[2024-01-24 11:13:49,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg063d2208-0223-4684-8ddd-ef71b5e4e4f0/dqc_reference
[2024-01-24 11:13:50,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,640] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,641] [INFO] Running command: gunzip -c /var/lib/cwl/stgaac3b84c-cf4f-46df-b79f-7b7a701de9ad/GCF_900444945.1_50450_B01_genomic.fna.gz | prodigal -d GCF_900444945.1_50450_B01_genomic.fna/cds.fna -a GCF_900444945.1_50450_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:55,416] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:55,417] [INFO] Task started: HMMsearch
[2024-01-24 11:13:55,417] [INFO] Running command: hmmsearch --tblout GCF_900444945.1_50450_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg063d2208-0223-4684-8ddd-ef71b5e4e4f0/dqc_reference/reference_markers.hmm GCF_900444945.1_50450_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:55,644] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:55,646] [INFO] Found 6/6 markers.
[2024-01-24 11:13:55,671] [INFO] Query marker FASTA was written to GCF_900444945.1_50450_B01_genomic.fna/markers.fasta
[2024-01-24 11:13:55,671] [INFO] Task started: Blastn
[2024-01-24 11:13:55,671] [INFO] Running command: blastn -query GCF_900444945.1_50450_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg063d2208-0223-4684-8ddd-ef71b5e4e4f0/dqc_reference/reference_markers.fasta -out GCF_900444945.1_50450_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:56,351] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:56,354] [INFO] Selected 13 target genomes.
[2024-01-24 11:13:56,355] [INFO] Target genome list was writen to GCF_900444945.1_50450_B01_genomic.fna/target_genomes.txt
[2024-01-24 11:13:56,372] [INFO] Task started: fastANI
[2024-01-24 11:13:56,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac3b84c-cf4f-46df-b79f-7b7a701de9ad/GCF_900444945.1_50450_B01_genomic.fna.gz --refList GCF_900444945.1_50450_B01_genomic.fna/target_genomes.txt --output GCF_900444945.1_50450_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:04,536] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:04,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg063d2208-0223-4684-8ddd-ef71b5e4e4f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:04,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg063d2208-0223-4684-8ddd-ef71b5e4e4f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:04,548] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:14:04,548] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:14:04,548] [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
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	100.0	742	744	95	inconclusive
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	96.5653	681	744	95	inconclusive
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	96.5584	680	744	95	inconclusive
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	96.4093	636	744	95	inconclusive
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	88.6949	596	744	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	88.6234	596	744	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	88.3542	581	744	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	87.3251	575	744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:04,550] [INFO] DFAST Taxonomy check result was written to GCF_900444945.1_50450_B01_genomic.fna/tc_result.tsv
[2024-01-24 11:14:04,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:04,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:04,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg063d2208-0223-4684-8ddd-ef71b5e4e4f0/dqc_reference/checkm_data
[2024-01-24 11:14:04,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:04,579] [INFO] Task started: CheckM
[2024-01-24 11:14:04,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900444945.1_50450_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900444945.1_50450_B01_genomic.fna/checkm_input GCF_900444945.1_50450_B01_genomic.fna/checkm_result
[2024-01-24 11:14:25,500] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:25,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:25,515] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:25,515] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:25,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900444945.1_50450_B01_genomic.fna/markers.fasta)
[2024-01-24 11:14:25,516] [INFO] Task started: Blastn
[2024-01-24 11:14:25,516] [INFO] Running command: blastn -query GCF_900444945.1_50450_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg063d2208-0223-4684-8ddd-ef71b5e4e4f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900444945.1_50450_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:26,538] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:26,542] [INFO] Selected 6 target genomes.
[2024-01-24 11:14:26,542] [INFO] Target genome list was writen to GCF_900444945.1_50450_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:26,543] [INFO] Task started: fastANI
[2024-01-24 11:14:26,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac3b84c-cf4f-46df-b79f-7b7a701de9ad/GCF_900444945.1_50450_B01_genomic.fna.gz --refList GCF_900444945.1_50450_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900444945.1_50450_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:29,951] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:29,958] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:29,958] [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_900444945.1	s__Actinobacillus lignieresii	100.0	741	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	conclusive
GCF_000739435.1	s__Actinobacillus suis	88.6222	598	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_900636745.1	s__Actinobacillus equuli	88.3614	582	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_000188255.1	s__Actinobacillus ureae	87.3104	576	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_000374285.1	s__Actinobacillus capsulatus	87.1917	580	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901687125.1	s__Actinobacillus vicugnae	81.6672	495	744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:29,959] [INFO] GTDB search result was written to GCF_900444945.1_50450_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:29,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:29,962] [INFO] DFAST_QC result json was written to GCF_900444945.1_50450_B01_genomic.fna/dqc_result.json
[2024-01-24 11:14:29,963] [INFO] DFAST_QC completed!
[2024-01-24 11:14:29,963] [INFO] Total running time: 0h0m41s