[2024-01-24 10:47:06,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg24703b70-7b65-4cc9-9536-49047af93873/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg472272b8-3f48-4f35-be3a-09baefee7ba9/GCF_024622045.1_ASM2462204v1_genomic.fna.gz | prodigal -d GCF_024622045.1_ASM2462204v1_genomic.fna/cds.fna -a GCF_024622045.1_ASM2462204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:17,683] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:17,683] [INFO] Task started: HMMsearch
[2024-01-24 10:47:17,683] [INFO] Running command: hmmsearch --tblout GCF_024622045.1_ASM2462204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24703b70-7b65-4cc9-9536-49047af93873/dqc_reference/reference_markers.hmm GCF_024622045.1_ASM2462204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:17,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:17,952] [INFO] Found 6/6 markers.
[2024-01-24 10:47:17,980] [INFO] Query marker FASTA was written to GCF_024622045.1_ASM2462204v1_genomic.fna/markers.fasta
[2024-01-24 10:47:17,981] [INFO] Task started: Blastn
[2024-01-24 10:47:17,981] [INFO] Running command: blastn -query GCF_024622045.1_ASM2462204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24703b70-7b65-4cc9-9536-49047af93873/dqc_reference/reference_markers.fasta -out GCF_024622045.1_ASM2462204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,641] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,645] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:19,645] [INFO] Target genome list was writen to GCF_024622045.1_ASM2462204v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:19,709] [INFO] Task started: fastANI
[2024-01-24 10:47:19,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg472272b8-3f48-4f35-be3a-09baefee7ba9/GCF_024622045.1_ASM2462204v1_genomic.fna.gz --refList GCF_024622045.1_ASM2462204v1_genomic.fna/target_genomes.txt --output GCF_024622045.1_ASM2462204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:27,333] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:27,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24703b70-7b65-4cc9-9536-49047af93873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:27,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24703b70-7b65-4cc9-9536-49047af93873/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:27,345] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:27,345] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:27,345] [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
Rodentibacter mrazii	strain=Ppn418	GCA_001998825.1	1908257	1908257	type	True	88.7088	613	833	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	87.3942	636	833	95	below_threshold
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	87.3579	643	833	95	below_threshold
Rodentibacter ratti	strain=F75	GCA_002000485.1	1906745	1906745	type	True	86.0595	575	833	95	below_threshold
Rodentibacter trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	81.8228	495	833	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	80.6488	471	833	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	80.1484	468	833	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	78.9156	296	833	95	below_threshold
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	78.4128	213	833	95	below_threshold
Gallibacterium anatis	strain=NCTC11413	GCA_900450735.1	750	750	type	True	77.3726	122	833	95	below_threshold
Gallibacterium anatis	strain=F149	GCA_000772265.1	750	750	type	True	77.2932	117	833	95	below_threshold
Gallibacterium anatis	strain=DSM 16844	GCA_000379785.1	750	750	type	True	77.2459	119	833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:27,347] [INFO] DFAST Taxonomy check result was written to GCF_024622045.1_ASM2462204v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:27,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:27,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:27,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24703b70-7b65-4cc9-9536-49047af93873/dqc_reference/checkm_data
[2024-01-24 10:47:27,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:27,374] [INFO] Task started: CheckM
[2024-01-24 10:47:27,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024622045.1_ASM2462204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024622045.1_ASM2462204v1_genomic.fna/checkm_input GCF_024622045.1_ASM2462204v1_genomic.fna/checkm_result
[2024-01-24 10:47:52,219] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:52,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:52,240] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:52,240] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:52,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024622045.1_ASM2462204v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:52,241] [INFO] Task started: Blastn
[2024-01-24 10:47:52,241] [INFO] Running command: blastn -query GCF_024622045.1_ASM2462204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24703b70-7b65-4cc9-9536-49047af93873/dqc_reference/reference_markers_gtdb.fasta -out GCF_024622045.1_ASM2462204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:53,232] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:53,236] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:53,236] [INFO] Target genome list was writen to GCF_024622045.1_ASM2462204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:53,264] [INFO] Task started: fastANI
[2024-01-24 10:47:53,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg472272b8-3f48-4f35-be3a-09baefee7ba9/GCF_024622045.1_ASM2462204v1_genomic.fna.gz --refList GCF_024622045.1_ASM2462204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024622045.1_ASM2462204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:00,093] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:00,116] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:00,116] [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_001019715.1	s__Rodentibacter heylii	98.6459	789	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.70	95.96	0.96	0.90	9	conclusive
GCF_001999425.1	s__Rodentibacter sp001999425	92.4923	678	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999335.1	s__Rodentibacter sp001999335	92.0751	662	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998825.1	s__Rodentibacter mrazii	88.702	614	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
GCF_000379905.1	s__Rodentibacter pneumotropicus	87.362	643	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
GCF_002000485.1	s__Rodentibacter ratti	86.0595	575	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	96.24	96.11	0.85	0.81	4	-
GCF_001999285.1	s__Rodentibacter sp001999285	85.6922	540	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	97.96	97.96	0.90	0.90	3	-
GCF_001999305.1	s__Rodentibacter myodis	80.6395	471	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998905.1	s__Rodentibacter_A heylii_A	79.692	255	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002989035.1	s__Haemophilus influenzae_F	79.0133	259	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9474	98.22	97.14	0.92	0.83	74	-
GCF_001276515.1	s__Haemophilus sp001276515	78.968	305	833	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.49	95.48	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:00,118] [INFO] GTDB search result was written to GCF_024622045.1_ASM2462204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:00,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:00,125] [INFO] DFAST_QC result json was written to GCF_024622045.1_ASM2462204v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:00,126] [INFO] DFAST_QC completed!
[2024-01-24 10:48:00,126] [INFO] Total running time: 0h0m54s