[2024-01-24 14:54:55,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:55,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:55,816] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9ee42e2-8e3e-49dc-a546-0f1f41b2ff7c/dqc_reference
[2024-01-24 14:54:57,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,145] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c3a16cf-3bf4-4c34-852e-94059d620331/GCF_900636745.1_44087_C02_genomic.fna.gz | prodigal -d GCF_900636745.1_44087_C02_genomic.fna/cds.fna -a GCF_900636745.1_44087_C02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:02,698] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:02,698] [INFO] Task started: HMMsearch
[2024-01-24 14:55:02,698] [INFO] Running command: hmmsearch --tblout GCF_900636745.1_44087_C02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9ee42e2-8e3e-49dc-a546-0f1f41b2ff7c/dqc_reference/reference_markers.hmm GCF_900636745.1_44087_C02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:02,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:02,974] [INFO] Found 6/6 markers.
[2024-01-24 14:55:02,997] [INFO] Query marker FASTA was written to GCF_900636745.1_44087_C02_genomic.fna/markers.fasta
[2024-01-24 14:55:02,998] [INFO] Task started: Blastn
[2024-01-24 14:55:02,998] [INFO] Running command: blastn -query GCF_900636745.1_44087_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9ee42e2-8e3e-49dc-a546-0f1f41b2ff7c/dqc_reference/reference_markers.fasta -out GCF_900636745.1_44087_C02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:03,689] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:03,692] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:03,692] [INFO] Target genome list was writen to GCF_900636745.1_44087_C02_genomic.fna/target_genomes.txt
[2024-01-24 14:55:03,701] [INFO] Task started: fastANI
[2024-01-24 14:55:03,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3a16cf-3bf4-4c34-852e-94059d620331/GCF_900636745.1_44087_C02_genomic.fna.gz --refList GCF_900636745.1_44087_C02_genomic.fna/target_genomes.txt --output GCF_900636745.1_44087_C02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:12,737] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:12,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9ee42e2-8e3e-49dc-a546-0f1f41b2ff7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:12,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9ee42e2-8e3e-49dc-a546-0f1f41b2ff7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:12,749] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:12,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:12,750] [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 equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	100.0	814	817	95	conclusive
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	93.8549	711	817	95	below_threshold
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	93.8368	709	817	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	93.1263	687	817	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	92.7457	661	817	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	88.1931	585	817	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	88.1446	609	817	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	87.9113	547	817	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	79.3302	52	817	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	79.0713	59	817	95	below_threshold
Otariodibacter oris	strain=Baika1	GCA_009684715.1	1032623	1032623	type	True	78.9528	172	817	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.8896	166	817	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.3184	54	817	95	below_threshold
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	78.1365	173	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:12,751] [INFO] DFAST Taxonomy check result was written to GCF_900636745.1_44087_C02_genomic.fna/tc_result.tsv
[2024-01-24 14:55:12,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:12,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:12,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9ee42e2-8e3e-49dc-a546-0f1f41b2ff7c/dqc_reference/checkm_data
[2024-01-24 14:55:12,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:12,777] [INFO] Task started: CheckM
[2024-01-24 14:55:12,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900636745.1_44087_C02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900636745.1_44087_C02_genomic.fna/checkm_input GCF_900636745.1_44087_C02_genomic.fna/checkm_result
[2024-01-24 14:55:36,269] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:36,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:36,289] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:36,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:36,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900636745.1_44087_C02_genomic.fna/markers.fasta)
[2024-01-24 14:55:36,290] [INFO] Task started: Blastn
[2024-01-24 14:55:36,290] [INFO] Running command: blastn -query GCF_900636745.1_44087_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9ee42e2-8e3e-49dc-a546-0f1f41b2ff7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900636745.1_44087_C02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:37,158] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:37,161] [INFO] Selected 9 target genomes.
[2024-01-24 14:55:37,161] [INFO] Target genome list was writen to GCF_900636745.1_44087_C02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:37,170] [INFO] Task started: fastANI
[2024-01-24 14:55:37,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c3a16cf-3bf4-4c34-852e-94059d620331/GCF_900636745.1_44087_C02_genomic.fna.gz --refList GCF_900636745.1_44087_C02_genomic.fna/target_genomes_gtdb.txt --output GCF_900636745.1_44087_C02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:42,244] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:42,252] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:42,253] [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_900636745.1	s__Actinobacillus equuli	100.0	813	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	conclusive
GCF_000739435.1	s__Actinobacillus suis	93.849	710	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_000374285.1	s__Actinobacillus capsulatus	93.1263	687	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188255.1	s__Actinobacillus ureae	92.7457	661	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_900444945.1	s__Actinobacillus lignieresii	88.1837	582	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_901687125.1	s__Actinobacillus vicugnae	83.7235	597	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377195.1	s__Bisgaardia hudsonensis	79.5615	116	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900444965.1	s__Basfia_A rossii	79.0941	185	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262245.1	s__Basfia bettyae	78.1227	133	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:42,254] [INFO] GTDB search result was written to GCF_900636745.1_44087_C02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:42,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:42,258] [INFO] DFAST_QC result json was written to GCF_900636745.1_44087_C02_genomic.fna/dqc_result.json
[2024-01-24 14:55:42,259] [INFO] DFAST_QC completed!
[2024-01-24 14:55:42,259] [INFO] Total running time: 0h0m46s