[2024-01-24 12:44:43,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg628b1bfc-6db7-413b-8577-820cc02cf247/dqc_reference
[2024-01-24 12:44:44,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,967] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,968] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ebdb532-e337-4805-81d2-cfd4fbc87730/GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/cds.fna -a GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:58,170] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:58,170] [INFO] Task started: HMMsearch
[2024-01-24 12:44:58,170] [INFO] Running command: hmmsearch --tblout GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg628b1bfc-6db7-413b-8577-820cc02cf247/dqc_reference/reference_markers.hmm GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:58,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:58,499] [INFO] Found 6/6 markers.
[2024-01-24 12:44:58,562] [INFO] Query marker FASTA was written to GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:44:58,563] [INFO] Task started: Blastn
[2024-01-24 12:44:58,563] [INFO] Running command: blastn -query GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg628b1bfc-6db7-413b-8577-820cc02cf247/dqc_reference/reference_markers.fasta -out GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:59,159] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:59,162] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:59,162] [INFO] Target genome list was writen to GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:44:59,175] [INFO] Task started: fastANI
[2024-01-24 12:44:59,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebdb532-e337-4805-81d2-cfd4fbc87730/GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna.gz --refList GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:14,098] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:14,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg628b1bfc-6db7-413b-8577-820cc02cf247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:14,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg628b1bfc-6db7-413b-8577-820cc02cf247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:14,110] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:14,110] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:14,110] [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
Fictibacillus solisalsi	strain=CGMCC 1.6854	GCA_900103485.1	459525	459525	type	True	100.0	1593	1595	95	conclusive
Fictibacillus enclensis	strain=NIO-1003	GCA_001457035.1	1017270	1017270	type	True	92.4609	1351	1595	95	below_threshold
Fictibacillus enclensis	strain=NIO-1003	GCA_900094955.1	1017270	1017270	type	True	92.4608	1351	1595	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	77.7882	122	1595	95	below_threshold
Fictibacillus barbaricus	strain=CCM 4982	GCA_014635025.1	182136	182136	type	True	77.7167	127	1595	95	below_threshold
Fictibacillus halophilus	strain=KCTC 33758	GCA_016401385.1	1610490	1610490	type	True	77.6991	110	1595	95	below_threshold
Fictibacillus barbaricus	strain=DSM 14730	GCA_017052555.1	182136	182136	type	True	77.6078	127	1595	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	77.2836	55	1595	95	below_threshold
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	76.5217	57	1595	95	below_threshold
Metabacillus kandeliae	strain=GX 13764	GCA_021166585.1	2900151	2900151	type	True	76.3674	65	1595	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:14,112] [INFO] DFAST Taxonomy check result was written to GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:45:14,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:14,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:14,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg628b1bfc-6db7-413b-8577-820cc02cf247/dqc_reference/checkm_data
[2024-01-24 12:45:14,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:14,166] [INFO] Task started: CheckM
[2024-01-24 12:45:14,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/checkm_input GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:45:55,714] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:55,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:55,743] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:55,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:55,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:45:55,745] [INFO] Task started: Blastn
[2024-01-24 12:45:55,745] [INFO] Running command: blastn -query GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg628b1bfc-6db7-413b-8577-820cc02cf247/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:56,518] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:56,522] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:56,522] [INFO] Target genome list was writen to GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:56,549] [INFO] Task started: fastANI
[2024-01-24 12:45:56,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebdb532-e337-4805-81d2-cfd4fbc87730/GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna.gz --refList GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:11,070] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:11,084] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:11,085] [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_900103485.1	s__Fictibacillus_C solisalsi	100.0	1593	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001457035.1	s__Fictibacillus_C enclensis	92.4494	1352	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus_C	95.0	99.48	98.95	0.97	0.95	3	-
GCF_001510655.1	s__Fictibacillus_C sp001510655	79.9972	677	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus_C	95.0	98.06	97.97	0.90	0.90	3	-
GCF_002245695.1	s__Fictibacillus aquaticus	77.9542	102	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216955.1	s__Fictibacillus sp004216955	77.7503	111	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635025.1	s__Fictibacillus barbaricus	77.7167	127	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016401385.1	s__Fictibacillus halophilus	77.6991	110	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642935.1	s__Fictibacillus arsenicus_B	77.4792	124	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016401345.1	s__Fictibacillus nanhaiensis_A	77.4211	115	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	97.66	97.26	0.91	0.88	5	-
GCF_001636425.1	s__Bacillus_AE acidicola	77.2323	56	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613125.1	s__Bacillus_D sp000613125	77.1255	50	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	77.1162	62	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_003316765.1	s__Bacillus_BM sp003316765	76.8544	53	1595	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	98.55	98.55	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:11,086] [INFO] GTDB search result was written to GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:11,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:11,091] [INFO] DFAST_QC result json was written to GCF_900103485.1_IMG-taxon_2619618871_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:46:11,091] [INFO] DFAST_QC completed!
[2024-01-24 12:46:11,091] [INFO] Total running time: 0h1m27s