[2024-01-24 12:09:05,862] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,864] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,865] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2039e1c-3c36-42e6-b90b-3507b2278fc9/dqc_reference
[2024-01-24 12:09:07,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:07,084] [INFO] Task started: Prodigal
[2024-01-24 12:09:07,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cbea9c5-db5f-4af8-ad22-ceaf96135356/GCF_002000545.1_ASM200054v1_genomic.fna.gz | prodigal -d GCF_002000545.1_ASM200054v1_genomic.fna/cds.fna -a GCF_002000545.1_ASM200054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:12,939] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:12,940] [INFO] Task started: HMMsearch
[2024-01-24 12:09:12,940] [INFO] Running command: hmmsearch --tblout GCF_002000545.1_ASM200054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2039e1c-3c36-42e6-b90b-3507b2278fc9/dqc_reference/reference_markers.hmm GCF_002000545.1_ASM200054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:13,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:13,187] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0cbea9c5-db5f-4af8-ad22-ceaf96135356/GCF_002000545.1_ASM200054v1_genomic.fna.gz]
[2024-01-24 12:09:13,212] [INFO] Query marker FASTA was written to GCF_002000545.1_ASM200054v1_genomic.fna/markers.fasta
[2024-01-24 12:09:13,212] [INFO] Task started: Blastn
[2024-01-24 12:09:13,212] [INFO] Running command: blastn -query GCF_002000545.1_ASM200054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2039e1c-3c36-42e6-b90b-3507b2278fc9/dqc_reference/reference_markers.fasta -out GCF_002000545.1_ASM200054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:13,799] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:13,802] [INFO] Selected 14 target genomes.
[2024-01-24 12:09:13,802] [INFO] Target genome list was writen to GCF_002000545.1_ASM200054v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:13,808] [INFO] Task started: fastANI
[2024-01-24 12:09:13,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cbea9c5-db5f-4af8-ad22-ceaf96135356/GCF_002000545.1_ASM200054v1_genomic.fna.gz --refList GCF_002000545.1_ASM200054v1_genomic.fna/target_genomes.txt --output GCF_002000545.1_ASM200054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:21,328] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:21,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2039e1c-3c36-42e6-b90b-3507b2278fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:21,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2039e1c-3c36-42e6-b90b-3507b2278fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:21,343] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:21,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:21,344] [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 trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	100.0	790	797	95	conclusive
Rodentibacter rarus	strain=CCUG 17206	GCA_001998965.1	1908260	1908260	type	True	89.5184	555	797	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	88.1029	526	797	95	below_threshold
Rodentibacter ratti	strain=F75	GCA_002000485.1	1906745	1906745	type	True	84.9379	497	797	95	below_threshold
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	83.5657	507	797	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	83.4786	509	797	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	80.6114	483	797	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.9611	435	797	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	78.1633	232	797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:21,345] [INFO] DFAST Taxonomy check result was written to GCF_002000545.1_ASM200054v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:21,346] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:21,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:21,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2039e1c-3c36-42e6-b90b-3507b2278fc9/dqc_reference/checkm_data
[2024-01-24 12:09:21,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:21,381] [INFO] Task started: CheckM
[2024-01-24 12:09:21,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002000545.1_ASM200054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002000545.1_ASM200054v1_genomic.fna/checkm_input GCF_002000545.1_ASM200054v1_genomic.fna/checkm_result
[2024-01-24 12:09:45,360] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:45,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:45,382] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:45,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:45,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002000545.1_ASM200054v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:45,383] [INFO] Task started: Blastn
[2024-01-24 12:09:45,383] [INFO] Running command: blastn -query GCF_002000545.1_ASM200054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2039e1c-3c36-42e6-b90b-3507b2278fc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002000545.1_ASM200054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:46,153] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:46,158] [INFO] Selected 15 target genomes.
[2024-01-24 12:09:46,158] [INFO] Target genome list was writen to GCF_002000545.1_ASM200054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:46,169] [INFO] Task started: fastANI
[2024-01-24 12:09:46,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cbea9c5-db5f-4af8-ad22-ceaf96135356/GCF_002000545.1_ASM200054v1_genomic.fna.gz --refList GCF_002000545.1_ASM200054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002000545.1_ASM200054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:53,798] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:53,815] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:53,815] [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_002000545.1	s__Rodentibacter trehalosifermentans	100.0	790	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.00	97.91	0.88	0.88	3	conclusive
GCF_001998965.1	s__Rodentibacter rarus	89.4792	557	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	99.19	99.19	0.90	0.90	2	-
GCF_002000125.1	s__Rodentibacter heidelbergensis	88.0844	527	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000485.1	s__Rodentibacter ratti	84.9362	498	797	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	83.8475	555	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	97.96	97.96	0.90	0.90	3	-
GCF_000379905.1	s__Rodentibacter pneumotropicus	83.5591	506	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
GCF_001999425.1	s__Rodentibacter sp001999425	82.641	504	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001019715.1	s__Rodentibacter heylii	82.3316	513	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.70	95.96	0.96	0.90	9	-
GCF_001999305.1	s__Rodentibacter myodis	80.6114	483	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356115.1	s__Rodentibacter sp015356115	79.9678	434	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901420285.1	s__Rodentibacter sp901420285	79.2603	320	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130075.1	s__Aggregatibacter segnis_A	78.2414	196	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.43	95.32	0.90	0.88	6	-
GCF_003130255.1	s__Aggregatibacter kilianii	78.1531	232	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	78.0674	180	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:53,817] [INFO] GTDB search result was written to GCF_002000545.1_ASM200054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:53,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:53,821] [INFO] DFAST_QC result json was written to GCF_002000545.1_ASM200054v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:53,821] [INFO] DFAST_QC completed!
[2024-01-24 12:09:53,821] [INFO] Total running time: 0h0m48s