[2024-01-25 19:57:35,651] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:35,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:35,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg134abaf7-aa4d-40d3-bbc0-dcf17ab63894/dqc_reference
[2024-01-25 19:57:36,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:36,767] [INFO] Task started: Prodigal
[2024-01-25 19:57:36,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a5214df-864b-473c-b97e-fdfb4f062d59/GCF_900452285.1_50861_B01_genomic.fna.gz | prodigal -d GCF_900452285.1_50861_B01_genomic.fna/cds.fna -a GCF_900452285.1_50861_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:42,237] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:42,237] [INFO] Task started: HMMsearch
[2024-01-25 19:57:42,238] [INFO] Running command: hmmsearch --tblout GCF_900452285.1_50861_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg134abaf7-aa4d-40d3-bbc0-dcf17ab63894/dqc_reference/reference_markers.hmm GCF_900452285.1_50861_B01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:42,454] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:42,456] [INFO] Found 6/6 markers.
[2024-01-25 19:57:42,480] [INFO] Query marker FASTA was written to GCF_900452285.1_50861_B01_genomic.fna/markers.fasta
[2024-01-25 19:57:42,481] [INFO] Task started: Blastn
[2024-01-25 19:57:42,481] [INFO] Running command: blastn -query GCF_900452285.1_50861_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg134abaf7-aa4d-40d3-bbc0-dcf17ab63894/dqc_reference/reference_markers.fasta -out GCF_900452285.1_50861_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:43,042] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:43,045] [INFO] Selected 11 target genomes.
[2024-01-25 19:57:43,045] [INFO] Target genome list was writen to GCF_900452285.1_50861_B01_genomic.fna/target_genomes.txt
[2024-01-25 19:57:43,049] [INFO] Task started: fastANI
[2024-01-25 19:57:43,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a5214df-864b-473c-b97e-fdfb4f062d59/GCF_900452285.1_50861_B01_genomic.fna.gz --refList GCF_900452285.1_50861_B01_genomic.fna/target_genomes.txt --output GCF_900452285.1_50861_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:50,835] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:50,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg134abaf7-aa4d-40d3-bbc0-dcf17ab63894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:50,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg134abaf7-aa4d-40d3-bbc0-dcf17ab63894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:50,843] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:57:50,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:50,843] [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=NCTC10597	GCA_900452285.1	1650	1650	type	True	100.0	995	996	95	conclusive
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	99.91	903	996	95	conclusive
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	99.9013	910	996	95	conclusive
Kurthia zopfii	strain=NBRC 101529	GCA_007989745.1	1650	1650	type	True	99.8472	863	996	95	conclusive
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	80.1837	436	996	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	78.7961	232	996	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	78.0861	189	996	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.6563	113	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:50,844] [INFO] DFAST Taxonomy check result was written to GCF_900452285.1_50861_B01_genomic.fna/tc_result.tsv
[2024-01-25 19:57:50,845] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:50,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:50,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg134abaf7-aa4d-40d3-bbc0-dcf17ab63894/dqc_reference/checkm_data
[2024-01-25 19:57:50,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:50,876] [INFO] Task started: CheckM
[2024-01-25 19:57:50,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900452285.1_50861_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900452285.1_50861_B01_genomic.fna/checkm_input GCF_900452285.1_50861_B01_genomic.fna/checkm_result
[2024-01-25 19:58:12,298] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:12,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:12,313] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:12,314] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:12,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900452285.1_50861_B01_genomic.fna/markers.fasta)
[2024-01-25 19:58:12,314] [INFO] Task started: Blastn
[2024-01-25 19:58:12,314] [INFO] Running command: blastn -query GCF_900452285.1_50861_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg134abaf7-aa4d-40d3-bbc0-dcf17ab63894/dqc_reference/reference_markers_gtdb.fasta -out GCF_900452285.1_50861_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:13,120] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:13,123] [INFO] Selected 16 target genomes.
[2024-01-25 19:58:13,123] [INFO] Target genome list was writen to GCF_900452285.1_50861_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:13,140] [INFO] Task started: fastANI
[2024-01-25 19:58:13,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a5214df-864b-473c-b97e-fdfb4f062d59/GCF_900452285.1_50861_B01_genomic.fna.gz --refList GCF_900452285.1_50861_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900452285.1_50861_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:24,927] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:24,937] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:24,938] [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	99.91	903	996	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	80.1888	436	996	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	80.0241	365	996	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	79.3599	370	996	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_002884495.1	s__Rummeliibacillus pycnus	79.2894	218	996	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_000505545.1	s__Kurthia huakuii	79.2486	242	996	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_002813185.1	s__Viridibacillus sp002813185	79.2483	211	996	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_002736105.1	s__Solibacillus sp002736105	79.0538	135	996	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_000285555.1	s__Kurthia massiliensis	78.8652	233	996	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	78.8329	230	996	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_003576525.1	s__Rummeliibacillus sp003576525	78.5462	183	996	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_003073375.1	s__Solibacillus sp003073375	78.5243	163	996	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_007896435.1	s__Rummeliibacillus suwonensis	77.9385	154	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
GCA_002973635.1	s__Lysinibacillus sp002973635	77.8718	133	996	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_001700315.1	s__Caryophanon tenue	77.5541	136	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Caryophanon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237755.1	s__Lysinibacillus sp002237755	77.5321	142	996	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	96.32	95.08	0.88	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:24,939] [INFO] GTDB search result was written to GCF_900452285.1_50861_B01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:24,940] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:24,942] [INFO] DFAST_QC result json was written to GCF_900452285.1_50861_B01_genomic.fna/dqc_result.json
[2024-01-25 19:58:24,943] [INFO] DFAST_QC completed!
[2024-01-25 19:58:24,943] [INFO] Total running time: 0h0m49s