[2024-01-24 12:30:18,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:18,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:18,703] [INFO] DQC Reference Directory: /var/lib/cwl/stgde4bae5c-3c83-4e70-9a0b-c32887d027f8/dqc_reference
[2024-01-24 12:30:20,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:20,045] [INFO] Task started: Prodigal
[2024-01-24 12:30:20,045] [INFO] Running command: gunzip -c /var/lib/cwl/stge31d64ce-37d3-4628-8c39-49d3f3396d36/GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/cds.fna -a GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:31,646] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:31,646] [INFO] Task started: HMMsearch
[2024-01-24 12:30:31,646] [INFO] Running command: hmmsearch --tblout GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde4bae5c-3c83-4e70-9a0b-c32887d027f8/dqc_reference/reference_markers.hmm GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:31,983] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:31,985] [INFO] Found 6/6 markers.
[2024-01-24 12:30:32,027] [INFO] Query marker FASTA was written to GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:30:32,028] [INFO] Task started: Blastn
[2024-01-24 12:30:32,028] [INFO] Running command: blastn -query GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgde4bae5c-3c83-4e70-9a0b-c32887d027f8/dqc_reference/reference_markers.fasta -out GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:32,698] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:32,702] [INFO] Selected 18 target genomes.
[2024-01-24 12:30:32,703] [INFO] Target genome list was writen to GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:30:32,713] [INFO] Task started: fastANI
[2024-01-24 12:30:32,713] [INFO] Running command: fastANI --query /var/lib/cwl/stge31d64ce-37d3-4628-8c39-49d3f3396d36/GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna.gz --refList GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:45,217] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:45,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde4bae5c-3c83-4e70-9a0b-c32887d027f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:45,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde4bae5c-3c83-4e70-9a0b-c32887d027f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:45,227] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:45,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:45,228] [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
Lihuaxuella thermophila	strain=DSM 46701	GCA_900110165.1	1173111	1173111	type	True	100.0	1244	1248	95	conclusive
Laceyella sediminis	strain=RHA1	GCA_003003125.1	573074	573074	type	True	77.5059	115	1248	95	below_threshold
Thermoactinomyces daqus	strain=H-18	GCA_000763315.1	1329516	1329516	type	True	77.4061	171	1248	95	below_threshold
Laceyella sacchari	strain=DSM 43356	GCA_004343255.1	37482	37482	type	True	77.3348	117	1248	95	below_threshold
Thermoactinomyces intermedius	strain=NRRL B-16979	GCA_013912365.1	2024	2024	type	True	77.2777	109	1248	95	below_threshold
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	76.7315	114	1248	95	below_threshold
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	76.7294	77	1248	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.1808	64	1248	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	76.0919	59	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:45,230] [INFO] DFAST Taxonomy check result was written to GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:30:45,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:45,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:45,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde4bae5c-3c83-4e70-9a0b-c32887d027f8/dqc_reference/checkm_data
[2024-01-24 12:30:45,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:45,280] [INFO] Task started: CheckM
[2024-01-24 12:30:45,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/checkm_input GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:31:22,908] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:22,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:22,928] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:22,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:22,929] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:31:22,929] [INFO] Task started: Blastn
[2024-01-24 12:31:22,929] [INFO] Running command: blastn -query GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgde4bae5c-3c83-4e70-9a0b-c32887d027f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:23,647] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:23,651] [INFO] Selected 18 target genomes.
[2024-01-24 12:31:23,651] [INFO] Target genome list was writen to GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:23,684] [INFO] Task started: fastANI
[2024-01-24 12:31:23,684] [INFO] Running command: fastANI --query /var/lib/cwl/stge31d64ce-37d3-4628-8c39-49d3f3396d36/GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna.gz --refList GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:36,359] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:36,369] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:36,369] [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_900110165.1	s__Lihuaxuella thermophila	100.0	1245	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Lihuaxuella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016055185.1	s__Paenactinomyces guangxiensis	78.0573	304	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Paenactinomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003003125.1	s__Laceyella sediminis	77.5059	115	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	97.79	97.73	0.93	0.93	3	-
GCF_000763315.1	s__Thermoactinomyces_A daqus	77.4061	171	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces_A	95.0	99.52	99.22	0.92	0.88	5	-
GCF_004343255.1	s__Laceyella sacchari	77.3096	118	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	96.84	96.83	0.94	0.94	3	-
GCF_014641195.1	s__Marinithermofilum abyssi	76.7294	77	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marinithermofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856495.1	s__Staphylospora marina	76.7109	115	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182565.1	s__Melghirimyces algeriensis	76.4832	50	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046315.1	s__Desmospora activa	76.1808	64	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Desmospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054245.1	s__Melghirimyces profundicolus	76.1092	60	1248	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:36,370] [INFO] GTDB search result was written to GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:36,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:36,375] [INFO] DFAST_QC result json was written to GCF_900110165.1_IMG-taxon_2675903160_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:31:36,376] [INFO] DFAST_QC completed!
[2024-01-24 12:31:36,376] [INFO] Total running time: 0h1m18s