[2024-01-24 12:36:35,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:35,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:35,754] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5da5455-57fb-4c74-a51b-4abc73ac4621/dqc_reference
[2024-01-24 12:36:36,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:36,932] [INFO] Task started: Prodigal
[2024-01-24 12:36:36,933] [INFO] Running command: gunzip -c /var/lib/cwl/stg581f1322-7613-4067-adfe-71107838d52a/GCF_013377235.1_ASM1337723v1_genomic.fna.gz | prodigal -d GCF_013377235.1_ASM1337723v1_genomic.fna/cds.fna -a GCF_013377235.1_ASM1337723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:41,822] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:41,822] [INFO] Task started: HMMsearch
[2024-01-24 12:36:41,822] [INFO] Running command: hmmsearch --tblout GCF_013377235.1_ASM1337723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5da5455-57fb-4c74-a51b-4abc73ac4621/dqc_reference/reference_markers.hmm GCF_013377235.1_ASM1337723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:42,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:42,087] [INFO] Found 6/6 markers.
[2024-01-24 12:36:42,112] [INFO] Query marker FASTA was written to GCF_013377235.1_ASM1337723v1_genomic.fna/markers.fasta
[2024-01-24 12:36:42,112] [INFO] Task started: Blastn
[2024-01-24 12:36:42,112] [INFO] Running command: blastn -query GCF_013377235.1_ASM1337723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5da5455-57fb-4c74-a51b-4abc73ac4621/dqc_reference/reference_markers.fasta -out GCF_013377235.1_ASM1337723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:42,794] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:42,799] [INFO] Selected 15 target genomes.
[2024-01-24 12:36:42,800] [INFO] Target genome list was writen to GCF_013377235.1_ASM1337723v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:42,881] [INFO] Task started: fastANI
[2024-01-24 12:36:42,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg581f1322-7613-4067-adfe-71107838d52a/GCF_013377235.1_ASM1337723v1_genomic.fna.gz --refList GCF_013377235.1_ASM1337723v1_genomic.fna/target_genomes.txt --output GCF_013377235.1_ASM1337723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:51,564] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:51,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5da5455-57fb-4c74-a51b-4abc73ac4621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:51,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5da5455-57fb-4c74-a51b-4abc73ac4621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:51,574] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:51,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:51,574] [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 varigena	strain=177	GCA_013377235.1	85404	85404	type	True	100.0	711	713	95	conclusive
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	88.2865	564	713	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	83.7666	522	713	95	below_threshold
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	83.7621	520	713	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	82.9744	573	713	95	below_threshold
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	82.7158	547	713	95	below_threshold
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	82.1716	509	713	95	below_threshold
Haemophilus parahaemolyticus	strain=FDAARGOS_1199	GCA_016889385.1	735	735	type	True	79.5699	236	713	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	79.2276	285	713	95	below_threshold
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	79.1311	241	713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:51,576] [INFO] DFAST Taxonomy check result was written to GCF_013377235.1_ASM1337723v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:51,577] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:51,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:51,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5da5455-57fb-4c74-a51b-4abc73ac4621/dqc_reference/checkm_data
[2024-01-24 12:36:51,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:51,601] [INFO] Task started: CheckM
[2024-01-24 12:36:51,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377235.1_ASM1337723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377235.1_ASM1337723v1_genomic.fna/checkm_input GCF_013377235.1_ASM1337723v1_genomic.fna/checkm_result
[2024-01-24 12:37:13,310] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:13,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:13,335] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:13,336] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:13,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377235.1_ASM1337723v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:13,337] [INFO] Task started: Blastn
[2024-01-24 12:37:13,337] [INFO] Running command: blastn -query GCF_013377235.1_ASM1337723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5da5455-57fb-4c74-a51b-4abc73ac4621/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377235.1_ASM1337723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:14,427] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:14,432] [INFO] Selected 8 target genomes.
[2024-01-24 12:37:14,432] [INFO] Target genome list was writen to GCF_013377235.1_ASM1337723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:14,454] [INFO] Task started: fastANI
[2024-01-24 12:37:14,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg581f1322-7613-4067-adfe-71107838d52a/GCF_013377235.1_ASM1337723v1_genomic.fna.gz --refList GCF_013377235.1_ASM1337723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377235.1_ASM1337723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:19,054] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:19,065] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:19,065] [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_013377235.1	s__Mannheimia varigena	100.0	712	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	conclusive
GCF_000521605.1	s__Mannheimia sp000521605	89.7331	593	713	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	88.3046	563	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377995.1	s__Mannheimia pernigra	83.736	523	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
GCF_004342115.1	s__Mannheimia haemolytica	82.7311	546	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_013377255.1	s__Mannheimia granulomatis	82.4115	513	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_011455695.1	s__Mannheimia granulomatis_A	81.8791	501	713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374285.1	s__Actinobacillus capsulatus	79.2402	285	713	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 12:37:19,067] [INFO] GTDB search result was written to GCF_013377235.1_ASM1337723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:19,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:19,071] [INFO] DFAST_QC result json was written to GCF_013377235.1_ASM1337723v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:19,071] [INFO] DFAST_QC completed!
[2024-01-24 12:37:19,072] [INFO] Total running time: 0h0m43s