hmm GCF_003143955.1_ASM314395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:26,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:26,380] [INFO] Found 6/6 markers.
[2024-01-24 12:30:26,412] [INFO] Query marker FASTA was written to GCF_003143955.1_ASM314395v1_genomic.fna/markers.fasta
[2024-01-24 12:30:26,413] [INFO] Task started: Blastn
[2024-01-24 12:30:26,413] [INFO] Running command: blastn -query GCF_003143955.1_ASM314395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aa257c3-163f-4ff0-992a-5f635aaa365b/dqc_reference/reference_markers.fasta -out GCF_003143955.1_ASM314395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:27,019] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:27,022] [INFO] Selected 11 target genomes.
[2024-01-24 12:30:27,022] [INFO] Target genome list was writen to GCF_003143955.1_ASM314395v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:27,026] [INFO] Task started: fastANI
[2024-01-24 12:30:27,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f76493f-88a1-48e4-8a87-cfa46ef5ae0a/GCF_003143955.1_ASM314395v1_genomic.fna.gz --refList GCF_003143955.1_ASM314395v1_genomic.fna/target_genomes.txt --output GCF_003143955.1_ASM314395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:33,692] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:33,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8aa257c3-163f-4ff0-992a-5f635aaa365b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:33,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8aa257c3-163f-4ff0-992a-5f635aaa365b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:33,701] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:30:33,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:33,702] [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 zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	100.0	908	912	95	conclusive
Kurthia zopfii	strain=NCTC10597	GCA_900452285.1	1650	1650	type	True	99.9925	911	912	95	conclusive
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	99.9817	881	912	95	conclusive
Kurthia zopfii	strain=NBRC 101529	GCA_007989745.1	1650	1650	type	True	99.9377	839	912	95	conclusive
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	80.1948	415	912	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	78.7502	218	912	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	78.1936	179	912	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.6196	107	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:33,705] [INFO] DFAST Taxonomy check result was written to GCF_003143955.1_ASM314395v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:33,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:33,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:33,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8aa257c3-163f-4ff0-992a-5f635aaa365b/dqc_reference/checkm_data
[2024-01-24 12:30:33,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:33,741] [INFO] Task started: CheckM
[2024-01-24 12:30:33,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003143955.1_ASM314395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003143955.1_ASM314395v1_genomic.fna/checkm_input GCF_003143955.1_ASM314395v1_genomic.fna/checkm_result
[2024-01-24 12:30:57,358] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:57,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:57,385] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:57,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:57,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003143955.1_ASM314395v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:57,386] [INFO] Task started: Blastn
[2024-01-24 12:30:57,386] [INFO] Running command: blastn -query GCF_003143955.1_ASM314395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8aa257c3-163f-4ff0-992a-5f635aaa365b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003143955.1_ASM314395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:58,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:58,191] [INFO] Selected 16 target genomes.
[2024-01-24 12:30:58,191] [INFO] Target genome list was writen to GCF_003143955.1_ASM314395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:58,204] [INFO] Task started: fastANI
[2024-01-24 12:30:58,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f76493f-88a1-48e4-8a87-cfa46ef5ae0a/GCF_003143955.1_ASM314395v1_genomic.fna.gz --refList GCF_003143955.1_ASM314395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003143955.1_ASM314395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:08,526] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:08,539] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:08,540] [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_003143955.1	s__Kurthia zopfii	100.0	908	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.54	98.21	0.97	0.90	5	conclusive
GCF_006539985.1	s__Kurthia gibsonii	80.2157	412	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	97.46	97.18	0.93	0.90	4	-
GCA_018065935.1	s__Kurthia sp018065935	79.9397	349	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143975.1	s__Kurthia sibirica	79.3676	361	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000285595.1	s__Kurthia senegalensis	78.7502	218	912	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_000285555.1	s__Kurthia massiliensis	78.7187	225	912	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_000505545.1	s__Kurthia huakuii	78.4278	235	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003576525.1	s__Rummeliibacillus sp003576525	78.345	184	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.66	98.66	0.89	0.89	2	-
GCF_002884495.1	s__Rummeliibacillus pycnus	78.0712	208	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813185.1	s__Viridibacillus sp002813185	78.0449	187	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
GCF_007896435.1	s__Rummeliibacillus suwonensis	77.7718	142	912	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_002736105.1	s__Solibacillus sp002736105	77.6337	115	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700315.1	s__Caryophanon tenue	77.5071	132	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Caryophanon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002973635.1	s__Lysinibacillus sp002973635	77.4625	112	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073375.1	s__Solibacillus sp003073375	77.4501	140	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002237755.1	s__Lysinibacillus sp002237755	77.4404	137	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	96.32	95.08	0.88	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:08,542] [INFO] GTDB search result was written to GCF_003143955.1_ASM314395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:08,542] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:08,547] [INFO] DFAST_QC result json was written to GCF_003143955.1_ASM314395v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:08,547] [INFO] DFAST_QC completed!
[2024-01-24 12:31:08,547] [INFO] Total running time: 0h0m49s