[2024-01-25 17:38:20,794] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:20,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:20,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg03a9977f-321c-4e35-a79a-cffdd2cb6d36/dqc_reference
[2024-01-25 17:38:21,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:21,981] [INFO] Task started: Prodigal
[2024-01-25 17:38:21,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg31cada6b-dfdf-4fbd-9664-bd17b335648b/GCF_002921155.1_ASM292115v1_genomic.fna.gz | prodigal -d GCF_002921155.1_ASM292115v1_genomic.fna/cds.fna -a GCF_002921155.1_ASM292115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:26,519] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:26,519] [INFO] Task started: HMMsearch
[2024-01-25 17:38:26,519] [INFO] Running command: hmmsearch --tblout GCF_002921155.1_ASM292115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03a9977f-321c-4e35-a79a-cffdd2cb6d36/dqc_reference/reference_markers.hmm GCF_002921155.1_ASM292115v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:26,727] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:26,729] [INFO] Found 6/6 markers.
[2024-01-25 17:38:26,754] [INFO] Query marker FASTA was written to GCF_002921155.1_ASM292115v1_genomic.fna/markers.fasta
[2024-01-25 17:38:26,754] [INFO] Task started: Blastn
[2024-01-25 17:38:26,754] [INFO] Running command: blastn -query GCF_002921155.1_ASM292115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03a9977f-321c-4e35-a79a-cffdd2cb6d36/dqc_reference/reference_markers.fasta -out GCF_002921155.1_ASM292115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:27,407] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:27,411] [INFO] Selected 13 target genomes.
[2024-01-25 17:38:27,411] [INFO] Target genome list was writen to GCF_002921155.1_ASM292115v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:27,415] [INFO] Task started: fastANI
[2024-01-25 17:38:27,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cada6b-dfdf-4fbd-9664-bd17b335648b/GCF_002921155.1_ASM292115v1_genomic.fna.gz --refList GCF_002921155.1_ASM292115v1_genomic.fna/target_genomes.txt --output GCF_002921155.1_ASM292115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:34,357] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:34,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03a9977f-321c-4e35-a79a-cffdd2cb6d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:34,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03a9977f-321c-4e35-a79a-cffdd2cb6d36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:34,364] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:38:34,364] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:34,364] [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=CCUG 12835	GCA_002921155.1	728	728	type	True	100.0	683	692	95	conclusive
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	99.992	692	692	95	conclusive
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	86.6972	425	692	95	below_threshold
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	86.2611	462	692	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	86.1033	440	692	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	85.7641	479	692	95	below_threshold
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	85.7424	479	692	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	85.6993	474	692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:34,366] [INFO] DFAST Taxonomy check result was written to GCF_002921155.1_ASM292115v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:34,367] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:34,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:34,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03a9977f-321c-4e35-a79a-cffdd2cb6d36/dqc_reference/checkm_data
[2024-01-25 17:38:34,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:34,397] [INFO] Task started: CheckM
[2024-01-25 17:38:34,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002921155.1_ASM292115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002921155.1_ASM292115v1_genomic.fna/checkm_input GCF_002921155.1_ASM292115v1_genomic.fna/checkm_result
[2024-01-25 17:38:53,699] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:53,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:53,743] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:53,743] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:53,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002921155.1_ASM292115v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:53,744] [INFO] Task started: Blastn
[2024-01-25 17:38:53,744] [INFO] Running command: blastn -query GCF_002921155.1_ASM292115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03a9977f-321c-4e35-a79a-cffdd2cb6d36/dqc_reference/reference_markers_gtdb.fasta -out GCF_002921155.1_ASM292115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:54,831] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:54,834] [INFO] Selected 5 target genomes.
[2024-01-25 17:38:54,834] [INFO] Target genome list was writen to GCF_002921155.1_ASM292115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:54,836] [INFO] Task started: fastANI
[2024-01-25 17:38:54,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cada6b-dfdf-4fbd-9664-bd17b335648b/GCF_002921155.1_ASM292115v1_genomic.fna.gz --refList GCF_002921155.1_ASM292115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002921155.1_ASM292115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:57,715] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:57,720] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:57,720] [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	99.992	692	692	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	86.7272	423	692	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	86.217	464	692	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	86.0815	440	692	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	85.7138	482	692	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 17:38:57,722] [INFO] GTDB search result was written to GCF_002921155.1_ASM292115v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:57,722] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:57,725] [INFO] DFAST_QC result json was written to GCF_002921155.1_ASM292115v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:57,726] [INFO] DFAST_QC completed!
[2024-01-25 17:38:57,726] [INFO] Total running time: 0h0m37s