[2024-01-24 13:13:39,507] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg2579fb26-76d6-4696-99c9-5f06d080a267/dqc_reference
[2024-01-24 13:13:40,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,847] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f297a9f-f1dc-464c-9b69-6052c259effb/GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/cds.fna -a GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:52,131] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:52,131] [INFO] Task started: HMMsearch
[2024-01-24 13:13:52,132] [INFO] Running command: hmmsearch --tblout GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2579fb26-76d6-4696-99c9-5f06d080a267/dqc_reference/reference_markers.hmm GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:52,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:52,418] [INFO] Found 6/6 markers.
[2024-01-24 13:13:52,447] [INFO] Query marker FASTA was written to GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:52,448] [INFO] Task started: Blastn
[2024-01-24 13:13:52,448] [INFO] Running command: blastn -query GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2579fb26-76d6-4696-99c9-5f06d080a267/dqc_reference/reference_markers.fasta -out GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:53,082] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:53,085] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:53,085] [INFO] Target genome list was writen to GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:53,091] [INFO] Task started: fastANI
[2024-01-24 13:13:53,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f297a9f-f1dc-464c-9b69-6052c259effb/GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna.gz --refList GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:04,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:04,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2579fb26-76d6-4696-99c9-5f06d080a267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:04,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2579fb26-76d6-4696-99c9-5f06d080a267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:04,129] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:04,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:04,130] [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
Laceyella sediminis	strain=RHA1	GCA_003003125.1	573074	573074	type	True	97.7682	1037	1103	95	conclusive
Laceyella sacchari	strain=DSM 43356	GCA_004343255.1	37482	37482	type	True	94.7806	989	1103	95	below_threshold
Thermoactinomyces daqus	strain=H-18	GCA_000763315.1	1329516	1329516	type	True	78.2698	140	1103	95	below_threshold
Lihuaxuella thermophila	strain=DSM 46701	GCA_900110165.1	1173111	1173111	type	True	77.2897	117	1103	95	below_threshold
Hazenella coriacea	strain=DSM 45707	GCA_004341825.1	1179467	1179467	type	True	77.0491	52	1103	95	below_threshold
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	77.0426	75	1103	95	below_threshold
Thermoflavimicrobium daqui	strain=FBKL4.011	GCA_003313465.1	2137476	2137476	type	True	76.9618	52	1103	95	below_threshold
Thermoactinomyces intermedius	strain=NRRL B-16979	GCA_013912365.1	2024	2024	type	True	76.8408	98	1103	95	below_threshold
Thermoactinomyces mirandus	strain=AMNI-1	GCA_013868055.1	2756294	2756294	type	True	76.75	80	1103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:04,131] [INFO] DFAST Taxonomy check result was written to GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:14:04,132] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:04,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:04,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2579fb26-76d6-4696-99c9-5f06d080a267/dqc_reference/checkm_data
[2024-01-24 13:14:04,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:04,165] [INFO] Task started: CheckM
[2024-01-24 13:14:04,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/checkm_input GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:14:41,346] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:41,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:41,365] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:41,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:41,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:14:41,366] [INFO] Task started: Blastn
[2024-01-24 13:14:41,366] [INFO] Running command: blastn -query GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2579fb26-76d6-4696-99c9-5f06d080a267/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:42,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:42,250] [INFO] Selected 19 target genomes.
[2024-01-24 13:14:42,250] [INFO] Target genome list was writen to GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:42,265] [INFO] Task started: fastANI
[2024-01-24 13:14:42,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f297a9f-f1dc-464c-9b69-6052c259effb/GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna.gz --refList GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:57,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:57,088] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:57,088] [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_003003125.1	s__Laceyella sediminis	97.7682	1037	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	97.79	97.73	0.93	0.93	3	conclusive
GCF_004343255.1	s__Laceyella sacchari	94.76	990	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	96.84	96.83	0.94	0.94	3	-
GCF_000763315.1	s__Thermoactinomyces_A daqus	78.2698	140	1103	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_900110165.1	s__Lihuaxuella thermophila	77.2927	116	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Lihuaxuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856495.1	s__Staphylospora marina	77.104	76	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341825.1	s__Hazenella coriacea	77.0491	52	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Hazenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868055.1	s__Thermoactinomyces mirandus	76.7772	79	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:57,097] [INFO] GTDB search result was written to GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:57,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:57,104] [INFO] DFAST_QC result json was written to GCF_900182735.1_IMG-taxon_2724679819_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:14:57,104] [INFO] DFAST_QC completed!
[2024-01-24 13:14:57,104] [INFO] Total running time: 0h1m18s