[2024-01-24 11:12:36,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg4440a2b9-ede7-41b8-a8dd-4fbe75bab556/dqc_reference
[2024-01-24 11:12:38,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,663] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg142e3beb-917f-4e3a-aba1-ca531baa72b7/GCF_002285635.2_ASM228563v2_genomic.fna.gz | prodigal -d GCF_002285635.2_ASM228563v2_genomic.fna/cds.fna -a GCF_002285635.2_ASM228563v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:53,684] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:53,685] [INFO] Task started: HMMsearch
[2024-01-24 11:12:53,685] [INFO] Running command: hmmsearch --tblout GCF_002285635.2_ASM228563v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4440a2b9-ede7-41b8-a8dd-4fbe75bab556/dqc_reference/reference_markers.hmm GCF_002285635.2_ASM228563v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:53,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:53,911] [INFO] Found 6/6 markers.
[2024-01-24 11:12:53,945] [INFO] Query marker FASTA was written to GCF_002285635.2_ASM228563v2_genomic.fna/markers.fasta
[2024-01-24 11:12:53,946] [INFO] Task started: Blastn
[2024-01-24 11:12:53,946] [INFO] Running command: blastn -query GCF_002285635.2_ASM228563v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4440a2b9-ede7-41b8-a8dd-4fbe75bab556/dqc_reference/reference_markers.fasta -out GCF_002285635.2_ASM228563v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:54,565] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:54,568] [INFO] Selected 19 target genomes.
[2024-01-24 11:12:54,568] [INFO] Target genome list was writen to GCF_002285635.2_ASM228563v2_genomic.fna/target_genomes.txt
[2024-01-24 11:12:54,576] [INFO] Task started: fastANI
[2024-01-24 11:12:54,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg142e3beb-917f-4e3a-aba1-ca531baa72b7/GCF_002285635.2_ASM228563v2_genomic.fna.gz --refList GCF_002285635.2_ASM228563v2_genomic.fna/target_genomes.txt --output GCF_002285635.2_ASM228563v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:12,491] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:12,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4440a2b9-ede7-41b8-a8dd-4fbe75bab556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:12,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4440a2b9-ede7-41b8-a8dd-4fbe75bab556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:12,505] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:12,505] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:12,505] [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
Chryseobacterium piperi	strain=ATCC BAA-1782	GCA_002285635.2	558152	558152	type	True	100.0	1497	1500	95	conclusive
Chryseobacterium piperi	strain=CTM	GCA_000737775.1	558152	558152	type	True	99.9525	1399	1500	95	conclusive
Chryseobacterium paridis	strain=YIM B02567	GCA_016595215.1	2800328	2800328	type	True	82.1546	986	1500	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	80.3198	722	1500	95	below_threshold
Chryseobacterium daecheongense	strain=DSM 15235	GCA_003729955.1	192389	192389	type	True	80.2564	659	1500	95	below_threshold
Chryseobacterium daecheongense	strain=DSM 15235	GCA_004365465.1	192389	192389	type	True	80.2336	661	1500	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	80.1608	709	1500	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.157	659	1500	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	80.1277	692	1500	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	80.1106	754	1500	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.0887	622	1500	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	80.0543	742	1500	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	80.0499	702	1500	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	79.9757	676	1500	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	79.9722	721	1500	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.9277	633	1500	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	79.8548	735	1500	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.3402	524	1500	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.1435	548	1500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:12,507] [INFO] DFAST Taxonomy check result was written to GCF_002285635.2_ASM228563v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:12,507] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:12,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:12,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4440a2b9-ede7-41b8-a8dd-4fbe75bab556/dqc_reference/checkm_data
[2024-01-24 11:13:12,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:12,549] [INFO] Task started: CheckM
[2024-01-24 11:13:12,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002285635.2_ASM228563v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002285635.2_ASM228563v2_genomic.fna/checkm_input GCF_002285635.2_ASM228563v2_genomic.fna/checkm_result
[2024-01-24 11:13:58,556] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:58,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:58,574] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:58,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:58,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002285635.2_ASM228563v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:58,575] [INFO] Task started: Blastn
[2024-01-24 11:13:58,575] [INFO] Running command: blastn -query GCF_002285635.2_ASM228563v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4440a2b9-ede7-41b8-a8dd-4fbe75bab556/dqc_reference/reference_markers_gtdb.fasta -out GCF_002285635.2_ASM228563v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:59,437] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:59,440] [INFO] Selected 7 target genomes.
[2024-01-24 11:13:59,440] [INFO] Target genome list was writen to GCF_002285635.2_ASM228563v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:59,445] [INFO] Task started: fastANI
[2024-01-24 11:13:59,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg142e3beb-917f-4e3a-aba1-ca531baa72b7/GCF_002285635.2_ASM228563v2_genomic.fna.gz --refList GCF_002285635.2_ASM228563v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002285635.2_ASM228563v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:08,042] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:08,050] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:08,050] [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_002285635.2	s__Chryseobacterium piperi	100.0	1498	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_018613715.1	s__Chryseobacterium sp018613715	82.3094	906	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595215.1	s__Chryseobacterium sp016595215	82.1448	987	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216065.1	s__Chryseobacterium sp002216065	81.9617	954	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184525.1	s__Chryseobacterium sp013184525	81.5208	937	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	80.0619	696	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCF_001045465.1	s__Chryseobacterium angstadtii	79.9887	674	1500	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:08,051] [INFO] GTDB search result was written to GCF_002285635.2_ASM228563v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:08,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:08,055] [INFO] DFAST_QC result json was written to GCF_002285635.2_ASM228563v2_genomic.fna/dqc_result.json
[2024-01-24 11:14:08,055] [INFO] DFAST_QC completed!
[2024-01-24 11:14:08,055] [INFO] Total running time: 0h1m32s