[2024-01-24 10:48:09,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,467] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,467] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5d45dfe-de87-44d1-a225-80a1bf2d5e36/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg972e5c4a-569b-4a24-9f12-8fb09279c002/GCF_000730685.1_ASM73068v1_genomic.fna.gz | prodigal -d GCF_000730685.1_ASM73068v1_genomic.fna/cds.fna -a GCF_000730685.1_ASM73068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:29,651] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:29,652] [INFO] Task started: HMMsearch
[2024-01-24 10:48:29,652] [INFO] Running command: hmmsearch --tblout GCF_000730685.1_ASM73068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5d45dfe-de87-44d1-a225-80a1bf2d5e36/dqc_reference/reference_markers.hmm GCF_000730685.1_ASM73068v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:29,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:29,934] [INFO] Found 6/6 markers.
[2024-01-24 10:48:29,961] [INFO] Query marker FASTA was written to GCF_000730685.1_ASM73068v1_genomic.fna/markers.fasta
[2024-01-24 10:48:29,961] [INFO] Task started: Blastn
[2024-01-24 10:48:29,962] [INFO] Running command: blastn -query GCF_000730685.1_ASM73068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5d45dfe-de87-44d1-a225-80a1bf2d5e36/dqc_reference/reference_markers.fasta -out GCF_000730685.1_ASM73068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:30,605] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:30,609] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:30,610] [INFO] Target genome list was writen to GCF_000730685.1_ASM73068v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:31,055] [INFO] Task started: fastANI
[2024-01-24 10:48:31,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg972e5c4a-569b-4a24-9f12-8fb09279c002/GCF_000730685.1_ASM73068v1_genomic.fna.gz --refList GCF_000730685.1_ASM73068v1_genomic.fna/target_genomes.txt --output GCF_000730685.1_ASM73068v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:40,469] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:40,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5d45dfe-de87-44d1-a225-80a1bf2d5e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:40,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5d45dfe-de87-44d1-a225-80a1bf2d5e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:40,480] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:40,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:40,480] [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 pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	100.0	797	806	95	conclusive
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	99.9521	743	806	95	conclusive
Rodentibacter mrazii	strain=Ppn418	GCA_001998825.1	1908257	1908257	type	True	90.4054	615	806	95	below_threshold
Rodentibacter ratti	strain=F75	GCA_002000485.1	1906745	1906745	type	True	89.8767	587	806	95	below_threshold
Rodentibacter rarus	strain=CCUG 17206	GCA_001998965.1	1908260	1908260	type	True	83.9631	500	806	95	below_threshold
Rodentibacter trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	83.6265	499	806	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	83.3342	493	806	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	80.8509	493	806	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	80.7317	477	806	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	79.5452	302	806	95	below_threshold
Haemophilus haemolyticus	strain=ATCC 33390	GCA_004368535.1	726	726	type	True	79.4598	300	806	95	below_threshold
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	79.3955	305	806	95	below_threshold
Canicola haemoglobinophilus	strain=NCTC1659	GCA_900450725.1	733	733	type	True	78.4816	174	806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:40,482] [INFO] DFAST Taxonomy check result was written to GCF_000730685.1_ASM73068v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:40,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:40,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:40,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5d45dfe-de87-44d1-a225-80a1bf2d5e36/dqc_reference/checkm_data
[2024-01-24 10:48:40,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:40,513] [INFO] Task started: CheckM
[2024-01-24 10:48:40,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000730685.1_ASM73068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000730685.1_ASM73068v1_genomic.fna/checkm_input GCF_000730685.1_ASM73068v1_genomic.fna/checkm_result
[2024-01-24 10:49:07,499] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:07,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:07,521] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:07,521] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:07,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000730685.1_ASM73068v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:07,522] [INFO] Task started: Blastn
[2024-01-24 10:49:07,522] [INFO] Running command: blastn -query GCF_000730685.1_ASM73068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5d45dfe-de87-44d1-a225-80a1bf2d5e36/dqc_reference/reference_markers_gtdb.fasta -out GCF_000730685.1_ASM73068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:08,325] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:08,329] [INFO] Selected 9 target genomes.
[2024-01-24 10:49:08,329] [INFO] Target genome list was writen to GCF_000730685.1_ASM73068v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:08,335] [INFO] Task started: fastANI
[2024-01-24 10:49:08,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg972e5c4a-569b-4a24-9f12-8fb09279c002/GCF_000730685.1_ASM73068v1_genomic.fna.gz --refList GCF_000730685.1_ASM73068v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000730685.1_ASM73068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:13,916] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:13,924] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:13,925] [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_000379905.1	s__Rodentibacter pneumotropicus	99.9521	743	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	conclusive
GCF_001998825.1	s__Rodentibacter mrazii	90.4054	615	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
GCF_002000485.1	s__Rodentibacter ratti	89.8767	587	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	96.24	96.11	0.85	0.81	4	-
GCF_001019715.1	s__Rodentibacter heylii	87.3307	649	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.70	95.96	0.96	0.90	9	-
GCF_001999425.1	s__Rodentibacter sp001999425	86.8146	609	806	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	86.1382	597	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999285.1	s__Rodentibacter sp001999285	85.649	544	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	97.96	97.96	0.90	0.90	3	-
GCF_001998965.1	s__Rodentibacter rarus	83.9457	501	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	99.19	99.19	0.90	0.90	2	-
GCF_001998905.1	s__Rodentibacter_A heylii_A	79.1073	233	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:13,930] [INFO] GTDB search result was written to GCF_000730685.1_ASM73068v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:13,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:13,934] [INFO] DFAST_QC result json was written to GCF_000730685.1_ASM73068v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:13,934] [INFO] DFAST_QC completed!
[2024-01-24 10:49:13,934] [INFO] Total running time: 0h1m4s