[2024-01-25 19:05:05,616] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:05,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:05,617] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1e54c63-c3a7-4a90-9703-0922ed607d88/dqc_reference
[2024-01-25 19:05:06,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:06,769] [INFO] Task started: Prodigal
[2024-01-25 19:05:06,769] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd339ac0-265a-445c-95de-4549d74b45c1/GCF_016908655.1_ASM1690865v1_genomic.fna.gz | prodigal -d GCF_016908655.1_ASM1690865v1_genomic.fna/cds.fna -a GCF_016908655.1_ASM1690865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:10,415] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:10,416] [INFO] Task started: HMMsearch
[2024-01-25 19:05:10,416] [INFO] Running command: hmmsearch --tblout GCF_016908655.1_ASM1690865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1e54c63-c3a7-4a90-9703-0922ed607d88/dqc_reference/reference_markers.hmm GCF_016908655.1_ASM1690865v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:10,622] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:10,623] [INFO] Found 6/6 markers.
[2024-01-25 19:05:10,644] [INFO] Query marker FASTA was written to GCF_016908655.1_ASM1690865v1_genomic.fna/markers.fasta
[2024-01-25 19:05:10,644] [INFO] Task started: Blastn
[2024-01-25 19:05:10,644] [INFO] Running command: blastn -query GCF_016908655.1_ASM1690865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1e54c63-c3a7-4a90-9703-0922ed607d88/dqc_reference/reference_markers.fasta -out GCF_016908655.1_ASM1690865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:11,224] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:11,227] [INFO] Selected 26 target genomes.
[2024-01-25 19:05:11,227] [INFO] Target genome list was writen to GCF_016908655.1_ASM1690865v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:11,244] [INFO] Task started: fastANI
[2024-01-25 19:05:11,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd339ac0-265a-445c-95de-4549d74b45c1/GCF_016908655.1_ASM1690865v1_genomic.fna.gz --refList GCF_016908655.1_ASM1690865v1_genomic.fna/target_genomes.txt --output GCF_016908655.1_ASM1690865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:20,284] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:20,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1e54c63-c3a7-4a90-9703-0922ed607d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:20,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1e54c63-c3a7-4a90-9703-0922ed607d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:20,300] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:05:20,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:20,300] [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 saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	100.0	646	647	95	conclusive
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	83.0566	390	647	95	below_threshold
Streptococcus salivarius	strain=NCTC8618	GCA_900636435.1	1304	1304	suspected-type	True	79.7349	177	647	95	below_threshold
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	79.6896	176	647	95	below_threshold
Streptococcus agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	79.6364	130	647	95	below_threshold
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	79.6308	180	647	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.5679	94	647	95	below_threshold
Streptococcus agalactiae	strain=ATCC 13813	GCA_000186445.1	1311	1311	type	True	79.5676	128	647	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	79.4593	157	647	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	79.444	102	647	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	79.4423	154	647	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	79.4275	159	647	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	79.2409	164	647	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	79.2195	80	647	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	79.1814	160	647	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	79.1565	160	647	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	79.1044	193	647	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.1039	93	647	95	below_threshold
Streptococcus didelphis	strain=DSM 15616	GCA_000380005.1	102886	102886	type	True	79.0856	86	647	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	79.062	107	647	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	78.9898	171	647	95	below_threshold
Streptococcus gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	78.975	172	647	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	78.8085	150	647	95	below_threshold
Streptococcus halotolerans	strain=HTS9	GCA_001598035.1	1814128	1814128	type	True	78.795	127	647	95	below_threshold
Streptococcus porcinus	strain=NCTC10999	GCA_900475415.1	1340	1340	type	True	78.7831	92	647	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.0699	91	647	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:20,301] [INFO] DFAST Taxonomy check result was written to GCF_016908655.1_ASM1690865v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:20,302] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:20,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:20,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1e54c63-c3a7-4a90-9703-0922ed607d88/dqc_reference/checkm_data
[2024-01-25 19:05:20,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:20,325] [INFO] Task started: CheckM
[2024-01-25 19:05:20,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908655.1_ASM1690865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908655.1_ASM1690865v1_genomic.fna/checkm_input GCF_016908655.1_ASM1690865v1_genomic.fna/checkm_result
[2024-01-25 19:05:37,681] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:37,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:37,702] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:37,703] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:37,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908655.1_ASM1690865v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:37,703] [INFO] Task started: Blastn
[2024-01-25 19:05:37,703] [INFO] Running command: blastn -query GCF_016908655.1_ASM1690865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1e54c63-c3a7-4a90-9703-0922ed607d88/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908655.1_ASM1690865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:38,478] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:38,481] [INFO] Selected 20 target genomes.
[2024-01-25 19:05:38,481] [INFO] Target genome list was writen to GCF_016908655.1_ASM1690865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:38,504] [INFO] Task started: fastANI
[2024-01-25 19:05:38,504] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd339ac0-265a-445c-95de-4549d74b45c1/GCF_016908655.1_ASM1690865v1_genomic.fna.gz --refList GCF_016908655.1_ASM1690865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908655.1_ASM1690865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:45,866] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:45,879] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:45,879] [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_016908655.1	s__Streptococcus saliviloxodontae	100.0	646	647	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_016908645.1	s__Streptococcus loxodontisalivarius	83.0499	391	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785515.1	s__Streptococcus salivarius	79.6896	176	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.08	95.32	0.88	0.82	131	-
GCF_010604095.1	s__Streptococcus sp000187445	79.624	166	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_000186445.1	s__Streptococcus agalactiae	79.5676	128	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_900101445.1	s__Streptococcus equinus_B	79.5145	157	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_000380125.1	s__Streptococcus ovis	79.444	102	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154985.1	s__Streptococcus infantarius	79.2409	164	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_900475675.1	s__Streptococcus lutetiensis	79.1528	161	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_015594605.1	s__Streptococcus sp015594605	79.1234	167	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000283635.1	s__Streptococcus macedonicus	79.0908	159	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_003686955.1	s__Streptococcus sp003686955	79.0654	151	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337175.1	s__Streptococcus gallolyticus_B	79.0626	151	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_003674745.1	s__Streptococcus iniae	79.0351	101	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_000380005.1	s__Streptococcus didelphis	79.0349	87	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000985.1	s__Streptococcus gallolyticus	78.965	172	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCF_900475415.1	s__Streptococcus porcinus	78.7831	92	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_902729355.1	s__Streptococcus sp902729355	78.7037	149	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_901542335.1	s__Streptococcus porcinus_A	78.6584	91	647	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_001431045.1	s__Streptococcus orisasini	77.6507	120	647	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 19:05:45,880] [INFO] GTDB search result was written to GCF_016908655.1_ASM1690865v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:45,881] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:45,887] [INFO] DFAST_QC result json was written to GCF_016908655.1_ASM1690865v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:45,887] [INFO] DFAST_QC completed!
[2024-01-25 19:05:45,888] [INFO] Total running time: 0h0m40s