[2024-01-24 14:19:31,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,742] [INFO] DQC Reference Directory: /var/lib/cwl/stge14db749-b044-4140-8aa4-052fd09aa90f/dqc_reference
[2024-01-24 14:19:33,198] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,199] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,199] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e4342f4-98b0-40fd-a945-d45c381012b8/GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/cds.fna -a GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:43,863] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:43,864] [INFO] Task started: HMMsearch
[2024-01-24 14:19:43,864] [INFO] Running command: hmmsearch --tblout GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge14db749-b044-4140-8aa4-052fd09aa90f/dqc_reference/reference_markers.hmm GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:44,163] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:44,164] [INFO] Found 6/6 markers.
[2024-01-24 14:19:44,195] [INFO] Query marker FASTA was written to GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:19:44,195] [INFO] Task started: Blastn
[2024-01-24 14:19:44,195] [INFO] Running command: blastn -query GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge14db749-b044-4140-8aa4-052fd09aa90f/dqc_reference/reference_markers.fasta -out GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:44,894] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:44,898] [INFO] Selected 17 target genomes.
[2024-01-24 14:19:44,898] [INFO] Target genome list was writen to GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:19:44,919] [INFO] Task started: fastANI
[2024-01-24 14:19:44,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e4342f4-98b0-40fd-a945-d45c381012b8/GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna.gz --refList GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:57,922] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:57,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge14db749-b044-4140-8aa4-052fd09aa90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:57,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge14db749-b044-4140-8aa4-052fd09aa90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:57,931] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:57,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:57,932] [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
Planifilum fulgidum	strain=DSM 44945	GCA_900113175.1	201973	201973	type	True	100.0	1096	1099	95	conclusive
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	89.656	935	1099	95	below_threshold
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	76.9966	78	1099	95	below_threshold
Polycladomyces abyssicola	strain=JIR-001	GCA_018326425.1	1125966	1125966	type	True	76.7671	109	1099	95	below_threshold
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	76.5232	105	1099	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.5168	60	1099	95	below_threshold
Paludifilum halophilum	strain=DSM 102817	GCA_002245355.1	1642702	1642702	type	True	76.0216	94	1099	95	below_threshold
Kroppenstedtia guangzhouensis	strain=CGMCC 1.12404	GCA_014637345.1	1274356	1274356	type	True	76.001	106	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,938] [INFO] DFAST Taxonomy check result was written to GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:19:57,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:57,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:57,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge14db749-b044-4140-8aa4-052fd09aa90f/dqc_reference/checkm_data
[2024-01-24 14:19:57,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:57,980] [INFO] Task started: CheckM
[2024-01-24 14:19:57,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/checkm_input GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:20:32,273] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:32,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:32,296] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:32,297] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:32,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:20:32,298] [INFO] Task started: Blastn
[2024-01-24 14:20:32,298] [INFO] Running command: blastn -query GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge14db749-b044-4140-8aa4-052fd09aa90f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:33,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:33,252] [INFO] Selected 17 target genomes.
[2024-01-24 14:20:33,252] [INFO] Target genome list was writen to GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:33,281] [INFO] Task started: fastANI
[2024-01-24 14:20:33,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e4342f4-98b0-40fd-a945-d45c381012b8/GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna.gz --refList GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:45,090] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:45,105] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:45,105] [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_900113175.1	s__Planifilum fulgidum	100.0	1096	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	99.34	99.26	0.97	0.97	3	conclusive
GCF_003001905.1	s__Planifilum fimeticola	89.656	935	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641195.1	s__Marinithermofilum abyssi	76.9966	78	1099	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_018326425.1	s__Polycladomyces abyssicola	76.7845	109	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__JIR-001;g__Polycladomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856495.1	s__Staphylospora marina	76.5422	105	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046315.1	s__Desmospora activa	76.5168	60	1099	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_014637345.1	s__Kroppenstedtia guangzhouensis	76.0223	106	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245355.1	s__Paludifilum halophilum	76.0216	94	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Paludifilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:45,107] [INFO] GTDB search result was written to GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:45,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:45,111] [INFO] DFAST_QC result json was written to GCF_900113175.1_IMG-taxon_2615840724_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:20:45,111] [INFO] DFAST_QC completed!
[2024-01-24 14:20:45,111] [INFO] Total running time: 0h1m13s