[2024-01-24 13:48:57,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:57,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:57,235] [INFO] DQC Reference Directory: /var/lib/cwl/stg635e44eb-2855-42b6-8239-2fb82c9fbdfd/dqc_reference
[2024-01-24 13:48:58,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:58,503] [INFO] Task started: Prodigal
[2024-01-24 13:48:58,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg618fad41-9657-4f4f-b33f-d042083f6597/GCF_004342115.1_ASM434211v1_genomic.fna.gz | prodigal -d GCF_004342115.1_ASM434211v1_genomic.fna/cds.fna -a GCF_004342115.1_ASM434211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:04,123] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:04,124] [INFO] Task started: HMMsearch
[2024-01-24 13:49:04,124] [INFO] Running command: hmmsearch --tblout GCF_004342115.1_ASM434211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg635e44eb-2855-42b6-8239-2fb82c9fbdfd/dqc_reference/reference_markers.hmm GCF_004342115.1_ASM434211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:04,367] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:04,369] [INFO] Found 6/6 markers.
[2024-01-24 13:49:04,393] [INFO] Query marker FASTA was written to GCF_004342115.1_ASM434211v1_genomic.fna/markers.fasta
[2024-01-24 13:49:04,394] [INFO] Task started: Blastn
[2024-01-24 13:49:04,394] [INFO] Running command: blastn -query GCF_004342115.1_ASM434211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635e44eb-2855-42b6-8239-2fb82c9fbdfd/dqc_reference/reference_markers.fasta -out GCF_004342115.1_ASM434211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:05,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:05,003] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:05,004] [INFO] Target genome list was writen to GCF_004342115.1_ASM434211v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:05,009] [INFO] Task started: fastANI
[2024-01-24 13:49:05,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg618fad41-9657-4f4f-b33f-d042083f6597/GCF_004342115.1_ASM434211v1_genomic.fna.gz --refList GCF_004342115.1_ASM434211v1_genomic.fna/target_genomes.txt --output GCF_004342115.1_ASM434211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:11,800] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:11,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg635e44eb-2855-42b6-8239-2fb82c9fbdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:11,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg635e44eb-2855-42b6-8239-2fb82c9fbdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:11,810] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:11,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:11,810] [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	100.0	822	826	95	conclusive
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	99.9988	826	826	95	conclusive
Mannheimia ovis	strain=ZY170218	GCA_009828705.1	2679994	2679994	type	True	83.645	516	826	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	82.7517	545	826	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	82.7113	558	826	95	below_threshold
Mannheimia pernigra	strain=17CN0883	GCA_013377995.1	111844	111844	type	True	82.0181	493	826	95	below_threshold
Mannheimia granulomatis	strain=DSM 19156	GCA_000621105.1	85402	85402	type	True	81.2995	540	826	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	79.1195	316	826	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	79.0398	302	826	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	78.7668	278	826	95	below_threshold
[Haemophilus] ducreyi	strain=CIP 54.2	GCA_001043455.1	730	730	type	True	78.0811	153	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:11,816] [INFO] DFAST Taxonomy check result was written to GCF_004342115.1_ASM434211v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:11,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:11,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:11,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg635e44eb-2855-42b6-8239-2fb82c9fbdfd/dqc_reference/checkm_data
[2024-01-24 13:49:11,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:11,847] [INFO] Task started: CheckM
[2024-01-24 13:49:11,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342115.1_ASM434211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342115.1_ASM434211v1_genomic.fna/checkm_input GCF_004342115.1_ASM434211v1_genomic.fna/checkm_result
[2024-01-24 13:49:35,333] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:35,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:35,360] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:35,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:35,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342115.1_ASM434211v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:35,361] [INFO] Task started: Blastn
[2024-01-24 13:49:35,362] [INFO] Running command: blastn -query GCF_004342115.1_ASM434211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg635e44eb-2855-42b6-8239-2fb82c9fbdfd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342115.1_ASM434211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:36,282] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:36,290] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:36,291] [INFO] Target genome list was writen to GCF_004342115.1_ASM434211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:36,304] [INFO] Task started: fastANI
[2024-01-24 13:49:36,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg618fad41-9657-4f4f-b33f-d042083f6597/GCF_004342115.1_ASM434211v1_genomic.fna.gz --refList GCF_004342115.1_ASM434211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342115.1_ASM434211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:44,526] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:44,541] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:44,542] [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	100.0	822	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	conclusive
GCF_000521605.1	s__Mannheimia sp000521605	83.1806	576	826	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	82.7517	545	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	82.7113	558	826	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	82.0179	493	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
GCF_011455695.1	s__Mannheimia granulomatis_A	81.4112	492	826	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	81.3736	539	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.35	95.73	0.92	0.88	5	-
GCF_000175195.1	s__Actinobacillus_A minor	79.2087	270	826	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_000188255.1	s__Actinobacillus ureae	79.1761	285	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_900636745.1	s__Actinobacillus equuli	79.1045	317	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	79.0934	276	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_000739435.1	s__Actinobacillus suis	79.0878	311	826	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	79.0544	301	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109315.1	s__Haemophilus_B ducreyi	78.0536	153	826	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 13:49:44,544] [INFO] GTDB search result was written to GCF_004342115.1_ASM434211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:44,544] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:44,551] [INFO] DFAST_QC result json was written to GCF_004342115.1_ASM434211v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:44,551] [INFO] DFAST_QC completed!
[2024-01-24 13:49:44,551] [INFO] Total running time: 0h0m47s