[2024-01-24 13:47:12,035] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:12,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:12,037] [INFO] DQC Reference Directory: /var/lib/cwl/stga0542b2d-1c4b-407d-830f-7412e12d248d/dqc_reference
[2024-01-24 13:47:13,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,418] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgbca884c7-2dc0-4bc8-b12b-2ec9debdf0e7/GCF_007988965.1_ASM798896v1_genomic.fna.gz | prodigal -d GCF_007988965.1_ASM798896v1_genomic.fna/cds.fna -a GCF_007988965.1_ASM798896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:20,777] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:20,777] [INFO] Task started: HMMsearch
[2024-01-24 13:47:20,778] [INFO] Running command: hmmsearch --tblout GCF_007988965.1_ASM798896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0542b2d-1c4b-407d-830f-7412e12d248d/dqc_reference/reference_markers.hmm GCF_007988965.1_ASM798896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:21,071] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:21,072] [INFO] Found 6/6 markers.
[2024-01-24 13:47:21,109] [INFO] Query marker FASTA was written to GCF_007988965.1_ASM798896v1_genomic.fna/markers.fasta
[2024-01-24 13:47:21,110] [INFO] Task started: Blastn
[2024-01-24 13:47:21,110] [INFO] Running command: blastn -query GCF_007988965.1_ASM798896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0542b2d-1c4b-407d-830f-7412e12d248d/dqc_reference/reference_markers.fasta -out GCF_007988965.1_ASM798896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:21,761] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:21,764] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:21,765] [INFO] Target genome list was writen to GCF_007988965.1_ASM798896v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:21,776] [INFO] Task started: fastANI
[2024-01-24 13:47:21,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca884c7-2dc0-4bc8-b12b-2ec9debdf0e7/GCF_007988965.1_ASM798896v1_genomic.fna.gz --refList GCF_007988965.1_ASM798896v1_genomic.fna/target_genomes.txt --output GCF_007988965.1_ASM798896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:31,330] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:31,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0542b2d-1c4b-407d-830f-7412e12d248d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:31,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0542b2d-1c4b-407d-830f-7412e12d248d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:31,344] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:31,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:31,344] [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
Rummeliibacillus stabekisii	strain=NBRC 104870	GCA_007988965.1	241244	241244	type	True	100.0	1075	1076	95	conclusive
Rummeliibacillus stabekisii	strain=DSM 25578	GCA_014202625.1	241244	241244	type	True	99.9989	1075	1076	95	conclusive
Rummeliibacillus pycnus	strain=DSM 15030	GCA_002884495.1	101070	101070	type	True	79.2939	304	1076	95	below_threshold
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	78.8626	261	1076	95	below_threshold
Kurthia massiliensis	strain=JC30	GCA_000285555.1	1033739	1033739	type	True	78.6265	106	1076	95	below_threshold
Caryophanon latum	strain=DSM 14151	GCA_001700325.1	33977	33977	type	True	78.4278	55	1076	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	78.3124	106	1076	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	78.0926	177	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:31,346] [INFO] DFAST Taxonomy check result was written to GCF_007988965.1_ASM798896v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:31,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:31,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:31,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0542b2d-1c4b-407d-830f-7412e12d248d/dqc_reference/checkm_data
[2024-01-24 13:47:31,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:31,383] [INFO] Task started: CheckM
[2024-01-24 13:47:31,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007988965.1_ASM798896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007988965.1_ASM798896v1_genomic.fna/checkm_input GCF_007988965.1_ASM798896v1_genomic.fna/checkm_result
[2024-01-24 13:47:57,804] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:57,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:57,824] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:57,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:57,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007988965.1_ASM798896v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:57,825] [INFO] Task started: Blastn
[2024-01-24 13:47:57,825] [INFO] Running command: blastn -query GCF_007988965.1_ASM798896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0542b2d-1c4b-407d-830f-7412e12d248d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007988965.1_ASM798896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:58,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:58,593] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:58,593] [INFO] Target genome list was writen to GCF_007988965.1_ASM798896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:58,623] [INFO] Task started: fastANI
[2024-01-24 13:47:58,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca884c7-2dc0-4bc8-b12b-2ec9debdf0e7/GCF_007988965.1_ASM798896v1_genomic.fna.gz --refList GCF_007988965.1_ASM798896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007988965.1_ASM798896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:09,699] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:09,710] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:09,710] [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_007988965.1	s__Rummeliibacillus stabekisii	100.0	1075	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.11	96.96	0.93	0.90	5	conclusive
GCF_002884495.1	s__Rummeliibacillus pycnus	79.3017	303	1076	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_003576525.1	s__Rummeliibacillus sp003576525	79.1963	290	1076	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_007896435.1	s__Rummeliibacillus suwonensis	78.846	262	1076	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_000285555.1	s__Kurthia massiliensis	78.5873	107	1076	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_001955655.1	s__Viridibacillus arenosi	78.3775	169	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	99.71	99.53	0.97	0.96	4	-
GCF_000285595.1	s__Kurthia senegalensis	78.2994	107	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015999545.1	s__Lysinibacillus sp002340205	78.1023	124	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.79	97.71	0.94	0.94	5	-
GCF_002813185.1	s__Viridibacillus sp002813185	77.9967	171	1076	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_003991225.1	s__Kurthia intestinigallinarum	77.9081	113	1076	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_000612805.1	s__Metasolibacillus ndiopicus	77.1734	102	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049505.1	s__Metasolibacillus meyeri	76.9457	95	1076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metasolibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:09,712] [INFO] GTDB search result was written to GCF_007988965.1_ASM798896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:09,712] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:09,716] [INFO] DFAST_QC result json was written to GCF_007988965.1_ASM798896v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:09,716] [INFO] DFAST_QC completed!
[2024-01-24 13:48:09,716] [INFO] Total running time: 0h0m58s