[2024-01-24 12:21:44,638] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg668ebda9-e9bb-47e3-8086-e590b58893c6/dqc_reference
[2024-01-24 12:21:46,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,012] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg290092e1-9d53-44ff-b4bf-dfff9ec0114e/GCF_002000485.1_ASM200048v1_genomic.fna.gz | prodigal -d GCF_002000485.1_ASM200048v1_genomic.fna/cds.fna -a GCF_002000485.1_ASM200048v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:50,724] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:50,725] [INFO] Task started: HMMsearch
[2024-01-24 12:21:50,725] [INFO] Running command: hmmsearch --tblout GCF_002000485.1_ASM200048v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg668ebda9-e9bb-47e3-8086-e590b58893c6/dqc_reference/reference_markers.hmm GCF_002000485.1_ASM200048v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:50,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:50,979] [INFO] Found 6/6 markers.
[2024-01-24 12:21:51,037] [INFO] Query marker FASTA was written to GCF_002000485.1_ASM200048v1_genomic.fna/markers.fasta
[2024-01-24 12:21:51,037] [INFO] Task started: Blastn
[2024-01-24 12:21:51,038] [INFO] Running command: blastn -query GCF_002000485.1_ASM200048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg668ebda9-e9bb-47e3-8086-e590b58893c6/dqc_reference/reference_markers.fasta -out GCF_002000485.1_ASM200048v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:51,713] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:51,716] [INFO] Selected 17 target genomes.
[2024-01-24 12:21:51,716] [INFO] Target genome list was writen to GCF_002000485.1_ASM200048v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:51,761] [INFO] Task started: fastANI
[2024-01-24 12:21:51,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg290092e1-9d53-44ff-b4bf-dfff9ec0114e/GCF_002000485.1_ASM200048v1_genomic.fna.gz --refList GCF_002000485.1_ASM200048v1_genomic.fna/target_genomes.txt --output GCF_002000485.1_ASM200048v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:59,919] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:59,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg668ebda9-e9bb-47e3-8086-e590b58893c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:59,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg668ebda9-e9bb-47e3-8086-e590b58893c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:59,930] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:21:59,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:59,930] [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 ratti	strain=F75	GCA_002000485.1	1906745	1906745	type	True	100.0	661	665	95	conclusive
Rodentibacter mrazii	strain=Ppn418	GCA_001998825.1	1908257	1908257	type	True	90.4948	551	665	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	89.8929	583	665	95	below_threshold
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	89.8787	586	665	95	below_threshold
Rodentibacter rarus	strain=CCUG 17206	GCA_001998965.1	1908260	1908260	type	True	85.6891	481	665	95	below_threshold
Rodentibacter trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	84.7626	494	665	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	80.904	440	665	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	80.3184	445	665	95	below_threshold
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	79.0296	315	665	95	below_threshold
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	78.3135	216	665	95	below_threshold
Pasteurella multocida subsp. gallicida	strain=NCTC10204	GCA_900636625.1	123812	747	type	True	77.6488	181	665	95	below_threshold
Pasteurella multocida subsp. septica	strain=NCTC11995	GCA_900454845.1	115545	747	type	True	77.5772	191	665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:59,932] [INFO] DFAST Taxonomy check result was written to GCF_002000485.1_ASM200048v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:59,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:59,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:59,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg668ebda9-e9bb-47e3-8086-e590b58893c6/dqc_reference/checkm_data
[2024-01-24 12:21:59,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:59,960] [INFO] Task started: CheckM
[2024-01-24 12:21:59,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002000485.1_ASM200048v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002000485.1_ASM200048v1_genomic.fna/checkm_input GCF_002000485.1_ASM200048v1_genomic.fna/checkm_result
[2024-01-24 12:22:22,606] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:22,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:22,631] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:22,632] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:22,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002000485.1_ASM200048v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:22,632] [INFO] Task started: Blastn
[2024-01-24 12:22:22,633] [INFO] Running command: blastn -query GCF_002000485.1_ASM200048v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg668ebda9-e9bb-47e3-8086-e590b58893c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002000485.1_ASM200048v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:23,452] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:23,456] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:23,456] [INFO] Target genome list was writen to GCF_002000485.1_ASM200048v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:23,462] [INFO] Task started: fastANI
[2024-01-24 12:22:23,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg290092e1-9d53-44ff-b4bf-dfff9ec0114e/GCF_002000485.1_ASM200048v1_genomic.fna.gz --refList GCF_002000485.1_ASM200048v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002000485.1_ASM200048v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:28,371] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:28,384] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:28,384] [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_002000485.1	s__Rodentibacter ratti	100.0	661	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	96.24	96.11	0.85	0.81	4	conclusive
GCF_001998825.1	s__Rodentibacter mrazii	90.4948	551	665	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	89.8787	586	665	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	86.7472	571	665	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	86.0919	573	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.70	95.96	0.96	0.90	9	-
GCF_001999335.1	s__Rodentibacter sp001999335	85.9147	563	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998965.1	s__Rodentibacter rarus	85.6833	481	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	99.19	99.19	0.90	0.90	2	-
GCF_001999285.1	s__Rodentibacter sp001999285	85.651	530	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	97.96	97.96	0.90	0.90	3	-
GCF_002000125.1	s__Rodentibacter heidelbergensis	84.5771	481	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:28,387] [INFO] GTDB search result was written to GCF_002000485.1_ASM200048v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:28,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:28,392] [INFO] DFAST_QC result json was written to GCF_002000485.1_ASM200048v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:28,392] [INFO] DFAST_QC completed!
[2024-01-24 12:22:28,392] [INFO] Total running time: 0h0m44s