[2024-01-24 12:16:03,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:03,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:03,403] [INFO] DQC Reference Directory: /var/lib/cwl/stge99ca886-f594-4ab4-b844-7744468bbe06/dqc_reference
[2024-01-24 12:16:04,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:04,606] [INFO] Task started: Prodigal
[2024-01-24 12:16:04,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg73938df3-3374-4c93-94f8-b539464d7bb8/GCF_900187255.1_51184_F02_genomic.fna.gz | prodigal -d GCF_900187255.1_51184_F02_genomic.fna/cds.fna -a GCF_900187255.1_51184_F02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:17,508] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:17,509] [INFO] Task started: HMMsearch
[2024-01-24 12:16:17,509] [INFO] Running command: hmmsearch --tblout GCF_900187255.1_51184_F02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge99ca886-f594-4ab4-b844-7744468bbe06/dqc_reference/reference_markers.hmm GCF_900187255.1_51184_F02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:17,747] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:17,748] [INFO] Found 6/6 markers.
[2024-01-24 12:16:17,777] [INFO] Query marker FASTA was written to GCF_900187255.1_51184_F02_genomic.fna/markers.fasta
[2024-01-24 12:16:17,778] [INFO] Task started: Blastn
[2024-01-24 12:16:17,778] [INFO] Running command: blastn -query GCF_900187255.1_51184_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stge99ca886-f594-4ab4-b844-7744468bbe06/dqc_reference/reference_markers.fasta -out GCF_900187255.1_51184_F02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:18,357] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:18,361] [INFO] Selected 13 target genomes.
[2024-01-24 12:16:18,362] [INFO] Target genome list was writen to GCF_900187255.1_51184_F02_genomic.fna/target_genomes.txt
[2024-01-24 12:16:18,374] [INFO] Task started: fastANI
[2024-01-24 12:16:18,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg73938df3-3374-4c93-94f8-b539464d7bb8/GCF_900187255.1_51184_F02_genomic.fna.gz --refList GCF_900187255.1_51184_F02_genomic.fna/target_genomes.txt --output GCF_900187255.1_51184_F02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:25,917] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:25,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge99ca886-f594-4ab4-b844-7744468bbe06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:25,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge99ca886-f594-4ab4-b844-7744468bbe06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:25,931] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:16:25,931] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:25,931] [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
Capnocytophaga haemolytica	strain=NCTC12947	GCA_900187255.1	45243	45243	type	True	100.0	896	896	95	conclusive
Capnocytophaga haemolytica	strain=CCUG 32990	GCA_001553545.1	45243	45243	type	True	99.9951	896	896	95	conclusive
Capnocytophaga haemolytica	strain=DSM 11385	GCA_900115315.1	45243	45243	type	True	99.9828	862	896	95	conclusive
Capnocytophaga ochracea	strain=DSM 7271	GCA_000023285.1	1018	1018	type	True	80.3109	152	896	95	below_threshold
Capnocytophaga ochracea	strain=FDAARGOS_1468	GCA_019930725.1	1018	1018	type	True	80.2621	156	896	95	below_threshold
Capnocytophaga periodontitidis	strain=p1a2	GCA_016126015.1	2795027	2795027	type	True	78.8664	160	896	95	below_threshold
Capnocytophaga sputigena	strain=NCTC11653	GCA_900446695.1	1019	1019	type	True	78.7347	146	896	95	below_threshold
Capnocytophaga granulosa	strain=DSM 11449	GCA_900106575.1	45242	45242	type	True	78.2179	52	896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:25,933] [INFO] DFAST Taxonomy check result was written to GCF_900187255.1_51184_F02_genomic.fna/tc_result.tsv
[2024-01-24 12:16:25,933] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:25,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:25,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge99ca886-f594-4ab4-b844-7744468bbe06/dqc_reference/checkm_data
[2024-01-24 12:16:25,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:25,967] [INFO] Task started: CheckM
[2024-01-24 12:16:25,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187255.1_51184_F02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187255.1_51184_F02_genomic.fna/checkm_input GCF_900187255.1_51184_F02_genomic.fna/checkm_result
[2024-01-24 12:17:05,811] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:05,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:05,831] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:05,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:05,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187255.1_51184_F02_genomic.fna/markers.fasta)
[2024-01-24 12:17:05,832] [INFO] Task started: Blastn
[2024-01-24 12:17:05,832] [INFO] Running command: blastn -query GCF_900187255.1_51184_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stge99ca886-f594-4ab4-b844-7744468bbe06/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187255.1_51184_F02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:06,636] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:06,639] [INFO] Selected 26 target genomes.
[2024-01-24 12:17:06,639] [INFO] Target genome list was writen to GCF_900187255.1_51184_F02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:06,674] [INFO] Task started: fastANI
[2024-01-24 12:17:06,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg73938df3-3374-4c93-94f8-b539464d7bb8/GCF_900187255.1_51184_F02_genomic.fna.gz --refList GCF_900187255.1_51184_F02_genomic.fna/target_genomes_gtdb.txt --output GCF_900187255.1_51184_F02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:19,471] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:19,480] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:19,480] [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_001553545.1	s__Capnocytophaga haemolytica	99.9951	896	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000023285.1	s__Capnocytophaga ochracea	80.2289	151	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.34	96.09	0.90	0.87	17	-
GCF_002209445.1	s__Capnocytophaga endodontalis	78.874	156	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.66	96.51	0.90	0.87	9	-
GCF_900446695.1	s__Capnocytophaga sputigena	78.723	147	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.52	96.32	0.92	0.88	8	-
GCF_002999135.1	s__Capnocytophaga sp002999135	78.5684	119	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:19,482] [INFO] GTDB search result was written to GCF_900187255.1_51184_F02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:19,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:19,485] [INFO] DFAST_QC result json was written to GCF_900187255.1_51184_F02_genomic.fna/dqc_result.json
[2024-01-24 12:17:19,485] [INFO] DFAST_QC completed!
[2024-01-24 12:17:19,485] [INFO] Total running time: 0h1m16s