[2024-01-24 13:42:57,603] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,605] [INFO] DQC Reference Directory: /var/lib/cwl/stga0b91d0f-2c57-4ae6-bc3b-df7ec4103137/dqc_reference
[2024-01-24 13:42:58,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,826] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,826] [INFO] Running command: gunzip -c /var/lib/cwl/stgc009136c-c9e6-4552-8306-28c4a817e32f/GCF_000023285.1_ASM2328v1_genomic.fna.gz | prodigal -d GCF_000023285.1_ASM2328v1_genomic.fna/cds.fna -a GCF_000023285.1_ASM2328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:09,740] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:09,740] [INFO] Task started: HMMsearch
[2024-01-24 13:43:09,741] [INFO] Running command: hmmsearch --tblout GCF_000023285.1_ASM2328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0b91d0f-2c57-4ae6-bc3b-df7ec4103137/dqc_reference/reference_markers.hmm GCF_000023285.1_ASM2328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:09,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:09,983] [INFO] Found 6/6 markers.
[2024-01-24 13:43:10,009] [INFO] Query marker FASTA was written to GCF_000023285.1_ASM2328v1_genomic.fna/markers.fasta
[2024-01-24 13:43:10,009] [INFO] Task started: Blastn
[2024-01-24 13:43:10,010] [INFO] Running command: blastn -query GCF_000023285.1_ASM2328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b91d0f-2c57-4ae6-bc3b-df7ec4103137/dqc_reference/reference_markers.fasta -out GCF_000023285.1_ASM2328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:10,602] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:10,605] [INFO] Selected 13 target genomes.
[2024-01-24 13:43:10,606] [INFO] Target genome list was writen to GCF_000023285.1_ASM2328v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:10,627] [INFO] Task started: fastANI
[2024-01-24 13:43:10,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgc009136c-c9e6-4552-8306-28c4a817e32f/GCF_000023285.1_ASM2328v1_genomic.fna.gz --refList GCF_000023285.1_ASM2328v1_genomic.fna/target_genomes.txt --output GCF_000023285.1_ASM2328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:20,738] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:20,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0b91d0f-2c57-4ae6-bc3b-df7ec4103137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:20,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0b91d0f-2c57-4ae6-bc3b-df7ec4103137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:20,753] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:43:20,753] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:20,753] [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 ochracea	strain=DSM 7271	GCA_000023285.1	1018	1018	type	True	100.0	868	870	95	conclusive
Capnocytophaga ochracea	strain=FDAARGOS_1468	GCA_019930725.1	1018	1018	type	True	99.9995	868	870	95	conclusive
Capnocytophaga endodontalis	strain=ChDC OS43	GCA_002209445.1	2708117	2708117	type	True	86.0222	594	870	95	below_threshold
Capnocytophaga periodontitidis	strain=p1a2	GCA_016126015.1	2795027	2795027	type	True	85.7668	587	870	95	below_threshold
Capnocytophaga sputigena	strain=NCTC11653	GCA_900446695.1	1019	1019	type	True	84.6926	575	870	95	below_threshold
Capnocytophaga leadbetteri	strain=DSM 22902	GCA_003054025.1	327575	327575	type	True	79.6651	347	870	95	below_threshold
Capnocytophaga bilenii	strain=Marseille-Q4570	GCA_017565765.1	2819369	2819369	type	True	78.9867	265	870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:20,755] [INFO] DFAST Taxonomy check result was written to GCF_000023285.1_ASM2328v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:20,756] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:20,756] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:20,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0b91d0f-2c57-4ae6-bc3b-df7ec4103137/dqc_reference/checkm_data
[2024-01-24 13:43:20,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:20,786] [INFO] Task started: CheckM
[2024-01-24 13:43:20,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000023285.1_ASM2328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000023285.1_ASM2328v1_genomic.fna/checkm_input GCF_000023285.1_ASM2328v1_genomic.fna/checkm_result
[2024-01-24 13:43:55,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:55,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:55,371] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:55,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:55,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000023285.1_ASM2328v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:55,372] [INFO] Task started: Blastn
[2024-01-24 13:43:55,372] [INFO] Running command: blastn -query GCF_000023285.1_ASM2328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b91d0f-2c57-4ae6-bc3b-df7ec4103137/dqc_reference/reference_markers_gtdb.fasta -out GCF_000023285.1_ASM2328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:56,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:56,149] [INFO] Selected 16 target genomes.
[2024-01-24 13:43:56,149] [INFO] Target genome list was writen to GCF_000023285.1_ASM2328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:56,184] [INFO] Task started: fastANI
[2024-01-24 13:43:56,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgc009136c-c9e6-4552-8306-28c4a817e32f/GCF_000023285.1_ASM2328v1_genomic.fna.gz --refList GCF_000023285.1_ASM2328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000023285.1_ASM2328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:07,079] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:07,090] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:07,091] [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_000023285.1	s__Capnocytophaga ochracea	100.0	868	870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.34	96.09	0.90	0.87	17	conclusive
GCF_002209445.1	s__Capnocytophaga endodontalis	86.1275	586	870	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	84.7297	572	870	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	80.403	347	870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054025.1	s__Capnocytophaga leadbetteri	79.659	347	870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	95.46	95.36	0.86	0.85	6	-
GCF_017565765.1	s__Capnocytophaga bilenii	79.0212	263	870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.25	97.25	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:07,092] [INFO] GTDB search result was written to GCF_000023285.1_ASM2328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:07,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:07,095] [INFO] DFAST_QC result json was written to GCF_000023285.1_ASM2328v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:07,096] [INFO] DFAST_QC completed!
[2024-01-24 13:44:07,096] [INFO] Total running time: 0h1m9s