[2024-01-24 11:26:19,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:19,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:19,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg46c0a361-2afd-43ce-b169-cf7c4650b29b/dqc_reference
[2024-01-24 11:26:20,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:20,623] [INFO] Task started: Prodigal
[2024-01-24 11:26:20,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c41857f-c8d3-456d-9494-b31bb6581ae6/GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/cds.fna -a GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:27,336] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:27,337] [INFO] Task started: HMMsearch
[2024-01-24 11:26:27,337] [INFO] Running command: hmmsearch --tblout GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46c0a361-2afd-43ce-b169-cf7c4650b29b/dqc_reference/reference_markers.hmm GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:27,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:27,642] [INFO] Found 6/6 markers.
[2024-01-24 11:26:27,670] [INFO] Query marker FASTA was written to GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:26:27,670] [INFO] Task started: Blastn
[2024-01-24 11:26:27,670] [INFO] Running command: blastn -query GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c0a361-2afd-43ce-b169-cf7c4650b29b/dqc_reference/reference_markers.fasta -out GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:28,260] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:28,264] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:28,265] [INFO] Target genome list was writen to GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:26:28,282] [INFO] Task started: fastANI
[2024-01-24 11:26:28,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c41857f-c8d3-456d-9494-b31bb6581ae6/GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna.gz --refList GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:35,295] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:35,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46c0a361-2afd-43ce-b169-cf7c4650b29b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:35,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46c0a361-2afd-43ce-b169-cf7c4650b29b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:35,305] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:35,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:35,305] [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
Megasphaera paucivorans	strain=DSM 16981	GCA_900103535.1	349095	349095	type	True	100.0	929	930	95	conclusive
Megasphaera cerevisiae	strain=DSM 20462	GCA_900167325.1	39029	39029	type	True	79.8587	161	930	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	79.7036	168	930	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	77.6841	64	930	95	below_threshold
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	77.651	69	930	95	below_threshold
Megasphaera lornae	strain=UPII 199-6	GCA_000214495.2	1000568	1000568	type	True	77.1874	58	930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:35,307] [INFO] DFAST Taxonomy check result was written to GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:26:35,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:35,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:35,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46c0a361-2afd-43ce-b169-cf7c4650b29b/dqc_reference/checkm_data
[2024-01-24 11:26:35,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:35,339] [INFO] Task started: CheckM
[2024-01-24 11:26:35,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/checkm_input GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:27:01,881] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:01,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:01,904] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:01,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:01,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:27:01,905] [INFO] Task started: Blastn
[2024-01-24 11:27:01,905] [INFO] Running command: blastn -query GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c0a361-2afd-43ce-b169-cf7c4650b29b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:02,756] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:02,761] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:02,761] [INFO] Target genome list was writen to GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:02,807] [INFO] Task started: fastANI
[2024-01-24 11:27:02,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c41857f-c8d3-456d-9494-b31bb6581ae6/GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna.gz --refList GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:12,190] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:12,202] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:12,203] [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_900103535.1	s__Megasphaera_A paucivorans	100.0	929	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001045675.1	s__Megasphaera cerevisiae	79.722	167	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.73	99.50	0.95	0.92	3	-
GCA_900539295.1	s__Megasphaera sp900539295	77.8289	56	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900752195.1	s__Caecibacter sp900549385	77.7471	56	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.73	99.52	0.95	0.92	4	-
GCA_900540735.1	s__Megasphaera sp900540735	77.6382	55	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.96	0.96	0.96	2	-
GCF_003467125.1	s__Caecibacter sp003467125	77.6329	76	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.80	97.67	0.92	0.89	5	-
GCF_014269395.1	s__Caecibacter hominis	77.4394	70	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.84	99.81	0.96	0.95	4	-
GCF_000214495.1	s__Megasphaera lornae	77.1874	58	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.01	98.81	0.95	0.94	5	-
GCA_002431345.1	s__Megasphaera sp002431345	77.1245	90	930	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.44	99.22	0.90	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:12,204] [INFO] GTDB search result was written to GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:12,205] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:12,207] [INFO] DFAST_QC result json was written to GCF_900103535.1_IMG-taxon_2596583540_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:27:12,207] [INFO] DFAST_QC completed!
[2024-01-24 11:27:12,207] [INFO] Total running time: 0h0m53s