[2024-01-24 14:28:16,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:16,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:16,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg74423c48-8383-4019-bdd2-27d4a4d3dce0/dqc_reference
[2024-01-24 14:28:17,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,367] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,367] [INFO] Running command: gunzip -c /var/lib/cwl/stg56cfda59-be62-4c68-9453-824c77e8133d/GCF_004362535.1_ASM436253v1_genomic.fna.gz | prodigal -d GCF_004362535.1_ASM436253v1_genomic.fna/cds.fna -a GCF_004362535.1_ASM436253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:23,264] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:23,265] [INFO] Task started: HMMsearch
[2024-01-24 14:28:23,265] [INFO] Running command: hmmsearch --tblout GCF_004362535.1_ASM436253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74423c48-8383-4019-bdd2-27d4a4d3dce0/dqc_reference/reference_markers.hmm GCF_004362535.1_ASM436253v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:23,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:23,554] [INFO] Found 6/6 markers.
[2024-01-24 14:28:23,595] [INFO] Query marker FASTA was written to GCF_004362535.1_ASM436253v1_genomic.fna/markers.fasta
[2024-01-24 14:28:23,596] [INFO] Task started: Blastn
[2024-01-24 14:28:23,596] [INFO] Running command: blastn -query GCF_004362535.1_ASM436253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74423c48-8383-4019-bdd2-27d4a4d3dce0/dqc_reference/reference_markers.fasta -out GCF_004362535.1_ASM436253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:24,251] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:24,254] [INFO] Selected 11 target genomes.
[2024-01-24 14:28:24,254] [INFO] Target genome list was writen to GCF_004362535.1_ASM436253v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:24,264] [INFO] Task started: fastANI
[2024-01-24 14:28:24,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cfda59-be62-4c68-9453-824c77e8133d/GCF_004362535.1_ASM436253v1_genomic.fna.gz --refList GCF_004362535.1_ASM436253v1_genomic.fna/target_genomes.txt --output GCF_004362535.1_ASM436253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:32,465] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:32,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74423c48-8383-4019-bdd2-27d4a4d3dce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:32,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74423c48-8383-4019-bdd2-27d4a4d3dce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:32,474] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:28:32,474] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:28:32,474] [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 gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	100.0	771	772	95	inconclusive
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	99.9949	772	772	95	inconclusive
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	99.9718	754	772	95	inconclusive
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	95.5128	659	772	95	inconclusive
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	95.3953	613	772	95	inconclusive
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	93.942	597	772	95	below_threshold
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	85.5964	528	772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:32,476] [INFO] DFAST Taxonomy check result was written to GCF_004362535.1_ASM436253v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:32,477] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:32,477] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:32,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74423c48-8383-4019-bdd2-27d4a4d3dce0/dqc_reference/checkm_data
[2024-01-24 14:28:32,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:32,506] [INFO] Task started: CheckM
[2024-01-24 14:28:32,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362535.1_ASM436253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362535.1_ASM436253v1_genomic.fna/checkm_input GCF_004362535.1_ASM436253v1_genomic.fna/checkm_result
[2024-01-24 14:28:57,270] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:57,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:57,286] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:57,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:57,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362535.1_ASM436253v1_genomic.fna/markers.fasta)
[2024-01-24 14:28:57,287] [INFO] Task started: Blastn
[2024-01-24 14:28:57,287] [INFO] Running command: blastn -query GCF_004362535.1_ASM436253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74423c48-8383-4019-bdd2-27d4a4d3dce0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362535.1_ASM436253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:58,262] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:58,266] [INFO] Selected 5 target genomes.
[2024-01-24 14:28:58,266] [INFO] Target genome list was writen to GCF_004362535.1_ASM436253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:58,275] [INFO] Task started: fastANI
[2024-01-24 14:28:58,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cfda59-be62-4c68-9453-824c77e8133d/GCF_004362535.1_ASM436253v1_genomic.fna.gz --refList GCF_004362535.1_ASM436253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362535.1_ASM436253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:01,815] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:01,826] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:01,827] [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_002921135.1	s__Avibacterium gallinarum	99.9718	754	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	conclusive
GCF_900635775.1	s__Avibacterium volantium	95.4833	660	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCF_002921145.1	s__Avibacterium endocarditidis	95.3953	613	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	-
GCF_900454535.1	s__Avibacterium avium	93.9438	598	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_900450705.1	s__Avibacterium paragallinarum	85.5774	529	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	97.58	96.82	0.90	0.82	41	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:01,828] [INFO] GTDB search result was written to GCF_004362535.1_ASM436253v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:01,829] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:01,831] [INFO] DFAST_QC result json was written to GCF_004362535.1_ASM436253v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:01,831] [INFO] DFAST_QC completed!
[2024-01-24 14:29:01,832] [INFO] Total running time: 0h0m46s