[2023-06-04 20:37:27,148] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:37:27,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:37:27,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg992bc7ae-06f0-47e9-8d4f-563945c1afcd/dqc_reference
[2023-06-04 20:37:28,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:37:28,545] [INFO] Task started: Prodigal
[2023-06-04 20:37:28,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a0373a9-76e7-4fc7-b611-de14c89b11f2/GCA_004555475.1_ASM455547v1_genomic.fna.gz | prodigal -d GCA_004555475.1_ASM455547v1_genomic.fna/cds.fna -a GCA_004555475.1_ASM455547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:37:33,445] [INFO] Task succeeded: Prodigal
[2023-06-04 20:37:33,445] [INFO] Task started: HMMsearch
[2023-06-04 20:37:33,446] [INFO] Running command: hmmsearch --tblout GCA_004555475.1_ASM455547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg992bc7ae-06f0-47e9-8d4f-563945c1afcd/dqc_reference/reference_markers.hmm GCA_004555475.1_ASM455547v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:37:33,697] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:37:33,699] [INFO] Found 6/6 markers.
[2023-06-04 20:37:33,726] [INFO] Query marker FASTA was written to GCA_004555475.1_ASM455547v1_genomic.fna/markers.fasta
[2023-06-04 20:37:33,727] [INFO] Task started: Blastn
[2023-06-04 20:37:33,727] [INFO] Running command: blastn -query GCA_004555475.1_ASM455547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg992bc7ae-06f0-47e9-8d4f-563945c1afcd/dqc_reference/reference_markers.fasta -out GCA_004555475.1_ASM455547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:37:34,350] [INFO] Task succeeded: Blastn
[2023-06-04 20:37:34,356] [INFO] Selected 15 target genomes.
[2023-06-04 20:37:34,357] [INFO] Target genome list was writen to GCA_004555475.1_ASM455547v1_genomic.fna/target_genomes.txt
[2023-06-04 20:37:34,362] [INFO] Task started: fastANI
[2023-06-04 20:37:34,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0373a9-76e7-4fc7-b611-de14c89b11f2/GCA_004555475.1_ASM455547v1_genomic.fna.gz --refList GCA_004555475.1_ASM455547v1_genomic.fna/target_genomes.txt --output GCA_004555475.1_ASM455547v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:37:39,849] [INFO] Task succeeded: fastANI
[2023-06-04 20:37:39,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg992bc7ae-06f0-47e9-8d4f-563945c1afcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:37:39,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg992bc7ae-06f0-47e9-8d4f-563945c1afcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:37:39,861] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-04 20:37:39,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 20:37:39,862] [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
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	98.4358	541	750	95	conclusive
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	81.0931	331	750	95	below_threshold
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	81.0829	333	750	95	below_threshold
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	81.0367	338	750	95	below_threshold
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	80.874	339	750	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	80.6717	314	750	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	80.39	307	750	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	80.3488	309	750	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	80.2793	317	750	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	80.1811	300	750	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	80.0084	293	750	95	below_threshold
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	80.0064	310	750	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	79.8942	307	750	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:37:39,864] [INFO] DFAST Taxonomy check result was written to GCA_004555475.1_ASM455547v1_genomic.fna/tc_result.tsv
[2023-06-04 20:37:39,864] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:37:39,864] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:37:39,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg992bc7ae-06f0-47e9-8d4f-563945c1afcd/dqc_reference/checkm_data
[2023-06-04 20:37:39,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:37:39,893] [INFO] Task started: CheckM
[2023-06-04 20:37:39,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004555475.1_ASM455547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004555475.1_ASM455547v1_genomic.fna/checkm_input GCA_004555475.1_ASM455547v1_genomic.fna/checkm_result
[2023-06-04 20:38:01,991] [INFO] Task succeeded: CheckM
[2023-06-04 20:38:01,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:38:02,020] [INFO] ===== Completeness check finished =====
[2023-06-04 20:38:02,020] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:38:02,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004555475.1_ASM455547v1_genomic.fna/markers.fasta)
[2023-06-04 20:38:02,021] [INFO] Task started: Blastn
[2023-06-04 20:38:02,022] [INFO] Running command: blastn -query GCA_004555475.1_ASM455547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg992bc7ae-06f0-47e9-8d4f-563945c1afcd/dqc_reference/reference_markers_gtdb.fasta -out GCA_004555475.1_ASM455547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:38:02,824] [INFO] Task succeeded: Blastn
[2023-06-04 20:38:02,829] [INFO] Selected 20 target genomes.
[2023-06-04 20:38:02,829] [INFO] Target genome list was writen to GCA_004555475.1_ASM455547v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:38:02,891] [INFO] Task started: fastANI
[2023-06-04 20:38:02,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0373a9-76e7-4fc7-b611-de14c89b11f2/GCA_004555475.1_ASM455547v1_genomic.fna.gz --refList GCA_004555475.1_ASM455547v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004555475.1_ASM455547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:38:09,880] [INFO] Task succeeded: fastANI
[2023-06-04 20:38:09,896] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:38:09,897] [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_003992125.1	s__Veillonella caviae	98.4358	541	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.44	98.44	0.87	0.87	2	conclusive
GCF_002959915.1	s__Veillonella atypica	81.095	332	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	-
GCF_001078375.1	s__Veillonella tobetsuensis	80.874	339	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.55	97.11	0.92	0.91	7	-
GCF_013393365.1	s__Veillonella nakazawae	80.6604	315	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.23	95.05	0.93	0.87	33	-
GCA_905214495.1	s__Veillonella sp905214495	80.5318	271	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002959755.1	s__Veillonella sp002959755	80.4184	304	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552445.1	s__Veillonella sp900552445	80.3566	163	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	97.10	0.94	0.94	2	-
GCF_002959895.1	s__Veillonella infantium	80.3468	310	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
GCA_900538355.1	s__Veillonella sp900538355	80.3305	306	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637515.1	s__Veillonella dispar	80.2793	317	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.54	95.48	0.96	0.91	7	-
GCF_002959775.1	s__Veillonella rogosae	80.1811	300	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
GCF_000024945.1	s__Veillonella parvula	79.894	307	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	98.96	96.87	0.98	0.94	4	-
GCA_900549845.1	s__Veillonella sp900549845	79.8514	230	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209685.1	s__Veillonella sp905209685	79.7069	242	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.07	95.07	0.78	0.78	2	-
GCA_018367495.1	s__Veillonella sp018367495	79.103	269	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902834965.1	s__Veillonella sp902834965	78.9733	161	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545795.1	s__Veillonella_A sp900545795	77.6604	93	750	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:38:09,899] [INFO] GTDB search result was written to GCA_004555475.1_ASM455547v1_genomic.fna/result_gtdb.tsv
[2023-06-04 20:38:09,899] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:38:09,904] [INFO] DFAST_QC result json was written to GCA_004555475.1_ASM455547v1_genomic.fna/dqc_result.json
[2023-06-04 20:38:09,904] [INFO] DFAST_QC completed!
[2023-06-04 20:38:09,904] [INFO] Total running time: 0h0m43s