[2024-01-25 19:46:35,923] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:35,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:35,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg446364d3-80a0-423e-aa7e-e86a7f5593f0/dqc_reference
[2024-01-25 19:46:37,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:37,036] [INFO] Task started: Prodigal
[2024-01-25 19:46:37,036] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c3aec42-1083-40b5-b011-5f7892ede900/GCF_900450705.1_54424_E01_genomic.fna.gz | prodigal -d GCF_900450705.1_54424_E01_genomic.fna/cds.fna -a GCF_900450705.1_54424_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:43,052] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:43,052] [INFO] Task started: HMMsearch
[2024-01-25 19:46:43,052] [INFO] Running command: hmmsearch --tblout GCF_900450705.1_54424_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg446364d3-80a0-423e-aa7e-e86a7f5593f0/dqc_reference/reference_markers.hmm GCF_900450705.1_54424_E01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:43,294] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:43,295] [INFO] Found 6/6 markers.
[2024-01-25 19:46:43,319] [INFO] Query marker FASTA was written to GCF_900450705.1_54424_E01_genomic.fna/markers.fasta
[2024-01-25 19:46:43,319] [INFO] Task started: Blastn
[2024-01-25 19:46:43,319] [INFO] Running command: blastn -query GCF_900450705.1_54424_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg446364d3-80a0-423e-aa7e-e86a7f5593f0/dqc_reference/reference_markers.fasta -out GCF_900450705.1_54424_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:43,977] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:43,979] [INFO] Selected 13 target genomes.
[2024-01-25 19:46:43,980] [INFO] Target genome list was writen to GCF_900450705.1_54424_E01_genomic.fna/target_genomes.txt
[2024-01-25 19:46:43,990] [INFO] Task started: fastANI
[2024-01-25 19:46:43,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c3aec42-1083-40b5-b011-5f7892ede900/GCF_900450705.1_54424_E01_genomic.fna.gz --refList GCF_900450705.1_54424_E01_genomic.fna/target_genomes.txt --output GCF_900450705.1_54424_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:54,773] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:54,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg446364d3-80a0-423e-aa7e-e86a7f5593f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:54,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg446364d3-80a0-423e-aa7e-e86a7f5593f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:54,780] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:46:54,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:54,780] [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
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	100.0	940	952	95	conclusive
Avibacterium paragallinarum	strain=CCUG 12835	GCA_002921155.1	728	728	type	True	99.6977	687	952	95	conclusive
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	86.913	440	952	95	below_threshold
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	86.7655	484	952	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	86.1978	510	952	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	86.1238	474	952	95	below_threshold
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	86.0266	497	952	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	85.797	510	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:54,781] [INFO] DFAST Taxonomy check result was written to GCF_900450705.1_54424_E01_genomic.fna/tc_result.tsv
[2024-01-25 19:46:54,782] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:54,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:54,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg446364d3-80a0-423e-aa7e-e86a7f5593f0/dqc_reference/checkm_data
[2024-01-25 19:46:54,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:54,812] [INFO] Task started: CheckM
[2024-01-25 19:46:54,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900450705.1_54424_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900450705.1_54424_E01_genomic.fna/checkm_input GCF_900450705.1_54424_E01_genomic.fna/checkm_result
[2024-01-25 19:47:17,069] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:17,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:17,084] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:17,085] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:17,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900450705.1_54424_E01_genomic.fna/markers.fasta)
[2024-01-25 19:47:17,085] [INFO] Task started: Blastn
[2024-01-25 19:47:17,085] [INFO] Running command: blastn -query GCF_900450705.1_54424_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg446364d3-80a0-423e-aa7e-e86a7f5593f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900450705.1_54424_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:18,164] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:18,166] [INFO] Selected 5 target genomes.
[2024-01-25 19:47:18,166] [INFO] Target genome list was writen to GCF_900450705.1_54424_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:18,171] [INFO] Task started: fastANI
[2024-01-25 19:47:18,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c3aec42-1083-40b5-b011-5f7892ede900/GCF_900450705.1_54424_E01_genomic.fna.gz --refList GCF_900450705.1_54424_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900450705.1_54424_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:24,371] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:24,375] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:24,375] [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_900450705.1	s__Avibacterium paragallinarum	100.0	941	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	97.58	96.82	0.90	0.82	41	conclusive
GCF_002921145.1	s__Avibacterium endocarditidis	86.9318	439	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	-
GCF_900635775.1	s__Avibacterium volantium	86.7792	488	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCF_900454535.1	s__Avibacterium avium	86.0639	478	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_002921135.1	s__Avibacterium gallinarum	85.983	500	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:24,376] [INFO] GTDB search result was written to GCF_900450705.1_54424_E01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:24,377] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:24,379] [INFO] DFAST_QC result json was written to GCF_900450705.1_54424_E01_genomic.fna/dqc_result.json
[2024-01-25 19:47:24,379] [INFO] DFAST_QC completed!
[2024-01-25 19:47:24,379] [INFO] Total running time: 0h0m48s