[2024-01-24 12:22:48,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,180] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a850575-44f3-406b-99fc-98d5f872e2b8/dqc_reference
[2024-01-24 12:22:49,284] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,285] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,285] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2773b76-2245-4e64-aa5e-6e096f8fc8b4/GCF_000421785.1_ASM42178v1_genomic.fna.gz | prodigal -d GCF_000421785.1_ASM42178v1_genomic.fna/cds.fna -a GCF_000421785.1_ASM42178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:52,590] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:52,590] [INFO] Task started: HMMsearch
[2024-01-24 12:22:52,590] [INFO] Running command: hmmsearch --tblout GCF_000421785.1_ASM42178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a850575-44f3-406b-99fc-98d5f872e2b8/dqc_reference/reference_markers.hmm GCF_000421785.1_ASM42178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:52,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:52,792] [INFO] Found 6/6 markers.
[2024-01-24 12:22:52,811] [INFO] Query marker FASTA was written to GCF_000421785.1_ASM42178v1_genomic.fna/markers.fasta
[2024-01-24 12:22:52,811] [INFO] Task started: Blastn
[2024-01-24 12:22:52,811] [INFO] Running command: blastn -query GCF_000421785.1_ASM42178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a850575-44f3-406b-99fc-98d5f872e2b8/dqc_reference/reference_markers.fasta -out GCF_000421785.1_ASM42178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:53,352] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:53,355] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:53,355] [INFO] Target genome list was writen to GCF_000421785.1_ASM42178v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:53,413] [INFO] Task started: fastANI
[2024-01-24 12:22:53,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2773b76-2245-4e64-aa5e-6e096f8fc8b4/GCF_000421785.1_ASM42178v1_genomic.fna.gz --refList GCF_000421785.1_ASM42178v1_genomic.fna/target_genomes.txt --output GCF_000421785.1_ASM42178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:58,868] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:58,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a850575-44f3-406b-99fc-98d5f872e2b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:58,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a850575-44f3-406b-99fc-98d5f872e2b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:58,877] [INFO] Found 13 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:22:58,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:58,877] [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 pyogenes	strain=DSM 20565	GCA_000421785.1	1314	1314	type	True	100.0	603	603	95	conclusive
Streptococcus pyogenes	strain=CCUG 4207	GCA_004028355.1	1314	1314	type	True	99.9918	602	603	95	conclusive
Streptococcus pyogenes	strain=NCTC8198	GCA_002055535.1	1314	1314	type	True	99.9918	602	603	95	conclusive
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	99.9914	602	603	95	conclusive
Streptococcus pyogenes	strain=FDAARGOS_774	GCA_006364235.1	1314	1314	type	True	99.9913	602	603	95	conclusive
Streptococcus pyogenes	strain=CCUG 4207	GCA_001982785.1	1314	1314	type	True	99.9764	587	603	95	conclusive
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	87.2089	437	603	95	below_threshold
Streptococcus dysgalactiae subsp. dysgalactiae	strain=NCTC13731	GCA_900459225.1	99822	1334	type	True	87.1866	431	603	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	86.4033	430	603	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	79.4434	178	603	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.1825	85	603	95	below_threshold
Streptococcus phocae	strain=ATCC 51973	GCA_001302265.1	119224	119224	type	True	79.0548	209	603	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.045	58	603	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:58,878] [INFO] DFAST Taxonomy check result was written to GCF_000421785.1_ASM42178v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:58,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:58,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:58,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a850575-44f3-406b-99fc-98d5f872e2b8/dqc_reference/checkm_data
[2024-01-24 12:22:58,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:58,900] [INFO] Task started: CheckM
[2024-01-24 12:22:58,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421785.1_ASM42178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421785.1_ASM42178v1_genomic.fna/checkm_input GCF_000421785.1_ASM42178v1_genomic.fna/checkm_result
[2024-01-24 12:23:15,012] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:15,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:15,030] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:15,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:15,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421785.1_ASM42178v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:15,031] [INFO] Task started: Blastn
[2024-01-24 12:23:15,031] [INFO] Running command: blastn -query GCF_000421785.1_ASM42178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a850575-44f3-406b-99fc-98d5f872e2b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421785.1_ASM42178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:15,837] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:15,840] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:15,840] [INFO] Target genome list was writen to GCF_000421785.1_ASM42178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:15,848] [INFO] Task started: fastANI
[2024-01-24 12:23:15,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2773b76-2245-4e64-aa5e-6e096f8fc8b4/GCF_000421785.1_ASM42178v1_genomic.fna.gz --refList GCF_000421785.1_ASM42178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421785.1_ASM42178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:22,363] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:22,370] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:22,370] [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_002055535.1	s__Streptococcus pyogenes	99.9918	602	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.85	98.36	0.95	0.87	2144	conclusive
GCF_900459225.1	s__Streptococcus dysgalactiae	87.2156	430	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_900636575.1	s__Streptococcus canis	86.4181	429	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_000425025.1	s__Streptococcus castoreus	80.986	313	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188015.2	s__Streptococcus ictaluri	80.669	278	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011421455.1	s__Streptococcus catagoni	79.6364	171	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003674745.1	s__Streptococcus iniae	79.4232	160	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_902729355.1	s__Streptococcus sp902729355	79.0938	103	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_001302265.1	s__Streptococcus phocae	79.0548	209	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.05	97.05	0.87	0.87	2	-
GCF_900475415.1	s__Streptococcus porcinus	78.6228	172	603	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:22,371] [INFO] GTDB search result was written to GCF_000421785.1_ASM42178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:22,372] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:22,374] [INFO] DFAST_QC result json was written to GCF_000421785.1_ASM42178v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:22,374] [INFO] DFAST_QC completed!
[2024-01-24 12:23:22,375] [INFO] Total running time: 0h0m34s