[2024-01-24 12:47:25,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:25,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:25,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg3616332f-7330-4970-bbf7-fc8fb67839fb/dqc_reference
[2024-01-24 12:47:27,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:27,149] [INFO] Task started: Prodigal
[2024-01-24 12:47:27,149] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7eb5678-9d9b-4c37-9143-405713d44aaf/GCF_000379985.1_ASM37998v1_genomic.fna.gz | prodigal -d GCF_000379985.1_ASM37998v1_genomic.fna/cds.fna -a GCF_000379985.1_ASM37998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:32,023] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:32,023] [INFO] Task started: HMMsearch
[2024-01-24 12:47:32,023] [INFO] Running command: hmmsearch --tblout GCF_000379985.1_ASM37998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3616332f-7330-4970-bbf7-fc8fb67839fb/dqc_reference/reference_markers.hmm GCF_000379985.1_ASM37998v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:32,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:32,272] [INFO] Found 6/6 markers.
[2024-01-24 12:47:32,297] [INFO] Query marker FASTA was written to GCF_000379985.1_ASM37998v1_genomic.fna/markers.fasta
[2024-01-24 12:47:32,297] [INFO] Task started: Blastn
[2024-01-24 12:47:32,297] [INFO] Running command: blastn -query GCF_000379985.1_ASM37998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3616332f-7330-4970-bbf7-fc8fb67839fb/dqc_reference/reference_markers.fasta -out GCF_000379985.1_ASM37998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:32,931] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:32,934] [INFO] Selected 23 target genomes.
[2024-01-24 12:47:32,934] [INFO] Target genome list was writen to GCF_000379985.1_ASM37998v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:32,949] [INFO] Task started: fastANI
[2024-01-24 12:47:32,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7eb5678-9d9b-4c37-9143-405713d44aaf/GCF_000379985.1_ASM37998v1_genomic.fna.gz --refList GCF_000379985.1_ASM37998v1_genomic.fna/target_genomes.txt --output GCF_000379985.1_ASM37998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:41,521] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:41,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3616332f-7330-4970-bbf7-fc8fb67839fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:41,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3616332f-7330-4970-bbf7-fc8fb67839fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:41,538] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:41,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:41,539] [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 caballi	strain=DSM 19004	GCA_000379985.1	439220	439220	type	True	100.0	676	679	95	conclusive
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	82.4917	276	679	95	below_threshold
Streptococcus gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	80.4678	249	679	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	80.3995	249	679	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	79.9317	209	679	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	79.9287	202	679	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	79.7977	198	679	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	79.7738	211	679	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	79.6621	206	679	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	79.471	216	679	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	79.4125	210	679	95	below_threshold
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	79.1675	112	679	95	below_threshold
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	79.1408	83	679	95	below_threshold
Streptococcus dysgalactiae subsp. dysgalactiae	strain=NCTC13731	GCA_900459225.1	99822	1334	type	True	79.0079	115	679	95	below_threshold
Streptococcus agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	78.9452	111	679	95	below_threshold
Streptococcus agalactiae	strain=ATCC 13813	GCA_000186445.1	1311	1311	type	True	78.8874	119	679	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.7143	99	679	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	78.5878	218	679	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.514	67	679	95	below_threshold
Streptococcus mutans	strain=NCTC10449	GCA_900475095.1	1309	1309	type	True	78.3331	159	679	95	below_threshold
Streptococcus mutans	strain=DSM 20523	GCA_000375505.1	1309	1309	type	True	78.1523	159	679	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	77.6708	88	679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:41,540] [INFO] DFAST Taxonomy check result was written to GCF_000379985.1_ASM37998v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:41,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:41,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:41,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3616332f-7330-4970-bbf7-fc8fb67839fb/dqc_reference/checkm_data
[2024-01-24 12:47:41,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:41,580] [INFO] Task started: CheckM
[2024-01-24 12:47:41,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000379985.1_ASM37998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000379985.1_ASM37998v1_genomic.fna/checkm_input GCF_000379985.1_ASM37998v1_genomic.fna/checkm_result
[2024-01-24 12:48:04,113] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:04,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:04,138] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:04,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:04,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000379985.1_ASM37998v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:04,139] [INFO] Task started: Blastn
[2024-01-24 12:48:04,139] [INFO] Running command: blastn -query GCF_000379985.1_ASM37998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3616332f-7330-4970-bbf7-fc8fb67839fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000379985.1_ASM37998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:04,966] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:04,970] [INFO] Selected 17 target genomes.
[2024-01-24 12:48:04,970] [INFO] Target genome list was writen to GCF_000379985.1_ASM37998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:04,981] [INFO] Task started: fastANI
[2024-01-24 12:48:04,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7eb5678-9d9b-4c37-9143-405713d44aaf/GCF_000379985.1_ASM37998v1_genomic.fna.gz --refList GCF_000379985.1_ASM37998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000379985.1_ASM37998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:12,125] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:12,141] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:12,142] [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_000379985.1	s__Streptococcus caballi	100.0	676	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000380105.1	s__Streptococcus orisratti	82.5024	277	679	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	80.45	218	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
GCF_002000985.1	s__Streptococcus gallolyticus	80.3995	249	679	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	80.1417	230	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_015594605.1	s__Streptococcus sp015594605	80.0273	235	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286075.1	s__Streptococcus ratti	79.9717	177	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_000154985.1	s__Streptococcus infantarius	79.9023	203	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_000187265.1	s__Streptococcus equinus	79.7977	198	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	-
GCF_016461705.1	s__Streptococcus vicugnae	79.6735	206	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_900104225.1	s__Streptococcus equinus_D	79.5897	212	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101445.1	s__Streptococcus equinus_B	79.3137	213	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_900459225.1	s__Streptococcus dysgalactiae	79.0123	114	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_000186445.1	s__Streptococcus agalactiae	78.9047	118	679	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	78.5877	218	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	78.5052	195	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006739205.1	s__Streptococcus mutans	78.3168	159	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.12	98.73	0.95	0.87	261	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:12,144] [INFO] GTDB search result was written to GCF_000379985.1_ASM37998v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:12,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:12,149] [INFO] DFAST_QC result json was written to GCF_000379985.1_ASM37998v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:12,150] [INFO] DFAST_QC completed!
[2024-01-24 12:48:12,150] [INFO] Total running time: 0h0m46s