[2024-01-24 13:50:10,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,881] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8e5dcd6-ff66-493d-b73c-74928cc5b3de/dqc_reference
[2024-01-24 13:50:12,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:12,189] [INFO] Task started: Prodigal
[2024-01-24 13:50:12,190] [INFO] Running command: gunzip -c /var/lib/cwl/stgf28f3553-d33f-442d-9c4a-499f731fbbe6/GCF_028649535.1_ASM2864953v1_genomic.fna.gz | prodigal -d GCF_028649535.1_ASM2864953v1_genomic.fna/cds.fna -a GCF_028649535.1_ASM2864953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:17,173] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:17,174] [INFO] Task started: HMMsearch
[2024-01-24 13:50:17,174] [INFO] Running command: hmmsearch --tblout GCF_028649535.1_ASM2864953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8e5dcd6-ff66-493d-b73c-74928cc5b3de/dqc_reference/reference_markers.hmm GCF_028649535.1_ASM2864953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:17,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:17,430] [INFO] Found 6/6 markers.
[2024-01-24 13:50:17,453] [INFO] Query marker FASTA was written to GCF_028649535.1_ASM2864953v1_genomic.fna/markers.fasta
[2024-01-24 13:50:17,453] [INFO] Task started: Blastn
[2024-01-24 13:50:17,453] [INFO] Running command: blastn -query GCF_028649535.1_ASM2864953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8e5dcd6-ff66-493d-b73c-74928cc5b3de/dqc_reference/reference_markers.fasta -out GCF_028649535.1_ASM2864953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:18,243] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:18,246] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:18,246] [INFO] Target genome list was writen to GCF_028649535.1_ASM2864953v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:18,252] [INFO] Task started: fastANI
[2024-01-24 13:50:18,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28f3553-d33f-442d-9c4a-499f731fbbe6/GCF_028649535.1_ASM2864953v1_genomic.fna.gz --refList GCF_028649535.1_ASM2864953v1_genomic.fna/target_genomes.txt --output GCF_028649535.1_ASM2864953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:26,555] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:26,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8e5dcd6-ff66-493d-b73c-74928cc5b3de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:26,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8e5dcd6-ff66-493d-b73c-74928cc5b3de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:26,570] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:26,570] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:26,570] [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
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	81.1565	475	760	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	81.1553	491	760	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	81.0587	469	760	95	below_threshold
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	80.9525	459	760	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	80.7112	460	760	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	80.4908	412	760	95	below_threshold
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	80.4017	420	760	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	79.1937	312	760	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	79.1845	302	760	95	below_threshold
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	79.1443	269	760	95	below_threshold
[Haemophilus] ducreyi	strain=CIP 54.2	GCA_001043455.1	730	730	type	True	78.2567	172	760	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	77.8745	124	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,572] [INFO] DFAST Taxonomy check result was written to GCF_028649535.1_ASM2864953v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:26,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:26,573] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:26,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8e5dcd6-ff66-493d-b73c-74928cc5b3de/dqc_reference/checkm_data
[2024-01-24 13:50:26,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:26,605] [INFO] Task started: CheckM
[2024-01-24 13:50:26,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028649535.1_ASM2864953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028649535.1_ASM2864953v1_genomic.fna/checkm_input GCF_028649535.1_ASM2864953v1_genomic.fna/checkm_result
[2024-01-24 13:50:47,865] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:47,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,884] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:47,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:47,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028649535.1_ASM2864953v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:47,885] [INFO] Task started: Blastn
[2024-01-24 13:50:47,885] [INFO] Running command: blastn -query GCF_028649535.1_ASM2864953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8e5dcd6-ff66-493d-b73c-74928cc5b3de/dqc_reference/reference_markers_gtdb.fasta -out GCF_028649535.1_ASM2864953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:48,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:48,936] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:48,937] [INFO] Target genome list was writen to GCF_028649535.1_ASM2864953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:48,953] [INFO] Task started: fastANI
[2024-01-24 13:50:48,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28f3553-d33f-442d-9c4a-499f731fbbe6/GCF_028649535.1_ASM2864953v1_genomic.fna.gz --refList GCF_028649535.1_ASM2864953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028649535.1_ASM2864953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:54,496] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:54,520] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:54,520] [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_004342115.1	s__Mannheimia haemolytica	81.1648	475	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_000521605.1	s__Mannheimia sp000521605	81.085	486	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014541205.1	s__Mannheimia bovis	81.0771	468	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455695.1	s__Mannheimia granulomatis_A	81.0229	453	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377255.1	s__Mannheimia granulomatis	80.989	460	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_013377235.1	s__Mannheimia varigena	80.7309	458	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_013377995.1	s__Mannheimia pernigra	80.4601	415	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
GCF_901687125.1	s__Actinobacillus vicugnae	79.1517	315	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175195.1	s__Actinobacillus_A minor	79.1348	270	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	79.0694	284	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCA_002002485.1	s__GCF-002002485 sp002002485	78.6945	257	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__GCF-002002485	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109315.1	s__Haemophilus_B ducreyi	78.3164	177	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_B	95.0	98.41	97.61	0.95	0.91	31	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:54,522] [INFO] GTDB search result was written to GCF_028649535.1_ASM2864953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:54,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:54,528] [INFO] DFAST_QC result json was written to GCF_028649535.1_ASM2864953v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:54,528] [INFO] DFAST_QC completed!
[2024-01-24 13:50:54,528] [INFO] Total running time: 0h0m44s