[2024-01-25 19:56:35,475] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:35,477] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:35,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f834139-8a07-4ddb-8172-0ec407f02326/dqc_reference
[2024-01-25 19:56:36,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:36,598] [INFO] Task started: Prodigal
[2024-01-25 19:56:36,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a613ba6-4eeb-421c-a702-63ab473535ab/GCF_024814375.1_ASM2481437v1_genomic.fna.gz | prodigal -d GCF_024814375.1_ASM2481437v1_genomic.fna/cds.fna -a GCF_024814375.1_ASM2481437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:39,802] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:39,802] [INFO] Task started: HMMsearch
[2024-01-25 19:56:39,802] [INFO] Running command: hmmsearch --tblout GCF_024814375.1_ASM2481437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f834139-8a07-4ddb-8172-0ec407f02326/dqc_reference/reference_markers.hmm GCF_024814375.1_ASM2481437v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:40,030] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:40,032] [INFO] Found 6/6 markers.
[2024-01-25 19:56:40,052] [INFO] Query marker FASTA was written to GCF_024814375.1_ASM2481437v1_genomic.fna/markers.fasta
[2024-01-25 19:56:40,052] [INFO] Task started: Blastn
[2024-01-25 19:56:40,052] [INFO] Running command: blastn -query GCF_024814375.1_ASM2481437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f834139-8a07-4ddb-8172-0ec407f02326/dqc_reference/reference_markers.fasta -out GCF_024814375.1_ASM2481437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:40,605] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:40,609] [INFO] Selected 28 target genomes.
[2024-01-25 19:56:40,609] [INFO] Target genome list was writen to GCF_024814375.1_ASM2481437v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:40,654] [INFO] Task started: fastANI
[2024-01-25 19:56:40,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a613ba6-4eeb-421c-a702-63ab473535ab/GCF_024814375.1_ASM2481437v1_genomic.fna.gz --refList GCF_024814375.1_ASM2481437v1_genomic.fna/target_genomes.txt --output GCF_024814375.1_ASM2481437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:49,287] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:49,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f834139-8a07-4ddb-8172-0ec407f02326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:49,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f834139-8a07-4ddb-8172-0ec407f02326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:49,302] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:56:49,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:56:49,302] [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
Streptococcus hyointestinalis	strain=NCTC12224	GCA_900459405.1	1337	1337	type	True	81.4512	355	554	95	below_threshold
Streptococcus gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	81.0783	139	554	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	80.9893	140	554	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	79.7719	118	554	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	79.7312	126	554	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	79.7017	120	554	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	79.4815	116	554	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	79.4568	119	554	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	79.4476	118	554	95	below_threshold
Streptococcus caballi	strain=DSM 19004	GCA_000379985.1	439220	439220	type	True	79.027	123	554	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	78.9799	116	554	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.8825	52	554	95	below_threshold
Streptococcus pyogenes	strain=CCUG 4207	GCA_004028355.1	1314	1314	type	True	78.8199	78	554	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	78.7475	111	554	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	78.626	84	554	95	below_threshold
Streptococcus halotolerans	strain=HTS9	GCA_001598035.1	1814128	1814128	type	True	78.6174	78	554	95	below_threshold
Streptococcus pyogenes	strain=DSM 20565	GCA_000421785.1	1314	1314	type	True	78.5948	75	554	95	below_threshold
Streptococcus agalactiae	strain=ATCC 13813	GCA_000186445.1	1311	1311	type	True	78.4026	94	554	95	below_threshold
Streptococcus agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	78.3866	98	554	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.2719	69	554	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	78.2543	97	554	95	below_threshold
Streptococcus urinalis	strain=NCTC13766	GCA_900636885.1	149016	149016	type	True	78.2267	87	554	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	77.999	79	554	95	below_threshold
Streptococcus urinalis	strain=2285-97	GCA_000188055.3	149016	149016	type	True	77.9654	91	554	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	77.9406	70	554	95	below_threshold
Streptococcus marimammalium	strain=DSM 18627	GCA_000380045.1	269666	269666	type	True	77.69	58	554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:49,304] [INFO] DFAST Taxonomy check result was written to GCF_024814375.1_ASM2481437v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:49,304] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:49,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:49,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f834139-8a07-4ddb-8172-0ec407f02326/dqc_reference/checkm_data
[2024-01-25 19:56:49,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:49,326] [INFO] Task started: CheckM
[2024-01-25 19:56:49,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024814375.1_ASM2481437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024814375.1_ASM2481437v1_genomic.fna/checkm_input GCF_024814375.1_ASM2481437v1_genomic.fna/checkm_result
[2024-01-25 19:57:05,464] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:05,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:05,478] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:05,478] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:05,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024814375.1_ASM2481437v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:05,478] [INFO] Task started: Blastn
[2024-01-25 19:57:05,478] [INFO] Running command: blastn -query GCF_024814375.1_ASM2481437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f834139-8a07-4ddb-8172-0ec407f02326/dqc_reference/reference_markers_gtdb.fasta -out GCF_024814375.1_ASM2481437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:06,267] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:06,270] [INFO] Selected 25 target genomes.
[2024-01-25 19:57:06,270] [INFO] Target genome list was writen to GCF_024814375.1_ASM2481437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:06,291] [INFO] Task started: fastANI
[2024-01-25 19:57:06,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a613ba6-4eeb-421c-a702-63ab473535ab/GCF_024814375.1_ASM2481437v1_genomic.fna.gz --refList GCF_024814375.1_ASM2481437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024814375.1_ASM2481437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:15,012] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:15,027] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:57:15,028] [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_900459405.1	s__Streptococcus hyointestinalis	81.4617	356	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011039275.1	s__Streptococcus hyointestinalis_A	81.3614	342	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900478025.1	s__Streptococcus pasteurianus	81.2899	129	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
GCF_003337175.1	s__Streptococcus gallolyticus_B	81.007	140	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_002000985.1	s__Streptococcus gallolyticus	80.9893	140	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCA_000283635.1	s__Streptococcus macedonicus	80.989	133	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_000154985.1	s__Streptococcus infantarius	79.7017	120	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_001708305.1	s__Streptococcus himalayensis	79.397	63	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004570575.1	s__Streptococcus cuniculi_A	79.1337	79	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000379985.1	s__Streptococcus caballi	79.027	123	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002055535.1	s__Streptococcus pyogenes	78.8199	78	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.85	98.36	0.95	0.87	2144	-
GCF_000380105.1	s__Streptococcus orisratti	78.7475	111	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921845.1	s__Streptococcus cuniculi	78.7148	62	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598035.1	s__Streptococcus halotolerans	78.6479	79	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	78.626	84	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010120595.1	s__Streptococcus thermophilus	78.4806	90	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.46	97.47	0.91	0.81	130	-
GCF_000186445.1	s__Streptococcus agalactiae	78.4026	94	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_000376985.1	s__Streptococcus henryi	78.2543	97	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_010604095.1	s__Streptococcus sp000187445	78.2027	94	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_001921825.1	s__Streptococcus acidominimus	78.0622	66	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.52	97.98	0.90	0.85	5	-
GCF_000188055.2	s__Streptococcus urinalis	77.9654	91	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.98	99.96	0.98	0.97	3	-
GCF_000380125.1	s__Streptococcus ovis	77.9406	70	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984715.1	s__Streptococcus azizii	77.8993	60	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.97	99.96	0.99	0.99	5	-
GCF_001814775.1	s__Streptococcus sp001814775	77.8822	73	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380045.1	s__Streptococcus marimammalium	77.6747	59	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:15,029] [INFO] GTDB search result was written to GCF_024814375.1_ASM2481437v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:15,030] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:15,034] [INFO] DFAST_QC result json was written to GCF_024814375.1_ASM2481437v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:15,034] [INFO] DFAST_QC completed!
[2024-01-25 19:57:15,034] [INFO] Total running time: 0h0m40s